From 7d7b6b86ec3fd14d915b69136c4102c02d200ce7 Mon Sep 17 00:00:00 2001
From: xkoloma1 <xkoloma1@node.mendelu.cz>
Date: Fri, 24 Nov 2023 10:37:19 +0000
Subject: [PATCH] Resolve "Move frontend to separate project"
---
.browserslistrc | 3 +
.eslintrc.js | 27 +
.gitignore | 24 +
.gitlab-ci.yml | 140 +
.npmrc | 1 +
Dockerfile | 13 +
README.md | 111 +-
babel.config.js | 3 +
docker-compose.yml | 61 +
jest.config.js | 3 +
package-lock.json | 14579 ++++++++++++++++
package.json | 45 +
public/favicon.ico | Bin 0 -> 73070 bytes
public/index.html | 17 +
src/assets/favicon.ico | Bin 0 -> 73070 bytes
src/assets/loader.gif | Bin 0 -> 673 bytes
src/axios.js | 6 +
src/components/core/app-form.vue | 73 +
src/components/core/app-menu.vue | 159 +
src/components/core/app.vue | 39 +
src/components/core/checkable-list.vue | 58 +
src/components/core/form-result.vue | 40 +
src/components/core/http-error.vue | 32 +
src/components/core/index.vue | 47 +
src/components/core/modal-alert.vue | 64 +
src/components/core/modal-confirm.vue | 74 +
src/components/core/not-found.vue | 15 +
src/components/core/pagination.vue | 88 +
src/components/core/result-editor.vue | 50 +
src/components/core/sequence.vue | 72 +
src/components/core/sort-toggle.vue | 55 +
.../core/visualisation/heatchart.vue | 306 +
src/components/core/visualisation/heatmap.vue | 177 +
.../core/visualisation/highlight.vue | 102 +
.../core/visualisation/mini-chart.vue | 84 +
.../core/visualisation/sequence-view.vue | 73 +
src/components/core/work-progress/store.js | 28 +
.../core/work-progress/work-progress.vue | 101 +
src/components/cruciform/cruciform.vue | 22 +
src/components/cruciform/heatmap.vue | 7 +
src/components/cruciform/input-form.vue | 62 +
src/components/cruciform/results-list.vue | 7 +
src/components/g4killer/backup.vue | 222 +
src/components/g4killer/form-multiple.vue | 223 +
src/components/g4killer/form-single.vue | 217 +
src/components/g4killer/g4killer-detail.vue | 59 +
src/components/g4killer/g4killer-tool.vue | 29 +
src/components/help/about.vue | 37 +
src/components/help/faq.vue | 65 +
src/components/help/help-cruciform.vue | 63 +
src/components/help/help-g4killer.vue | 62 +
src/components/help/help-import.vue | 29 +
src/components/help/help-p53.vue | 42 +
src/components/help/help-quadruplex.vue | 150 +
src/components/help/help-rloopr.vue | 156 +
src/components/help/help-zdna.vue | 156 +
src/components/help/help.vue | 9 +
src/components/help/status.vue | 42 +
src/components/p53predictor/form-best.vue | 135 +
src/components/p53predictor/form-multiple.vue | 120 +
src/components/p53predictor/form-single.vue | 99 +
src/components/p53predictor/p53-form.vue | 57 +
.../p53predictor/p53-predictor-results.vue | 118 +
.../p53predictor/p53-predictor-tool.vue | 45 +
src/components/p53predictor/p53-predictor.vue | 129 +
.../p53predictor/stored-results-detail.vue | 54 +
.../p53predictor/stored-results.vue | 196 +
.../quadruplex/quadruplex-details.vue | 66 +
src/components/quadruplex/quadruplex-form.vue | 166 +
.../quadruplex/quadruplex-results.vue | 344 +
src/components/quadruplex/quadruplex.vue | 132 +
.../quadruplex/stored-results-details.vue | 57 +
src/components/quadruplex/stored-results.vue | 243 +
src/components/rloopr/rloopr-form.vue | 63 +
src/components/rloopr/rloopr-results.vue | 339 +
src/components/rloopr/rloopr.vue | 132 +
.../rloopr/stored-results-details.vue | 55 +
src/components/rloopr/stored-results.vue | 202 +
.../sequence/helpers/sequence-stats.js | 46 +
src/components/sequence/list-with-action.vue | 258 +
src/components/sequence/list.vue | 317 +
src/components/sequence/ncbi-import-multi.vue | 118 +
src/components/sequence/ncbi-import.vue | 118 +
src/components/sequence/overview.vue | 159 +
src/components/sequence/paste.vue | 92 +
src/components/sequence/sequence-editor.vue | 49 +
src/components/sequence/sequence-info.vue | 83 +
src/components/sequence/sequence-selector.vue | 42 +
src/components/sequence/sequence.vue | 44 +
src/components/sequence/upload.vue | 165 +
src/components/test/test.vue | 73 +
src/components/user/change-password.vue | 97 +
src/components/user/login.vue | 83 +
src/components/user/register.vue | 99 +
src/components/user/reset-password.vue | 77 +
.../zdna/stored-results-details.vue | 55 +
src/components/zdna/stored-results.vue | 205 +
src/components/zdna/zdna-form.vue | 75 +
src/components/zdna/zdna-results.vue | 287 +
src/components/zdna/zdna.vue | 130 +
src/config.js | 23 +
src/formatters.js | 46 +
src/helpers.js | 20 +
src/less/custom.less | 65 +
src/main.js | 69 +
src/router.js | 258 +
src/services/auth-store.js | 32 +
src/services/auth-token.js | 43 +
src/services/batch-watcher.js | 64 +
src/services/filetype-detector.js | 25 +
src/services/token-updater.js | 23 +
src/services/user-auth.js | 119 +
src/store/index.js | 38 +
src/utils.js | 14 +
tests/unit/example.spec.js | 12 +
vue.config.js | 13 +
116 files changed, 24638 insertions(+), 79 deletions(-)
create mode 100644 .browserslistrc
create mode 100644 .eslintrc.js
create mode 100644 .gitignore
create mode 100644 .gitlab-ci.yml
create mode 100644 .npmrc
create mode 100644 Dockerfile
create mode 100644 babel.config.js
create mode 100644 docker-compose.yml
create mode 100644 jest.config.js
create mode 100644 package-lock.json
create mode 100644 package.json
create mode 100644 public/favicon.ico
create mode 100644 public/index.html
create mode 100644 src/assets/favicon.ico
create mode 100644 src/assets/loader.gif
create mode 100644 src/axios.js
create mode 100644 src/components/core/app-form.vue
create mode 100644 src/components/core/app-menu.vue
create mode 100644 src/components/core/app.vue
create mode 100644 src/components/core/checkable-list.vue
create mode 100644 src/components/core/form-result.vue
create mode 100644 src/components/core/http-error.vue
create mode 100644 src/components/core/index.vue
create mode 100644 src/components/core/modal-alert.vue
create mode 100644 src/components/core/modal-confirm.vue
create mode 100644 src/components/core/not-found.vue
create mode 100644 src/components/core/pagination.vue
create mode 100644 src/components/core/result-editor.vue
create mode 100644 src/components/core/sequence.vue
create mode 100644 src/components/core/sort-toggle.vue
create mode 100644 src/components/core/visualisation/heatchart.vue
create mode 100644 src/components/core/visualisation/heatmap.vue
create mode 100644 src/components/core/visualisation/highlight.vue
create mode 100644 src/components/core/visualisation/mini-chart.vue
create mode 100644 src/components/core/visualisation/sequence-view.vue
create mode 100644 src/components/core/work-progress/store.js
create mode 100644 src/components/core/work-progress/work-progress.vue
create mode 100644 src/components/cruciform/cruciform.vue
create mode 100644 src/components/cruciform/heatmap.vue
create mode 100644 src/components/cruciform/input-form.vue
create mode 100644 src/components/cruciform/results-list.vue
create mode 100644 src/components/g4killer/backup.vue
create mode 100644 src/components/g4killer/form-multiple.vue
create mode 100644 src/components/g4killer/form-single.vue
create mode 100644 src/components/g4killer/g4killer-detail.vue
create mode 100644 src/components/g4killer/g4killer-tool.vue
create mode 100644 src/components/help/about.vue
create mode 100644 src/components/help/faq.vue
create mode 100644 src/components/help/help-cruciform.vue
create mode 100644 src/components/help/help-g4killer.vue
create mode 100644 src/components/help/help-import.vue
create mode 100644 src/components/help/help-p53.vue
create mode 100644 src/components/help/help-quadruplex.vue
create mode 100644 src/components/help/help-rloopr.vue
create mode 100644 src/components/help/help-zdna.vue
create mode 100644 src/components/help/help.vue
create mode 100644 src/components/help/status.vue
create mode 100644 src/components/p53predictor/form-best.vue
create mode 100644 src/components/p53predictor/form-multiple.vue
create mode 100644 src/components/p53predictor/form-single.vue
create mode 100644 src/components/p53predictor/p53-form.vue
create mode 100644 src/components/p53predictor/p53-predictor-results.vue
create mode 100644 src/components/p53predictor/p53-predictor-tool.vue
create mode 100644 src/components/p53predictor/p53-predictor.vue
create mode 100644 src/components/p53predictor/stored-results-detail.vue
create mode 100644 src/components/p53predictor/stored-results.vue
create mode 100644 src/components/quadruplex/quadruplex-details.vue
create mode 100644 src/components/quadruplex/quadruplex-form.vue
create mode 100644 src/components/quadruplex/quadruplex-results.vue
create mode 100644 src/components/quadruplex/quadruplex.vue
create mode 100644 src/components/quadruplex/stored-results-details.vue
create mode 100644 src/components/quadruplex/stored-results.vue
create mode 100644 src/components/rloopr/rloopr-form.vue
create mode 100644 src/components/rloopr/rloopr-results.vue
create mode 100644 src/components/rloopr/rloopr.vue
create mode 100644 src/components/rloopr/stored-results-details.vue
create mode 100644 src/components/rloopr/stored-results.vue
create mode 100644 src/components/sequence/helpers/sequence-stats.js
create mode 100644 src/components/sequence/list-with-action.vue
create mode 100644 src/components/sequence/list.vue
create mode 100644 src/components/sequence/ncbi-import-multi.vue
create mode 100644 src/components/sequence/ncbi-import.vue
create mode 100644 src/components/sequence/overview.vue
create mode 100644 src/components/sequence/paste.vue
create mode 100644 src/components/sequence/sequence-editor.vue
create mode 100644 src/components/sequence/sequence-info.vue
create mode 100644 src/components/sequence/sequence-selector.vue
create mode 100644 src/components/sequence/sequence.vue
create mode 100644 src/components/sequence/upload.vue
create mode 100644 src/components/test/test.vue
create mode 100644 src/components/user/change-password.vue
create mode 100644 src/components/user/login.vue
create mode 100644 src/components/user/register.vue
create mode 100644 src/components/user/reset-password.vue
create mode 100644 src/components/zdna/stored-results-details.vue
create mode 100644 src/components/zdna/stored-results.vue
create mode 100644 src/components/zdna/zdna-form.vue
create mode 100644 src/components/zdna/zdna-results.vue
create mode 100644 src/components/zdna/zdna.vue
create mode 100644 src/config.js
create mode 100644 src/formatters.js
create mode 100644 src/helpers.js
create mode 100644 src/less/custom.less
create mode 100644 src/main.js
create mode 100644 src/router.js
create mode 100644 src/services/auth-store.js
create mode 100644 src/services/auth-token.js
create mode 100644 src/services/batch-watcher.js
create mode 100644 src/services/filetype-detector.js
create mode 100644 src/services/token-updater.js
create mode 100644 src/services/user-auth.js
create mode 100644 src/store/index.js
create mode 100644 src/utils.js
create mode 100644 tests/unit/example.spec.js
create mode 100644 vue.config.js
diff --git a/.browserslistrc b/.browserslistrc
new file mode 100644
index 0000000..214388f
--- /dev/null
+++ b/.browserslistrc
@@ -0,0 +1,3 @@
+> 1%
+last 2 versions
+not dead
diff --git a/.eslintrc.js b/.eslintrc.js
new file mode 100644
index 0000000..955bfea
--- /dev/null
+++ b/.eslintrc.js
@@ -0,0 +1,27 @@
+module.exports = {
+ root: true,
+ env: {
+ node: true,
+ },
+ extends: ['plugin:vue/strongly-recommended', 'eslint:recommended'],
+ parserOptions: {
+ parser: 'babel-eslint',
+ },
+ rules: {
+ 'no-console': process.env.NODE_ENV === 'production' ? 'warn' : 'off',
+ 'no-debugger': process.env.NODE_ENV === 'production' ? 'warn' : 'off',
+ 'vue/no-use-v-if-with-v-for': 'off',
+ 'vue/require-v-for-key': 'off',
+ 'vue/max-attributes-per-line': 'off',
+ 'vue/html-self-closing' : 'off',
+ 'vue/singleline-html-element-content-newline' : 'off',
+ },
+ overrides: [
+ {
+ files: ['**/__tests__/*.{j,t}s?(x)', '**/tests/unit/**/*.spec.{j,t}s?(x)'],
+ env: {
+ jest: true,
+ },
+ },
+ ],
+}
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..2b53524
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+.DS_Store
+node_modules
+/dist
+
+/tests/e2e/videos/
+/tests/e2e/screenshots/
+
+# local env files
+.env.local
+.env.*.local
+
+# Log files
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Editor directories and files
+.idea
+.vscode
+*.suo
+*.ntvs*
+*.njsproj
+*.sln
+*.sw?
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..99ca0b7
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,140 @@
+variables:
+ DOCKER_HOST: $DOCKER_HOST_BIO
+ PROJECT_NAME: "frontend"
+
+cache:
+ key: $CI_COMMIT_REF_NAME
+ paths:
+ - build/
+
+stages:
+ - analyse
+ - build
+ - publish
+ - deploy
+
+# ===========================================================================
+# Stage: analyse
+# ===========================================================================
+
+include:
+ - template: Code-Quality.gitlab-ci.yml
+
+code_quality:
+ stage: analyse
+ services: [] # Shut off Docker-in-Docker
+ variables:
+ REPORT_FORMAT: html
+ artifacts:
+ paths: [gl-code-quality-report.html]
+
+# second job has to be run to create both artefacts
+code_quality_json:
+ extends: code_quality
+ variables:
+ REPORT_FORMAT: json
+ artifacts:
+ paths: [gl-code-quality-report.json]
+
+
+# ===========================================================================
+# Stage: build
+# ===========================================================================
+
+docker-build-latest:
+ stage: build
+ image: docker:git
+ only:
+ refs:
+ - main
+ except:
+ variables:
+ - $CI_COMMIT_TAG
+ before_script:
+ - mkdir -p build
+ script:
+ - docker build -t $DOCKER_NAMESPACE/$PROJECT_NAME:latest .
+ - docker save -o build/image.tar $DOCKER_NAMESPACE/$PROJECT_NAME:latest
+ artifacts:
+ paths:
+ - build/image.tar
+ expire_in: 10 mins # Optional: Set an expiration time for the artifact
+
+docker-build-tag:
+ stage: build
+ image: docker:git
+ only:
+ variables:
+ - $CI_COMMIT_TAG
+ before_script:
+ - mkdir -p build
+ script:
+ - docker build -t $DOCKER_NAMESPACE/$PROJECT_NAME:$CI_COMMIT_TAG .
+ - docker save -o build/image.tar $DOCKER_NAMESPACE/$PROJECT_NAME:$CI_COMMIT_TAG
+ artifacts:
+ paths:
+ - build/image.tar
+ expire_in: 10 mins # Optional: Set an expiration time for the artifact
+
+
+# ===========================================================================
+# Stage: test
+#
+# TODO
+# ===========================================================================
+
+
+
+# ===========================================================================
+# Stage: publish
+# ===========================================================================
+
+docker-push-latest:
+ stage: publish
+ image: docker
+ only:
+ - main
+ before_script:
+ - docker login -u $DOCKER_USERNAME -p $DOCKER_TOKEN $DOCKER_REGISTRY
+ script:
+ - docker load -i build/image.tar
+ - docker push $DOCKER_NAMESPACE/$PROJECT_NAME:latest
+
+docker-push-tag:
+ stage: publish
+ image: docker
+ only:
+ variables:
+ - $CI_COMMIT_TAG
+ before_script:
+ - docker login -u $DOCKER_USERNAME -p $DOCKER_TOKEN $DOCKER_REGISTRY
+ script:
+ - docker load -i build/image.tar
+ - docker push $DOCKER_NAMESPACE/$PROJECT_NAME:$CI_COMMIT_TAG
+
+
+# ===========================================================================
+# Stage: deploy
+# ===========================================================================
+
+deploy-bioinformatika.pef.mendelu.cz:
+ stage: deploy
+ only:
+ - main
+ script:
+ - cp .env /home/bioinformatics/
+ - cd /home/bioinformatics/
+ - docker-compose config > docker-swarm.yml
+# - docker stack deploy -c docker-compose.yml test_stack
+# after_script:
+# - docker system prune -f
+
+deploy-bioinformatics.ibp.cz:
+ stage: deploy
+ only:
+ variables:
+ - $CI_COMMIT_TAG
+ script:
+ - scp .env root@bioinformatics.ibp.cz:/opt/
+ - scp docker-compose.yml root@bioinformatics.ibp.cz:/opt/
+ - ssh root@bioinformatics.ibp.cz "cd /opt && export $(xargs < .env) && docker stack deploy dna-analyser -c docker-compose.yml"
diff --git a/.npmrc b/.npmrc
new file mode 100644
index 0000000..cad5797
--- /dev/null
+++ b/.npmrc
@@ -0,0 +1 @@
+save-exact = true
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..39a6f85
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,13 @@
+# Build stage
+FROM node:14 as build-stage
+WORKDIR /app
+COPY package*.json ./
+RUN npm ci
+COPY . .
+RUN npm run build
+
+# production stage
+FROM nginx:stable-alpine as production-stage
+COPY --from=build-stage /app/dist /usr/share/nginx/html
+EXPOSE 80
+CMD ["nginx", "-g", "daemon off;"]
\ No newline at end of file
diff --git a/README.md b/README.md
index 22c5868..94f47d3 100644
--- a/README.md
+++ b/README.md
@@ -1,92 +1,45 @@
-# frontend-vue-2
-
-
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
+# DNA analyser frontend
+## Project setup
```
-cd existing_repo
-git remote add origin https://git.pef.mendelu.cz/bioinformatics/frontend-vue-2.git
-git branch -M main
-git push -uf origin main
+npm install
```
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://git.pef.mendelu.cz/bioinformatics/frontend-vue-2/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
+### Compiles and hot-reloads for development
+```
+npm run serve
+```
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
+### Compiles and minifies for production (backend/build/resources/main/static)
+```
+npm run build
+```
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
+### Run your unit tests
+```
+npm run test:unit
+```
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
+### Run your end-to-end tests
+```
+npm run test:e2e
+```
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
+### Lints and fixes files
+```
+npm run lint
+```
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
+## Code documentation
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
+### Store
+Global store handles user authorisation.
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
+Plugins:
+- Work progress components - `src/components/core/work-progress.vue`
-## License
-For open source projects, say how it is licensed.
+### Event bus global events
+Global event bus is created in `main.js`.
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
+- `reloadSequences` - handled in `src/components/sequences/list.vue`
+- `newSequence` - handled in `src/components/sequences/overview.vue`
diff --git a/babel.config.js b/babel.config.js
new file mode 100644
index 0000000..c1b783e
--- /dev/null
+++ b/babel.config.js
@@ -0,0 +1,3 @@
+module.exports = {
+ presets: ['@vue/cli-plugin-babel/preset'],
+}
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 0000000..363c82d
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,61 @@
+version: '3.0'
+
+services:
+
+ gateway:
+ image: dnapef/gateway:${TAG:-latest}
+ depends_on:
+ - backend
+ ports:
+ - 443:8443
+ volumes:
+ - gateway_config:/workspace/config
+
+ redirect:
+ image: dnapef/redirect
+ ports:
+ - 80:80
+
+ backend:
+ image: dnapef/backend:${TAG:-latest}
+ depends_on:
+ - postgres
+ volumes:
+ - backend_db:/home/app/db
+ - backend_logs:/home/app/logs
+ - backend_config:/home/app/config
+
+ postgres:
+ image: postgres:13
+ environment:
+ POSTGRES_DB: dna_analyser
+ POSTGRES_USER: ${POSTGRES_USER:-developer}
+ POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-password}
+ PGDATA: /data/postgres
+ volumes:
+ - postgres:/data/postgres
+ ports:
+ - 5432:5432
+
+ pgadmin:
+ image: dpage/pgadmin4:latest
+ depends_on:
+ - postgres
+ environment:
+ PGADMIN_DEFAULT_EMAIL: ${PGADMIN_DEFAULT_EMAIL:-user@mendelu.cz}
+ PGADMIN_DEFAULT_PASSWORD: ${PGADMIN_DEFAULT_PASSWORD:-user}
+ volumes:
+ - pgadmin:/root/.pgadmin
+ ports:
+ - 5050:80
+
+
+
+volumes:
+ postgres:
+ pgadmin:
+ gateway_config:
+ backend_db:
+ backend_logs:
+ backend_config:
+
diff --git a/jest.config.js b/jest.config.js
new file mode 100644
index 0000000..2dac575
--- /dev/null
+++ b/jest.config.js
@@ -0,0 +1,3 @@
+module.exports = {
+ preset: '@vue/cli-plugin-unit-jest',
+}
diff --git a/package-lock.json b/package-lock.json
new file mode 100644
index 0000000..5da9d88
--- /dev/null
+++ b/package-lock.json
@@ -0,0 +1,14579 @@
+{
+ "name": "dna-frontend",
+ "version": "2.0.0",
+ "lockfileVersion": 1,
+ "requires": true,
+ "dependencies": {
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+ "dev": true,
+ "requires": {
+ "@babel/highlight": "^7.8.3"
+ }
+ },
+ "@babel/compat-data": {
+ "version": "7.9.6",
+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.9.6.tgz",
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+ "dev": true,
+ "requires": {
+ "browserslist": "^4.11.1",
+ "invariant": "^2.2.4",
+ "semver": "^5.5.0"
+ }
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diff --git a/package.json b/package.json
new file mode 100644
index 0000000..9b581bc
--- /dev/null
+++ b/package.json
@@ -0,0 +1,45 @@
+{
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+ "version": "2.0.0",
+ "description": "DNA analyser frontend",
+ "private": true,
+ "scripts": {
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+ "build": "vue-cli-service build",
+ "test:unit": "vue-cli-service test:unit",
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+ },
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diff --git a/public/index.html b/public/index.html
new file mode 100644
index 0000000..388ccf0
--- /dev/null
+++ b/public/index.html
@@ -0,0 +1,17 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width,initial-scale=1.0">
+ <link rel="icon" href="<%= BASE_URL %>favicon.ico">
+ <title>DNA analyser</title>
+ </head>
+ <body>
+ <noscript>
+ <strong>We're sorry but DNA analyser doesn't work properly without JavaScript enabled. Please enable it to continue.</strong>
+ </noscript>
+ <div id="app"></div>
+ <!-- built files will be auto injected -->
+ </body>
+</html>
diff --git a/src/assets/favicon.ico b/src/assets/favicon.ico
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diff --git a/src/assets/loader.gif b/src/assets/loader.gif
new file mode 100644
index 0000000000000000000000000000000000000000..d0bce1542342e912da81a2c260562df172f30d73
GIT binary patch
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diff --git a/src/axios.js b/src/axios.js
new file mode 100644
index 0000000..29127bf
--- /dev/null
+++ b/src/axios.js
@@ -0,0 +1,6 @@
+import Axios from 'axios'
+
+const axios = Axios.create()
+axios.defaults.baseURL = '/api/'
+
+export default axios
diff --git a/src/components/core/app-form.vue b/src/components/core/app-form.vue
new file mode 100644
index 0000000..76533b2
--- /dev/null
+++ b/src/components/core/app-form.vue
@@ -0,0 +1,73 @@
+<template>
+ <form @submit.prevent="submit" :class="{ loader: formSubmitting }" novalidate>
+ <slot></slot>
+ </form>
+</template>
+
+<script>
+/**
+ * general form which displays overlay loader once submitted
+ *
+ * to remove the loader use enable() method
+ *
+ * pass validator via validator attribute to handle validation internally
+ *
+ * usage:
+ * <app-form @submit="uploadSequence" ref="uploadForm" :validator="$v">
+ * <!-- some inputs and submit element -->
+ * </app-form>
+ */
+export default {
+ props: ['validator'],
+ data() {
+ return {
+ formSubmitting: false,
+ }
+ },
+ methods: {
+ submit() {
+ this.disable()
+ if (this.validator) {
+ this.validator.$touch()
+ if (!this.validator.$invalid) {
+ this.$emit('submit')
+ this.validator.$reset()
+ } else {
+ this.enable()
+ }
+ } else {
+ this.$emit('submit')
+ }
+ },
+ disable() {
+ this.formSubmitting = true
+ },
+ enable() {
+ this.formSubmitting = false
+ },
+ },
+}
+</script>
+
+<style scoped lang="less">
+.loader {
+ position: relative;
+
+ &:after {
+ text-align: center;
+ line-height: 100%;
+ content: '';
+ display: block;
+ position: absolute;
+ top: 0px;
+ left: 0px;
+ right: 0px;
+ bottom: 0px;
+ background-color: #ffffff;
+ background-image: url('/static/loader.png');
+ background-position: center;
+ background-repeat: no-repeat;
+ opacity: 0.8;
+ }
+}
+</style>
diff --git a/src/components/core/app-menu.vue b/src/components/core/app-menu.vue
new file mode 100644
index 0000000..e45cc95
--- /dev/null
+++ b/src/components/core/app-menu.vue
@@ -0,0 +1,159 @@
+<template>
+ <div class="menu">
+ <b-navbar toggleable="md" type="dark" variant="info">
+ <b-navbar-toggle target="nav_collapse"></b-navbar-toggle>
+
+ <b-navbar-brand :to="{ name: 'index' }">
+ DNA analyser
+ </b-navbar-brand>
+
+ <b-collapse is-nav id="nav_collapse">
+ <b-navbar-nav>
+ <b-nav-item-dropdown text="Sequences">
+ <b-dropdown-item :to="{ name: 'sequence.tools' }">
+ My sequences
+ </b-dropdown-item>
+ </b-nav-item-dropdown>
+
+ <b-nav-item-dropdown text="Analyses">
+ <!--
+ <b-dropdown-item :to="{ name: 'analyse.cruciform' }">
+ Palindromes
+ </b-dropdown-item>
+ -->
+ <b-dropdown-item :to="{ name: 'analyse.quadruplex' }" v-if="config.analysis.g4hunter">
+ G4 hunter
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'results.quadruplex' }" v-if="config.analysis.g4hunter">
+ Stored results (G4Hunter)
+ </b-dropdown-item>
+ <!--
+ <div class="dropdown-divider"></div>
+ <b-dropdown-item :to="{ name: 'analyse.p53predictor' }">
+ p53 predictor
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'results.p53predictor' }">
+ Stored results
+ </b-dropdown-item>
+ -->
+ <div class="dropdown-divider" v-if="config.analysis.g4killer"></div>
+ <b-dropdown-item :to="{ name: 'analyse.g4killer' }" v-if="config.analysis.g4killer">
+ G4 killer
+ </b-dropdown-item>
+
+ <div class="dropdown-divider" v-if="config.analysis.p53predictor"></div>
+ <b-dropdown-item :to="{ name: 'tools.p53predictor' }" v-if="config.analysis.p53predictor">
+ P53 predictor
+ </b-dropdown-item>
+
+ <div class="dropdown-divider" v-if="config.analysis.rloopr"></div>
+
+ <b-dropdown-item :to="{ name: 'analyse.rloopr' }" v-if="config.analysis.rloopr">
+ R-loop tracker
+ </b-dropdown-item>
+
+ <b-dropdown-item :to="{ name: 'results.rloopr' }" v-if="config.analysis.rloopr">
+ Stored results (R-loop tracker)
+ </b-dropdown-item>
+ </b-nav-item-dropdown>
+
+ <b-nav-item-dropdown text="Help">
+ <b-dropdown-item :to="{ name: 'help.import' }">
+ Import
+ </b-dropdown-item>
+ <!--
+ <b-dropdown-item :to="{ name: 'help.cruciform' }">
+ Cruciform
+ </b-dropdown-item>
+ -->
+ <b-dropdown-item :to="{ name: 'help.quadruplex' }" v-if="config.analysis.g4hunter">
+ G4 hunter
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'help.g4killer' }" v-if="config.analysis.g4killer">
+ G4 Killer
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'help.p53' }" v-if="config.analysis.p53predictor">
+ P53 predictor
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'help.rloopr' }" v-if="config.analysis.rloopr">
+ R-loop tracker
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'help.faq' }">
+ FAQ
+ </b-dropdown-item>
+ <div class="dropdown-divider"></div>
+ <b-dropdown-item :to="{ name: 'help.about' }">
+ About
+ </b-dropdown-item>
+ <b-dropdown-item href="/adoc/index.html">
+ Documentation
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'help.status' }">
+ Status
+ </b-dropdown-item>
+ </b-nav-item-dropdown>
+
+ <b-nav-item href="http://palindromes.ibp.cz" target="__blank" rel="noopener noreferrer">
+ Palindrome analyser
+ </b-nav-item>
+ </b-navbar-nav>
+
+ <!-- Right aligned nav items -->
+ <b-navbar-nav class="ml-auto">
+ <b-nav-item-dropdown text="Users" right v-if="!user">
+ <b-dropdown-item :to="{ name: 'login' }">
+ Login
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'register' }">
+ Register
+ </b-dropdown-item>
+ <b-dropdown-item :to="{ name: 'reset-password' }">
+ Reset password
+ </b-dropdown-item>
+ </b-nav-item-dropdown>
+
+ <b-nav-item-dropdown :text="user.user" v-if="user">
+ <b-dropdown-item :to="{ name: 'change-password' }">
+ Change password
+ </b-dropdown-item>
+ <b-dropdown-item @click="logout()">
+ Logout
+ </b-dropdown-item>
+ </b-nav-item-dropdown>
+ </b-navbar-nav>
+ </b-collapse>
+ </b-navbar>
+ </div>
+</template>
+
+<script>
+export default {
+ inject: ['UserAuth', 'config'],
+ data: function() {
+ return {}
+ },
+ mounted: function() {},
+ methods: {
+ update: function() {},
+ logout: function() {
+ this.UserAuth.logout()
+ this.$router.push({ name: 'index' })
+ },
+ },
+ computed: {
+ user() {
+ if (this.$store.getters.isGuest) {
+ return null
+ } else {
+ return this.$store.state.user
+ }
+ },
+ },
+}
+</script>
+
+<style>
+.menu {
+ padding-bottom: 20px;
+}
+</style>
diff --git a/src/components/core/app.vue b/src/components/core/app.vue
new file mode 100644
index 0000000..5aa7d38
--- /dev/null
+++ b/src/components/core/app.vue
@@ -0,0 +1,39 @@
+<template>
+ <div>
+ <app-menu></app-menu>
+ <div class="container" v-if="isGuest">
+ <p class="alert alert-warning">
+ You are not logged in. All your work will be lost once you close the browser.
+ <router-link :to="{ name: 'register' }">Create an account</router-link>
+ or <router-link :to="{ name: 'login' }">log in</router-link> to prevent data loss.
+ </p>
+ </div>
+ <router-view></router-view>
+ <work-progress></work-progress>
+ </div>
+</template>
+
+<script>
+import AppMenu from '@/components/core/app-menu'
+import WorkProgress from '@/components/core/work-progress/work-progress'
+
+/**
+ * application main component
+ */
+export default {
+ name: 'app',
+ components: {
+ 'app-menu': AppMenu,
+ 'work-progress': WorkProgress,
+ },
+ computed: {
+ isGuest() {
+ return this.$store.getters.isGuest
+ },
+ },
+}
+</script>
+
+<style lang="less">
+@import '../../less/custom.less';
+</style>
diff --git a/src/components/core/checkable-list.vue b/src/components/core/checkable-list.vue
new file mode 100644
index 0000000..ef434fa
--- /dev/null
+++ b/src/components/core/checkable-list.vue
@@ -0,0 +1,58 @@
+<template>
+ <table v-if="items && items.length > 0" class="table table-hover table-striped">
+ <tbody>
+ <tr>
+ <slot name="header"></slot>
+ </tr>
+ <tr v-for="item of items" @click.stop="item.ui.checked = !item.ui.checked">
+ <td>
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" v-model="item.ui.checked" />
+ <label class="custom-control-label">
+ <slot name="item-name" :item="item"></slot>
+ </label>
+ </div>
+ </td>
+ <slot :item="item"></slot>
+ </tr>
+ </tbody>
+ </table>
+ <div v-else>
+ <slot name="no-items"></slot>
+ </div>
+</template>
+
+<script>
+import Helpers from '@/helpers'
+import Vue from 'vue'
+
+export default {
+ data() {
+ return {
+ items: null,
+ }
+ },
+ methods: {
+ setItems(items) {
+ Helpers.setUIState(items, 'checked', false)
+ this.items = items
+ },
+ getCheckedItems() {
+ return this.items.filter(item => {
+ return item.ui.checked
+ })
+ },
+ /**
+ * toggle check state of currently visible items
+ */
+ toggleSelection() {
+ this.items.forEach(result => {
+ Vue.set(result.ui, 'checked', !result.ui.checked)
+ })
+ },
+ },
+ mounted() {},
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/core/form-result.vue b/src/components/core/form-result.vue
new file mode 100644
index 0000000..14c6507
--- /dev/null
+++ b/src/components/core/form-result.vue
@@ -0,0 +1,40 @@
+<template>
+ <div>
+ <div class="alert alert-success" v-if="hasSuccess">
+ {{ result.success }}
+ </div>
+ <div class="alert alert-danger" v-if="hasFailure">
+ {{ result.failure }}
+ </div>
+ </div>
+</template>
+
+<script>
+export default {
+ data() {
+ return {
+ result: null,
+ }
+ },
+ methods: {
+ failure(msg) {
+ this.result = {
+ failure: msg,
+ }
+ },
+ success(msg) {
+ this.result = {
+ success: msg,
+ }
+ },
+ },
+ computed: {
+ hasSuccess() {
+ return this.result && this.result.success
+ },
+ hasFailure() {
+ return this.result && this.result.failure
+ },
+ },
+}
+</script>
diff --git a/src/components/core/http-error.vue b/src/components/core/http-error.vue
new file mode 100644
index 0000000..3ba8a94
--- /dev/null
+++ b/src/components/core/http-error.vue
@@ -0,0 +1,32 @@
+<template>
+ <div v-if="message">
+ <br />
+ <p class="alert alert-danger">
+ {{ message }}
+ </p>
+ </div>
+</template>
+
+<script>
+/**
+ * display readable explanation of http error from REST routes
+ */
+export default {
+ props: ['info'],
+ data() {
+ return {}
+ },
+ computed: {
+ message() {
+ if (this.info) {
+ if (this.info.response.status == 404) {
+ return 'Resource not found.'
+ } else if (this.info.response.status == 500) {
+ return 'Server failed to deliver results.'
+ }
+ }
+ return ''
+ },
+ },
+}
+</script>
diff --git a/src/components/core/index.vue b/src/components/core/index.vue
new file mode 100644
index 0000000..f695399
--- /dev/null
+++ b/src/components/core/index.vue
@@ -0,0 +1,47 @@
+<template>
+ <div class="container">
+ <h1>DNA analyser</h1>
+
+ <p class="well">
+ DNA Analyser is a web-based server for nucleotide sequence analysis. It has been developed thanks to cooperation
+ of Department of Informatics, Mendel’s University in Brno and Institute of Biophysics, Academy of Sciences of the
+ Czech Republic. The aim of this service is to provide a free and user-friendly tool for studying DNA features with
+ a focus on DNA local structures. The “Palindrome analyserâ€, which is capable to gather information about the
+ presence of inverted repeats in DNA sequences, was established as a first tool. Our unique application displays
+ and analyses detailed information about different parameters of this important DNA feature including inverted
+ repeats similarity, visualization and localization, just to mention a few.
+ </p>
+
+ <p class="well">
+ <strong>Please cite:</strong> Brazda, V., Kolomaznik, J., Lysek, J., Haronikova, L., Coufal, J. and Stastny, J.
+ (2016) Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide
+ sequences. Biochem Bioph Res Co, 478, 1739-1745.
+ <a href="http://dx.doi.org/10.1016/j.bbrc.2016.09.015" target="_blank">link</a>
+ </p>
+
+ <p class="well">
+ <strong>Please cite:</strong> Brázda, V., KolomaznÃk, J., Lýsek, J., Bartas, M., Fojta, M., Šťastný, J., and
+ Mergny, J.-L. (2019). G4Hunter web application: a web server for G-quadruplex prediction. Bioinformatics 35,
+ 3493–3495.
+ <a href="https://academic.oup.com/bioinformatics/article/35/18/3493/5306941" target="_blank">link</a>
+ </p>
+
+ <p class="well">
+ © {{ new Date().getFullYear() }}
+ prof. RNDr. Ing. Jiřà Šťastný, CSc.; Ing. Jan KolomaznÃk, Ph.D.; Ing. Jiřà Lýsek, Ph.D. /
+ <a href="http://informatika.mendelu.cz" target="_blank">ÚI PEF MENDELU</a>
+ <br />
+ doc. Mgr. Václav Brázda, Ph.D. /
+ <a href="http://www.ibp.cz" target="_blank">Biofyzikálnà ústav akademie věd ČR</a>
+ <br />
+ Feedback: <a href="mailto:palindrome@ibp.cz">palindrome@ibp.cz</a>
+ </p>
+ </div>
+</template>
+
+<script>
+/**
+ * main page
+ */
+export default {}
+</script>
diff --git a/src/components/core/modal-alert.vue b/src/components/core/modal-alert.vue
new file mode 100644
index 0000000..f0df669
--- /dev/null
+++ b/src/components/core/modal-alert.vue
@@ -0,0 +1,64 @@
+<template>
+ <b-modal ref="modal" :size="size">
+ <div slot="modal-header" class="modal-header">
+ <h4 class="modal-title">
+ <slot name="header">
+ Alert
+ </slot>
+ </h4>
+ </div>
+ <div class="modal-body">
+ <slot>Alert!</slot>
+ </div>
+ <div slot="modal-footer" class="modal-footer">
+ <b-button type="button" variant="success" @click="confirm">
+ <slot name="button">
+ OK
+ </slot>
+ </b-button>
+ </div>
+ </b-modal>
+</template>
+
+<script>
+/**
+ * modal alert component
+ *
+ * call display method which returns a promise and calls resolve upon dismiss
+ *
+ * usage:
+ * <modal-alert ref="alertModal">message</modal-alert>
+ *
+ * this.$refs.alertModal.display().then(() => {});
+ */
+export default {
+ props: {
+ size: {
+ default: 'sm',
+ type: String,
+ },
+ },
+ data: function() {
+ return {
+ confirmAction: null,
+ }
+ },
+ methods: {
+ confirm() {
+ if (this.confirmAction) {
+ this.confirmAction()
+ }
+ this.hide()
+ },
+ display() {
+ this.$refs.modal.show()
+ return new Promise(resolve => {
+ this.confirmAction = resolve
+ })
+ },
+ hide() {
+ this.$refs.modal.hide()
+ },
+ },
+}
+</script>
diff --git a/src/components/core/modal-confirm.vue b/src/components/core/modal-confirm.vue
new file mode 100644
index 0000000..6c2a2f7
--- /dev/null
+++ b/src/components/core/modal-confirm.vue
@@ -0,0 +1,74 @@
+<template>
+ <b-modal ref="modal" :size="size">
+ <div slot="modal-header" class="modal-header">
+ <h4 class="modal-title">
+ <slot name="header">
+ Confirmation
+ </slot>
+ </h4>
+ </div>
+ <div class="modal-body">
+ <slot>Do you confirm action?</slot>
+ </div>
+ <div slot="modal-footer" class="modal-footer">
+ <b-button type="button" variant="danger" @click="cancel">Cancel</b-button>
+ <b-button type="button" variant="success" @click="confirm">
+ <slot name="buttonConfirm">
+ OK
+ </slot>
+ </b-button>
+ </div>
+ </b-modal>
+</template>
+
+<script>
+/**
+ * modal confirm component
+ *
+ * call display method which returns a promise and calls resolve upon confirmation
+ *
+ * usage:
+ * <modal-confirm ref="confirmModal">message</modal-confirm>
+ *
+ * this.$refs.confirmModal.display().then(() => {});
+ *
+ */
+export default {
+ props: {
+ size: {
+ default: 'md',
+ type: String,
+ },
+ },
+ data: function() {
+ return {
+ confirmAction: null,
+ cancelAction: null,
+ }
+ },
+ methods: {
+ confirm() {
+ if (this.confirmAction) {
+ this.confirmAction()
+ }
+ this.hide()
+ },
+ cancel() {
+ if (this.cancelAction) {
+ this.cancelAction()
+ }
+ this.hide()
+ },
+ display() {
+ this.$refs.modal.show()
+ return new Promise((resolve, reject) => {
+ this.confirmAction = resolve
+ this.cancelAction = reject
+ })
+ },
+ hide() {
+ this.$refs.modal.hide()
+ },
+ },
+}
+</script>
diff --git a/src/components/core/not-found.vue b/src/components/core/not-found.vue
new file mode 100644
index 0000000..3306f6a
--- /dev/null
+++ b/src/components/core/not-found.vue
@@ -0,0 +1,15 @@
+<template>
+ <div class="container">
+ <h1>Page not found</h1>
+ <p>
+ Please use menu to select available module.
+ </p>
+ </div>
+</template>
+
+<script>
+/**
+ * not found page
+ */
+export default {}
+</script>
diff --git a/src/components/core/pagination.vue b/src/components/core/pagination.vue
new file mode 100644
index 0000000..cd71577
--- /dev/null
+++ b/src/components/core/pagination.vue
@@ -0,0 +1,88 @@
+<template>
+ <div>
+ <b-pagination
+ v-if="pageCount > pageSize && paginationTop"
+ align="center"
+ :total-rows="pageCount"
+ v-model="pageCurrent"
+ :per-page="pageSize"
+ @change="pageChange"
+ >
+ </b-pagination>
+
+ <slot></slot>
+
+ <b-pagination
+ v-if="pageCount > pageSize && paginationBottom"
+ align="center"
+ :total-rows="pageCount"
+ v-model="pageCurrent"
+ :per-page="pageSize"
+ @change="pageChange"
+ >
+ </b-pagination>
+ </div>
+</template>
+
+<script>
+/**
+ * pagination wrapper around a list
+ *
+ * usage:
+ * <pagination ref="pagination" @pageChange="reload" :page-size="20">
+ * <!-- any paginated content -->
+ * </pagination>
+ */
+export default {
+ props: {
+ pageSize: {
+ //size of each page
+ type: Number,
+ default: 10,
+ },
+ paginationTop: {
+ //display top pagination
+ type: Boolean,
+ default: false,
+ },
+ paginationBottom: {
+ //display bottom pagination
+ type: Boolean,
+ default: true,
+ },
+ },
+ data() {
+ return {
+ pageCount: 0, //amount of pages
+ pageCurrent: 1, //current page
+ }
+ },
+ methods: {
+ /**
+ * set total count of elements in list (not pages)
+ *
+ * @param c
+ */
+ setPageCount(c) {
+ this.pageCount = c
+ //move to first page in case of insufficient items
+ if (this.pageCount > 0 && Math.ceil(this.pageCount / this.pageSize) < this.pageCurrent) {
+ this.pageCurrent = 1
+ this.pageChange(this.pageCurrent)
+ }
+ },
+ getPageSize() {
+ return this.pageSize
+ },
+ getPageCurrent() {
+ return this.pageCurrent
+ },
+ pageChange(p) {
+ this.pageCurrent = p
+ this.$emit('pageChange', p)
+ },
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/core/result-editor.vue b/src/components/core/result-editor.vue
new file mode 100644
index 0000000..1d115f1
--- /dev/null
+++ b/src/components/core/result-editor.vue
@@ -0,0 +1,50 @@
+<template>
+ <form v-if="result">
+ <h5><sequence :sequence-id="result.sequenceId"></sequence></h5>
+ <br />
+ <label>Tags</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+ <button type="button" class="btn btn-danger" @click="clearTags">
+ <span class="fa fa-trash"></span> Remove all tags
+ </button>
+ </form>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+import Sequence from '@/components/core/sequence'
+
+export default {
+ props: ['result'],
+ data() {
+ return {
+ tags: [],
+ name: '',
+ }
+ },
+ methods: {
+ getTags() {
+ return this.tags
+ },
+ clearTags() {
+ this.tags = []
+ },
+ copySourceInfo() {
+ if (this.result) {
+ this.tags = this.result.tags
+ this.name = this.result.name
+ }
+ },
+ },
+ mounted() {
+ this.copySourceInfo()
+ },
+ components: {
+ 'input-tag': InputTag,
+ sequence: Sequence,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/core/sequence.vue b/src/components/core/sequence.vue
new file mode 100644
index 0000000..7ff5d6d
--- /dev/null
+++ b/src/components/core/sequence.vue
@@ -0,0 +1,72 @@
+<template>
+ <span :class="{ 'font-italic': !sequence }">
+ {{ sequenceTitle }}
+ </span>
+</template>
+
+<script>
+//cache for sequence objects
+var sequenceNameCache = new Map()
+
+/**
+ * display sequence info (name) when you know only ID of sequence
+ *
+ * TODO: hover can display details
+ *
+ * usage:
+ * <sequence :sequence-id="item.sequenceId"></sequence>
+ */
+export default {
+ props: ['sequenceId'],
+ data() {
+ return {
+ sequence: null,
+ sequenceTitle: '',
+ }
+ },
+ methods: {
+ setSequence(s) {
+ this.sequence = s
+ this.sequenceTitle = s.name
+ },
+ downloadSequence() {
+ var cached = sequenceNameCache.get(this.sequenceId)
+ if (cached) {
+ this.setSequence(cached)
+ } else {
+ this.$http.get('sequence/' + this.sequenceId).then(
+ response => {
+ sequenceNameCache.set(this.sequenceId, response.data.payload)
+ this.setSequence(response.data.payload)
+ },
+ err => {
+ if (err.response.status == 404) {
+ this.sequenceTitle = 'deleted sequence'
+ } else {
+ this.sequenceTitle = 'error'
+ }
+ }
+ )
+ }
+ },
+ /**
+ * return current sequence details
+ */
+ getSequence() {
+ return this.sequence
+ },
+ },
+ mounted() {
+ this.sequenceName = this.sequenceId
+ this.downloadSequence()
+ },
+ watch: {
+ sequenceId: function(newVal, oldVal) {
+ if (newVal != oldVal) {
+ this.sequenceName = newVal
+ this.downloadSequence()
+ }
+ },
+ },
+}
+</script>
diff --git a/src/components/core/sort-toggle.vue b/src/components/core/sort-toggle.vue
new file mode 100644
index 0000000..129b315
--- /dev/null
+++ b/src/components/core/sort-toggle.vue
@@ -0,0 +1,55 @@
+<template>
+ <div class="sortButton" @click="sortBy">
+ <span
+ class="fa"
+ :class="{
+ 'fa-sort-up': current.crit == crit && !asc,
+ 'fa-sort-down': current.crit == crit && asc,
+ 'fa-sort': current.crit != crit,
+ }"
+ ></span>
+ <slot></slot>
+ </div>
+</template>
+
+<script>
+/**
+ * sorting component for table headers
+ *
+ * attribute *current*: Object {crit: String, asc: Boolean} -- global sorting state
+ * attribute *crit*: String -- sorting criterion of current toggle
+ * event *sort*: sort click callback
+ *
+ * usage:
+ * <sort-toggle @sort="sortSequences" crit="name" :current="currentSort">Title</sort-toggle>
+ *
+ */
+export default {
+ props: ['crit', 'current'],
+ data() {
+ return {
+ asc: false,
+ }
+ },
+ methods: {
+ sortBy() {
+ this.asc = !this.asc
+ this.$emit('sort', {
+ crit: this.crit,
+ asc: this.asc,
+ })
+ },
+ },
+ mounted() {
+ if (this.current && this.current.crit && this.current.crit == this.crit) {
+ this.asc = this.current.asc
+ }
+ },
+}
+</script>
+
+<style scoped>
+.sortButton {
+ cursor: pointer;
+}
+</style>
diff --git a/src/components/core/visualisation/heatchart.vue b/src/components/core/visualisation/heatchart.vue
new file mode 100644
index 0000000..9a719e3
--- /dev/null
+++ b/src/components/core/visualisation/heatchart.vue
@@ -0,0 +1,306 @@
+<template>
+ <div>
+ <apexchart
+ v-if="type.includes('Coverage')"
+ type="line"
+ height="350"
+ :options="chartOptions"
+ :series="coverage"
+ ></apexchart>
+ <apexchart
+ v-if="type.includes('Count')"
+ type="line"
+ height="350"
+ :options="chartOptions"
+ :series="count"
+ ></apexchart>
+ <div class="button-wrapper">
+ <button type="button" class="btn btn-primary" @click="toggleData()">Coverage/Count</button>
+ <button type="button" class="btn btn-primary" @click="showInfo()">Info</button>
+ </div>
+ <b-modal ref="modalInfo">
+ <div slot="modal-header" class="modal-header">
+ <h4 class="modal-title">Heatmap info</h4>
+ </div>
+ <div class="modal-body">
+ <slot>
+ Segment count: {{ data.metaData.segmentCount }}
+ <br />
+ Segment size: {{ data.metaData.segmentSize }} bp
+ <br />
+ Min count: {{ data.metaData.min.count }}
+ <br />
+ Max count: {{ data.metaData.max.count }}
+ <br />
+ Min coverage: {{ (data.metaData.min.coverage * 100) | number(0) }} %
+ <br />
+ Max coverage: {{ (data.metaData.max.coverage * 100) | number(0) }} %
+ </slot>
+ </div>
+ <div slot="modal-footer" class="modal-footer">
+ <b-button type="button" variant="success" @click="hideInfo">OK</b-button>
+ </div>
+ </b-modal>
+ </div>
+</template>
+
+<script>
+import VueApexCharts from 'vue-apexcharts'
+import Formatters from '@/formatters'
+
+export default {
+ props: ['data'],
+
+ data() {
+ return {
+ type: 'Count',
+ number: Formatters.number,
+ coverage: [
+ {
+ name: 'Coverage',
+ data: [],
+ },
+ ],
+ count: [
+ {
+ name: 'Count',
+ data: [],
+ },
+ ],
+ loading: false,
+ from: 0,
+ to: 0,
+ total: 0,
+ chartOptions: {
+ chart: {
+ toolbar: {
+ tools: {
+ download: true,
+ selection: false,
+ zoom: true,
+ zoomin: false,
+ zoomout: false,
+ pan: false,
+ },
+ },
+ events: {
+ dataPointSelection: (e, chart, config) => {
+ this.dataPointClick(config.dataPointIndex)
+ },
+ zoomed: (chart, { xaxis }) => {
+ const { min, max } = xaxis
+ const { metaData, from, total } = this.data
+
+ chart.updateSeries([{ data: [] }])
+
+ if (!min && !max) {
+ this.onZoom(chart, 0, total)
+ } else {
+ const { segmentSize } = metaData
+ const zoomedMin = min * segmentSize + from
+ const zoomedMax = max * segmentSize + from
+ this.onZoom(chart, zoomedMin, zoomedMax)
+ }
+ },
+ },
+ },
+ colors: ['#ea271b', '#545454'],
+ stroke: {
+ curve: 'smooth',
+ width: 4,
+ },
+ grid: {
+ borderColor: '#e7e7e7',
+ row: {
+ colors: ['#f3f3f3', 'transparent'], // takes an array which will be repeated on columns
+ opacity: 0.5,
+ },
+ },
+ markers: {
+ size: 6,
+ strokeWidth: 3,
+ hover: {
+ sizeOffset: 4,
+ },
+ strokeOpacity: 0.9,
+ },
+ xaxis: {
+ categories: this.getXaxis,
+ title: {
+ text: 'Position (bp)',
+ style: {
+ fontSize: '14px',
+ },
+ },
+ tooltip: {
+ enabled: false,
+ },
+ },
+ yaxis: {
+ title: {
+ text: 'Count (Quadruplex)',
+ style: {
+ fontSize: '14px',
+ },
+ },
+ min: 0,
+ max: this.maxValue,
+ },
+ tooltip: {
+ intersect: true,
+ shared: false,
+ x: {
+ show: true,
+ formatter: (value, index) => {
+ return 'Position: ' + this.getXaxis?.[index.dataPointIndex]
+ },
+ },
+ y: {
+ formatter: function(value) {
+ return Math.trunc(value)
+ },
+ },
+ },
+ noData: {
+ text: 'Loading...',
+ },
+ title: {
+ text: '',
+ align: 'center',
+ },
+ states: {
+ active: {
+ filter: {
+ type: 'darken',
+ value: 0.3,
+ },
+ },
+ },
+ },
+ }
+ },
+ methods: {
+ reload() {
+ this.count[0].data = this.countData
+ this.coverage[0].data = this.coverageData
+
+ this.chartOptions = {
+ xaxis: {
+ categories: this.getXaxis,
+ },
+ }
+ },
+
+ onZoom(chart, from, to) {
+ this.$emit('onZoom', from, to, () => {
+ this.reload()
+ chart.updateSeries(this.type === 'Count' ? this.count : this.coverage)
+ chart.updateOptions(this.chartOptions, true, false, false)
+ })
+ },
+
+ toggleData() {
+ let color = null
+ if (this.type.includes('Count')) {
+ this.type = 'Coverage (%)'
+ color = this.getCoverageColor
+ } else {
+ this.type = 'Count (Quadruplex)'
+ color = this.getCountColor
+ }
+ this.chartOptions = {
+ yaxis: {
+ title: {
+ text: this.getYtitle,
+ style: {
+ fontSize: '14px',
+ },
+ },
+ },
+ colors: color,
+ }
+ },
+
+ showInfo() {
+ this.$refs.modalInfo.show()
+ },
+
+ hideInfo() {
+ this.$refs.modalInfo.hide()
+ },
+
+ dataPointClick(pos) {
+ this.$emit('dataPointClick', pos, this.data.metaData.segmentSize)
+ },
+ },
+
+ computed: {
+ countData() {
+ return this.segmentData.map(item => Math.trunc(item.count))
+ },
+
+ coverageData() {
+ return this.segmentData.map(item => (item.coverage * 100) | this.number(0))
+ },
+
+ getYtitle() {
+ return this.type
+ },
+
+ getXaxis() {
+ const { metaData, from } = this.data
+ const { segmentSize } = metaData
+
+ let data = []
+ for (let i = 1; i <= this.segments; i++) {
+ data.push(i * segmentSize + from)
+ }
+ return data
+ },
+
+ segmentData() {
+ return this.data.data
+ },
+ segments() {
+ return this.data.metaData.segmentCount
+ },
+ maxValue() {
+ return this.data.metaData.max.count
+ },
+
+ getCoverageColor() {
+ return ['#77B6EA', '#545454']
+ },
+
+ getCountColor() {
+ return ['#ea271b', '#545454']
+ },
+ },
+
+ mounted() {
+ this.reload()
+ },
+
+ filters: {
+ number: Formatters.number,
+ },
+
+ components: {
+ apexchart: VueApexCharts,
+ },
+}
+</script>
+
+<style scoped>
+.btn {
+ float: right;
+ margin-left: 10px;
+ position: relative;
+}
+
+.button-wrapper {
+ width: 100%;
+ height: 50px;
+ margin-top: -30px;
+}
+</style>
diff --git a/src/components/core/visualisation/heatmap.vue b/src/components/core/visualisation/heatmap.vue
new file mode 100644
index 0000000..4c1409d
--- /dev/null
+++ b/src/components/core/visualisation/heatmap.vue
@@ -0,0 +1,177 @@
+<template>
+ <div>
+ <div class="heatmap" v-if="type == 'count'">
+ <div
+ class="segment"
+ :style="calcStyleCount(info.count)"
+ :class="{ selected: selected == key }"
+ v-for="(info, key) of segmentData"
+ @click="segmentClick(key)"
+ >
+ <span>{{ info.count }}</span>
+ </div>
+ <div class="toggle" @click="showCoverage()" title="Show coverage">
+ <span>%</span>
+ </div>
+ <div class="info" @click="showInfo()" title="Show heatmap info">
+ <span class="fa fa-info"></span>
+ </div>
+ </div>
+ <div class="heatmap" v-if="type == 'coverage'">
+ <div
+ class="segment"
+ :title="'Coverage ' + number(info.coverage * 100) + '%'"
+ :class="{ selected: selected == key }"
+ :style="calcStyleCoverage(info.coverage)"
+ v-for="(info, key) of segmentData"
+ @click="segmentClick(key)"
+ >
+ <span>{{ (info.coverage * 100) | number(0) }}</span>
+ </div>
+ <div class="toggle" @click="showCount" title="Show absolute count">
+ <span>#</span>
+ </div>
+ <div class="info" @click="showInfo" title="Show heatmap info">
+ <span class="fa fa-info"></span>
+ </div>
+ </div>
+ <b-modal ref="modalInfo">
+ <div slot="modal-header" class="modal-header">
+ <h4 class="modal-title">Heatmap info</h4>
+ </div>
+ <div class="modal-body">
+ <slot>
+ Segment count: {{ data.metaData.segmentCount }}
+ <br />
+ Segment size: {{ data.metaData.segmentSize }} bp
+ <br />
+ Min count: {{ data.metaData.min.count }}
+ <br />
+ Max count: {{ data.metaData.max.count }}
+ <br />
+ Min coverage: {{ (data.metaData.min.coverage * 100) | number(0) }} %
+ <br />
+ Max coverage: {{ (data.metaData.max.coverage * 100) | number(0) }} %
+ </slot>
+ </div>
+ <div slot="modal-footer" class="modal-footer">
+ <b-button type="button" variant="success" @click="hideInfo">OK</b-button>
+ </div>
+ </b-modal>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+
+/**
+ * heatmap component
+ *
+ * usage:
+ * <heatmap :data="heatmapData" @segmentClick="showSegment" :selected="selectedSegment"></heatmap>
+ */
+export default {
+ props: ['data', 'selected'],
+ data() {
+ return {
+ type: 'count',
+ number: Formatters.number,
+ }
+ },
+ methods: {
+ calcStyleCount(count) {
+ var r = Math.round((count / this.maxValue) * 255)
+ return {
+ backgroundColor: 'rgb(' + r + ', 0, 0)',
+ width: 'calc(((100% - 4rem) / ' + this.segments + '))',
+ }
+ },
+ calcStyleCoverage(coverage) {
+ var avg = this.data.metaData.avg.coverage
+ var b
+ if (avg > coverage) {
+ b = Math.round((((coverage - avg) / avg) * 255) / 2 + 255 / 2)
+ } else {
+ b = Math.round(((coverage / avg) * 255) / 2)
+ }
+ return {
+ backgroundColor: 'rgb(0, 0, ' + b + ')',
+ width: 'calc(((100% - 4rem) / ' + this.segments + '))',
+ }
+ },
+ showCount() {
+ this.type = 'count'
+ },
+ showCoverage() {
+ this.type = 'coverage'
+ },
+ segmentClick(pos) {
+ this.$emit('segmentClick', pos, this.data.metaData.segmentSize)
+ },
+ showInfo() {
+ this.$refs.modalInfo.show()
+ },
+ hideInfo() {
+ this.$refs.modalInfo.hide()
+ },
+ },
+ computed: {
+ segmentData() {
+ return this.data.data
+ },
+ segments() {
+ return this.data.metaData.segmentCount
+ },
+ maxValue() {
+ return this.data.metaData.max.count
+ },
+ },
+ filters: {
+ number: Formatters.number,
+ },
+}
+</script>
+
+<style scoped>
+.heatmap {
+ margin: 0.5rem 0 0.5rem 0;
+ width: 100%;
+}
+.heatmap .segment,
+.heatmap .toggle,
+.heatmap .info {
+ height: 2rem;
+ border: 1px solid #666666;
+ display: inline-block;
+ margin: 0;
+}
+.heatmap .segment {
+ background: #000000;
+ cursor: pointer;
+}
+.heatmap .segment.selected {
+ border: 1px solid #00ff00;
+}
+.heatmap .toggle {
+ background: #999999;
+ width: 2rem;
+ cursor: pointer;
+}
+.heatmap .info {
+ background: #999999;
+ width: 2rem;
+ cursor: pointer;
+}
+.heatmap .segment span,
+.heatmap .toggle span,
+.heatmap .info span {
+ display: block;
+ text-align: center;
+ color: #ffffff;
+ line-height: 1.9rem;
+ font-size: 8pt;
+ height: 2rem;
+ width: 100%;
+ overflow: hidden;
+}
+</style>
diff --git a/src/components/core/visualisation/highlight.vue b/src/components/core/visualisation/highlight.vue
new file mode 100644
index 0000000..f75a336
--- /dev/null
+++ b/src/components/core/visualisation/highlight.vue
@@ -0,0 +1,102 @@
+<template>
+ <div class="highlight">
+ <span v-for="part of sequenceHighlight" :class="part.styleClass">{{ part.nuclide }}</span>
+ </div>
+</template>
+
+<script>
+export default {
+ props: ['sequence', 'mask'],
+ data() {
+ return {}
+ },
+ computed: {
+ sequenceHighlight() {
+ const styleClass = {
+ '0': 'other',
+ '1': 'len1 Gs',
+ '2': 'len2 Gs',
+ '3': 'len3 Gs',
+ '4': 'len4 Gs',
+ '5': 'len1 Cs',
+ '6': 'len2 Cs',
+ '7': 'len3 Cs',
+ '8': 'len4 Cs',
+ }
+
+ let codes = this.sequence
+ .toUpperCase()
+ .replace(/[ATU]/g, '0')
+ .replace(/G+/g, x =>
+ Math.min(4, x.length)
+ .toString()
+ .repeat(x.length)
+ )
+
+ .replace(/C+/g, x => (Math.min(4, x.length) + 4).toString().repeat(x.length))
+
+ var ret = []
+
+ for (var i = 0; i < this.sequence.length; i++) {
+ var code = codes[i]
+ ret.push({
+ styleClass: styleClass[code] + (this.mask && this.mask[i] === 'W' ? ' mutation' : ''),
+ nuclide: this.sequence[i].toUpperCase(),
+ })
+ }
+ return ret
+ },
+ },
+}
+</script>
+
+<style scoped>
+.mutation {
+ background-color: gold;
+ padding: 0.1rem;
+ border: 1px solid darkgoldenrod;
+ border-radius: 0.2rem;
+}
+
+.other {
+ color: #666666;
+}
+
+.len1.Gs {
+ color: #990000;
+}
+.len1.Cs {
+ color: #000099;
+}
+
+.len2.Gs {
+ color: #bb0000;
+}
+.len2.Cs {
+ color: #0000bb;
+}
+
+.len3.Gs {
+ color: #dd0000;
+}
+.len3.Cs {
+ color: #0000dd;
+}
+
+.len4.Gs {
+ color: #ff0000;
+}
+.len4.Cs {
+ color: #0000ff;
+}
+
+.highlight {
+ display: block;
+ word-wrap: break-word;
+ white-space: normal;
+ padding: 0;
+ margin: 0;
+ line-height: 1;
+ font-size: 1.3rem;
+}
+</style>
diff --git a/src/components/core/visualisation/mini-chart.vue b/src/components/core/visualisation/mini-chart.vue
new file mode 100644
index 0000000..f459336
--- /dev/null
+++ b/src/components/core/visualisation/mini-chart.vue
@@ -0,0 +1,84 @@
+<template>
+ <canvas :width="w" :height="h" ref="canvas"></canvas>
+</template>
+
+<script>
+/**
+ * mini chart that displays x axis (zero) and plots data from a 1D array
+ */
+export default {
+ props: ['w', 'h', 'data', 'min', 'max'],
+ data() {
+ return {
+ minVal: 0,
+ maxVal: 1,
+ range: 1,
+ ctx: null,
+ }
+ },
+ methods: {
+ _getYPos(p) {
+ return ((this.maxVal - p) / this.range) * this.h
+ },
+ drawZero() {
+ var ctx = this.ctx
+
+ ctx.strokeStyle = '#000000'
+
+ var y = this._getYPos(0)
+
+ ctx.beginPath()
+ ctx.moveTo(0, y)
+ ctx.lineTo(this.w, y)
+ ctx.stroke()
+ },
+ drawData() {
+ var ctx = this.ctx
+
+ ctx.strokeStyle = '#FF0000'
+ ctx.fillStyle = '#eca1a6'
+
+ ctx.beginPath()
+ ctx.moveTo(0, this._getYPos(0))
+ ctx.lineTo(0, this._getYPos(this.data[0]))
+ for (var i = 0; i < this.data.length; i++) {
+ var x = ((i + 1) / this.data.length) * this.w
+ var y = this._getYPos(this.data[i])
+ ctx.lineTo(x, y)
+ }
+ ctx.lineTo(this.w, this._getYPos(0))
+ ctx.lineTo(0, this._getYPos(0))
+ ctx.closePath()
+ ctx.stroke()
+ ctx.fill()
+ },
+ paint() {
+ var canvas = this.$refs.canvas
+ this.ctx = canvas.getContext('2d')
+ this.minVal = this.min ? this.min : Math.min(...this.data)
+ this.maxVal = this.max ? this.max : Math.max(...this.data)
+
+ if (this.minVal > 0 && this.maxVal > 0) {
+ this.minVal = 0
+ } else if (this.minVal < 0 && this.maxVal < 0) {
+ this.maxVal = 0
+ }
+
+ this.range = this.maxVal - this.minVal
+
+ this.ctx.clearRect(-1, -1, this.w + 1, this.h + 1)
+
+ this.drawData()
+ this.drawZero()
+ },
+ },
+ mounted() {
+ this.paint()
+ },
+ watch: {
+ data() {
+ this.paint()
+ },
+ },
+}
+</script>
diff --git a/src/components/core/visualisation/sequence-view.vue b/src/components/core/visualisation/sequence-view.vue
new file mode 100644
index 0000000..693c138
--- /dev/null
+++ b/src/components/core/visualisation/sequence-view.vue
@@ -0,0 +1,73 @@
+<template>
+ <div class="sequence text-monospace text-bold">
+ <slot :left="left" :feature="feature" :right="right"> {{ left }}{{ feature }}{{ right }} </slot>
+ </div>
+</template>
+
+<script>
+/**
+ * display surrounding of sequence
+ */
+export default {
+ data() {
+ return {
+ left: '',
+ feature: '',
+ right: '',
+ }
+ },
+ props: {
+ /**
+ * sequence object, must have id and length props
+ */
+ sequence: {
+ required: true,
+ },
+ /**
+ * position of feature
+ */
+ featurePos: {
+ type: Number,
+ required: true,
+ },
+ /**
+ * length of feature
+ */
+ featureLen: {
+ type: Number,
+ required: true,
+ },
+ /**
+ * amount of bases to display before and after
+ */
+ aroundLen: {
+ type: Number,
+ default: 15,
+ required: false,
+ },
+ },
+ methods: {},
+ mounted() {
+ var p = Math.max(0, this.featurePos - this.aroundLen)
+ var lenLeft = this.featurePos - p
+ var l = this.featureLen + lenLeft + this.aroundLen
+ this.$http.get(`sequence/${this.sequence.id}/data?pos=${p}&len=${l}`).then(response => {
+ this.left = response.data.substr(0, lenLeft)
+ this.feature = response.data.substr(lenLeft, this.featureLen)
+ this.right = response.data.substr(lenLeft + this.featureLen)
+ })
+ },
+}
+</script>
+
+<style scoped>
+.sequence {
+ max-width: 100%;
+ overflow: hidden;
+ text-overflow: ellipsis;
+ white-space: nowrap;
+ padding: 0;
+ margin: 0;
+ line-height: 1;
+}
+</style>
diff --git a/src/components/core/work-progress/store.js b/src/components/core/work-progress/store.js
new file mode 100644
index 0000000..41abc2b
--- /dev/null
+++ b/src/components/core/work-progress/store.js
@@ -0,0 +1,28 @@
+export default {
+ state: {
+ workItems: [],
+ },
+ mutations: {
+ /**
+ * adds work info to list of tasks
+ *
+ * must have `key` and `title` attributes
+ *
+ * @param state
+ * @param info payload
+ */
+ addWork(state, info) {
+ state.workItems.push(info)
+ },
+ /**
+ * removes
+ * @param state
+ * @param key
+ */
+ workDone(state, key) {
+ state.workItems = state.workItems.filter(item => {
+ return item.key != key
+ })
+ },
+ },
+}
diff --git a/src/components/core/work-progress/work-progress.vue b/src/components/core/work-progress/work-progress.vue
new file mode 100644
index 0000000..88b3e1f
--- /dev/null
+++ b/src/components/core/work-progress/work-progress.vue
@@ -0,0 +1,101 @@
+<template>
+ <div class="work-progress" :class="{ hidden: uiHidden }">
+ <div class="header">
+ Work progress ({{ count }})
+ <button @click="toggleVisible">
+ <span class="fa" :class="{ 'fa-arrow-down': !uiHidden, 'fa-arrow-up': uiHidden }"></span>
+ </button>
+ </div>
+ <div class="tasks">
+ <ul>
+ <li v-for="work of workItems">
+ <span class="fa fa-spinner animate"></span>
+ {{ work.title }}
+ </li>
+ </ul>
+ </div>
+ </div>
+</template>
+
+<script>
+/**
+ * display list of currently active backend tasks
+ *
+ */
+export default {
+ data() {
+ return {
+ uiHidden: true,
+ }
+ },
+ methods: {
+ toggleVisible() {
+ this.uiHidden = !this.uiHidden
+ },
+ },
+ mounted() {},
+ computed: {
+ workItems() {
+ return this.$store.state.workProgress.workItems
+ },
+ count() {
+ return this.$store.state.workProgress.workItems.length
+ },
+ },
+}
+</script>
+
+<style scoped lang="less">
+@headerHeight: 2.5rem;
+@minHeight: 160px;
+@maxHeight: 160px;
+
+.work-progress {
+ position: fixed;
+ bottom: 0;
+ right: 10vw;
+ width: 300px;
+ border: 1px solid #000000;
+ background: #ffffff;
+ max-height: @maxHeight;
+
+ &:not(.hidden) {
+ min-height: @minHeight;
+ }
+
+ &.hidden {
+ height: @headerHeight;
+ }
+
+ .header {
+ height: @headerHeight;
+ line-height: @headerHeight;
+ background: #17a2b8;
+ color: #ffffff;
+ padding-left: 0.5rem;
+
+ button {
+ background: none;
+ border: none;
+ height: @headerHeight;
+ color: #ffffff;
+ float: right;
+ width: @headerHeight;
+ cursor: pointer;
+ }
+ }
+
+ ul {
+ margin: 0;
+ padding: 0;
+ overflow: auto;
+ li {
+ list-style-type: none;
+ padding: 0.5rem;
+ margin: 0.2rem;
+ background: #cccccc;
+ border-radius: 0.5rem;
+ }
+ }
+}
+</style>
diff --git a/src/components/cruciform/cruciform.vue b/src/components/cruciform/cruciform.vue
new file mode 100644
index 0000000..36238d2
--- /dev/null
+++ b/src/components/cruciform/cruciform.vue
@@ -0,0 +1,22 @@
+<template>
+ <div class="container-fluid">
+ <h1>Palindrome analyser</h1>
+ <input-form></input-form>
+ <heatmap></heatmap>
+ <results-list></results-list>
+ </div>
+</template>
+
+<script>
+import InputForm from './input-form'
+import Heatmap from './heatmap'
+import ResultsList from './results-list'
+
+export default {
+ components: {
+ 'input-form': InputForm,
+ heatmap: Heatmap,
+ 'results-list': ResultsList,
+ },
+}
+</script>
diff --git a/src/components/cruciform/heatmap.vue b/src/components/cruciform/heatmap.vue
new file mode 100644
index 0000000..3b01247
--- /dev/null
+++ b/src/components/cruciform/heatmap.vue
@@ -0,0 +1,7 @@
+<template>
+ <div></div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/cruciform/input-form.vue b/src/components/cruciform/input-form.vue
new file mode 100644
index 0000000..19205b5
--- /dev/null
+++ b/src/components/cruciform/input-form.vue
@@ -0,0 +1,62 @@
+<template>
+ <form>
+ <div class="row">
+ <div class="col-sm-3">
+ <label>Size</label>
+ <div class="input-group">
+ <input class="form-control" type="tex" />
+ <div class="input-group-addon">range</div>
+ </div>
+ <br />
+ </div>
+ <div class="col-sm-3">
+ <label>Spacer</label>
+ <div class="input-group">
+ <input class="form-control" type="tex" />
+ <div class="input-group-addon">range</div>
+ </div>
+ <br />
+ </div>
+ <div class="col-sm-3">
+ <label>Mismatches</label>
+ <div class="input-group">
+ <input class="form-control" type="tex" />
+ <div class="input-group-addon">range</div>
+ </div>
+ <br />
+ </div>
+ <div class="col-sm-3">
+ <label>Options</label>
+
+ <br />
+
+ <label class="checkbox-inline">
+ <input type="checkbox" />
+ Circular input
+ </label>
+
+ <br />
+
+ <label class="checkbox-inline">
+ <input type="checkbox" />
+ Filter ATATATAT...
+ </label>
+
+ <br />
+ </div>
+ </div>
+
+ <textarea class="form-control" cols="80" rows="4"></textarea>
+ <br />
+
+ <div class="row">
+ <div class="col-sm-2 col-sm-offset-10">
+ <button class="btn btn-success btn-block" type="submit"><i class="fa fa-cog"></i> Analyse</button>
+ </div>
+ </div>
+ </form>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/cruciform/results-list.vue b/src/components/cruciform/results-list.vue
new file mode 100644
index 0000000..3b01247
--- /dev/null
+++ b/src/components/cruciform/results-list.vue
@@ -0,0 +1,7 @@
+<template>
+ <div></div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/g4killer/backup.vue b/src/components/g4killer/backup.vue
new file mode 100644
index 0000000..937a037
--- /dev/null
+++ b/src/components/g4killer/backup.vue
@@ -0,0 +1,222 @@
+<template>
+ <div class="container">
+ <!-- G4killer multiple form -->
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v">
+ <label class="mandatory">Sequences</label>
+ <!--Inputs -->
+ <textarea class="form-control" v-model="sequences" rows="10"></textarea>
+ <br />
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <!--Allert messages -->
+ <div v-if="!$v.sequences.required">Sequence is required.</div>
+ <div v-if="!$v.sequences.numLines">The limit is {{ $v.sequences.$params.numLines.amount }} rows.</div>
+ </div>
+ <label class="mandatory">Target G4 hunter score</label>
+ <div class="row">
+ <div class="col-md-3">
+ <input
+ type="number"
+ class="form-control"
+ step="0.1"
+ min="1.2"
+ max="2"
+ required
+ v-model="$v.threshold.$model"
+ />
+ </div>
+ <div class="col-md-2">
+ <button type="submit" class="btn btn-primary">Calculate</button>
+ </div>
+ </div>
+ </app-form>
+ <hr />
+
+ <!-- Results -->
+ <div v-if="results">
+ <h2>Results</h2>
+ <br />
+ <table v-for="result in results" class="table table-striped">
+ <tbody>
+ <!-- Result table header -->
+ <tr>
+ <th class="text-center">Original sequence</th>
+ <th class="text-center">Score</th>
+ <th class="text-center">Show mutations</th>
+ </tr>
+ <!-- Result table content -->
+ <tr>
+ <td class="sequence text-center text-bold">
+ <Highlight :sequence="result.originSequence"></Highlight>
+ </td>
+ <td class="text-center">{{ result.originScore | number }}</td>
+ <td class="text-center">
+ <!-- Button show mutation results -->
+ <b-button variant="primary" v-if="!result.showMutated" @click="toggleShowMutations(result)"
+ >Show</b-button
+ >
+ <b-button variant="primary" v-if="result.showMutated" @click="toggleShowMutations(result)">Hide</b-button>
+ </td>
+ </tr>
+ <!-- Mutated sequences header -->
+ <tr v-if="result.showMutated">
+ <th class="text-center">Mutated sequence</th>
+ <th class="text-center">Score</th>
+ <th class="text-center">Details</th>
+ </tr>
+ <!-- Mutated sequences content -->
+ <template v-for="mutationSequence in result.mutationSequences">
+ <tr v-if="result.showMutated">
+ <td class="sequence text-center text-bold">
+ <Highlight :sequence="mutationSequence.sequence"></Highlight>
+ </td>
+ <td class="text-center">{{ result.mutationScore | number }}</td>
+ <td class="text-center">
+ <b-button
+ variant="primary"
+ v-if="!mutationSequence.showDetail"
+ @click="toggleShowDetail(mutationSequence)"
+ >Show</b-button
+ >
+ <b-button
+ variant="primary"
+ v-if="mutationSequence.showDetail"
+ @click="toggleShowDetail(mutationSequence)"
+ >Hide</b-button
+ >
+ </td>
+ </tr>
+ <!-- Mutated sequences detail content -->
+ <tr v-if="mutationSequence.showDetail">
+ <td colspan="3">
+ <pre>
+ {{ mutationSequence.origin }}
+ {{ mutationSequence | difference }}
+ {{ mutationSequence.sequence }}
+ </pre>
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ </div>
+ </div>
+</template>
+
+<script>
+import Highlight from '@/components/core/visualisation/highlight'
+import Formatters from '@/formatters'
+import AppForm from '@/components/core/app-form'
+import { required, minValue, maxValue, decimal, helpers } from 'vuelidate/lib/validators'
+
+const numLines = lines => {
+ return helpers.withParams({ type: 'numLines', amount: lines }, s => {
+ return (
+ s.split('\n').filter(r => {
+ return r.trim() != ''
+ }).length <= lines
+ )
+ })
+}
+
+export default {
+ data() {
+ return {
+ sequences: '',
+ threshold: 1.4,
+ showRes: false,
+ results: null,
+ differences: '',
+ }
+ },
+ validations: {
+ sequences: {
+ required,
+ numLines: numLines(20),
+ },
+ threshold: {
+ required,
+ decimal,
+ minValue: minValue(1.2),
+ maxValue: maxValue(2),
+ },
+ },
+ components: {
+ Highlight,
+ AppForm,
+ },
+ filters: {
+ number: Formatters.number,
+ difference: function(mutationSequence) {
+ return mutationSequence.origin.replace(/W/g, '-').replace(/\w/g, '|')
+ },
+ },
+ methods: {
+ calculate() {
+ this.results = []
+ this.differences = []
+
+ let promises = []
+
+ this.sequences.split('\n').forEach(item => {
+ item = item.trim()
+
+ if (item.length > 0) {
+ let p = this.$http
+ .post('/analyse/g4killer', {
+ sequence: item,
+ threshold: this.threshold,
+ })
+ .then(
+ resp => {
+ let sequence = resp.data
+ console.log(sequence)
+ sequence.showMutated = false
+ sequence.mutationSequences = resp.data.mutationSequences.map(ms => ({
+ origin: ms,
+ sequence: this.replaceMutationSequence(ms),
+ showDetail: false,
+ }))
+ this.results.push(sequence)
+ },
+ () => {
+ //TODO
+ }
+ )
+ promises.push(p)
+ }
+ })
+ Promise.all(promises).finally(() => {
+ this.$refs.calculateForm.enable()
+ this.showRes = true
+ })
+ },
+ replaceMutationSequence(mutationSequence) {
+ const replacement = ['A', 'T']
+ return mutationSequence.replace(/W/g, () => {
+ return replacement[Math.floor(Math.random() * replacement.length)]
+ })
+ },
+ toggleShowDetail(mutationSequence) {
+ mutationSequence.showDetail = !mutationSequence.showDetail
+ },
+ toggleShowMutations(sequence) {
+ sequence.showMutated = !sequence.showMutated
+ },
+ },
+ mounted() {
+ if (this.$route.query.threshold) {
+ this.threshold = parseFloat(this.$route.query.threshold)
+ }
+ if (this.$route.query.sequence) {
+ this.sequence = this.$route.query.sequence
+ this.calculate()
+ }
+ },
+}
+</script>
+
+<style scoped>
+textarea {
+ font-family: monospace;
+}
+</style>
diff --git a/src/components/g4killer/form-multiple.vue b/src/components/g4killer/form-multiple.vue
new file mode 100644
index 0000000..82a3e30
--- /dev/null
+++ b/src/components/g4killer/form-multiple.vue
@@ -0,0 +1,223 @@
+<template>
+ <div class="container">
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v">
+ <div class="row">
+ <div class="col-md-12">
+ <label class="mandatory">Sequence</label>
+ <textarea class="form-control" @change="handleSequenceChange($event)" rows="10" cols="2"></textarea>
+ <br />
+ </div>
+ </div>
+ <label class="mandatory">Target G4 hunter score</label>
+ <div class="row">
+ <div class="col-md-3">
+ <input type="number" class="form-control" step="0.1" min="0" max="2" required v-model="$v.threshold.$model" />
+ <br />
+ </div>
+ <div class="col-md-2">
+ <button type="submit" class="btn btn-primary">Calculate</button>
+ <br />
+ </div>
+ </div>
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.threshold.maxValue">Maximal value of threshold is {{ $v.threshold.$params.maxValue.max }}.</div>
+ <div v-if="!$v.sequenceArray.required">Sequences are required.</div>
+ <div v-if="!$v.sequenceArray.maxLength">The limit is {{ $v.sequenceArray.$params.maxLength.max }} rows.</div>
+ <div v-if="$v.threshold.$model <= 1.2">
+ The probability of G-quadruplex formation with G4Hunter score below 1.2 is low.
+ </div>
+ <div v-if="!$v.threshold.required">Threshold is required.</div>
+ <div v-if="!$v.threshold.decimal">
+ Threshold must be decimal number.
+ </div>
+ <div v-if="!$v.threshold.decimal">
+ Threshold must be decimal number.
+ </div>
+ </div>
+ <div class="alert alert-danger" v-if="error">Analyse failed: {{ error[0].defaultMessage }}</div>
+ </app-form>
+
+ <hr />
+ <div v-if="Array.isArray(results) && results.length">
+ <h2>Results</h2>
+ <table class="table table-striped">
+ <tbody>
+ <tr>
+ <th class="text-left">#</th>
+ <th class="text-left">Original sequence</th>
+ <th class="text-center">Score</th>
+ <th class="text-left">Mutated sequence</th>
+ <th class="text-center">Mutated score</th>
+ <th class="text-center">Show mutations</th>
+ </tr>
+ <template v-for="(result, index) in results">
+ <tr v-if="result && result.mutationSequences">
+ <td>{{ index + 1 }}</td>
+ <td class="sequence text-left text-bold">
+ <Highlight :sequence="result.originSequence" />
+ </td>
+ <td class="text-center">{{ result.originScore | number }}</td>
+ <td class="sequence text-left text-bold">
+ <Highlight
+ :sequence="result.mutationSequences[0].sequence"
+ :mask="result.mutationSequences[0].origin"
+ >
+ </Highlight>
+ </td>
+ <td class="text-center">{{ result.mutationScore | number }}</td>
+ <td class="text-center">
+ <b-button
+ variant="primary"
+ v-if="!result.mutationSequences[0].showDetail"
+ @click="toggleShowDetail(result.mutationSequences[0])"
+ >
+ Show
+ </b-button>
+ <b-button
+ variant="primary"
+ v-if="result.mutationSequences[0].showDetail"
+ @click="toggleShowDetail(result.mutationSequences[0])"
+ >
+ Hide
+ </b-button>
+ </td>
+ </tr>
+ <tr v-else>
+ <td>{{ index + 1 }}</td>
+ <td class="sequence text-left text-bold">
+ <Highlight :sequence="result.originSequence" />
+ </td>
+ <td class="text-center">{{ result.originScore | number }}</td>
+
+ <td class="alert-warning text-center" colspan="3">
+ The target score {{ threshold }} is below the G4Hunter score of the sequence.
+ <b>No mutation is needed!</b>
+ </td>
+ </tr>
+ <tr v-if="result && result.mutationSequences && result.mutationSequences[0].showDetail">
+ <td class="text-center" colspan="6">
+ <G4KillerDetail :sequence="result.originSequence" :mutation="result.mutationSequences[0]" />
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ <hr />
+ </div>
+ <div class="card bg-light">
+ <div class="card-body">
+ In the case that there are more options for mutation – only one is shown here. For more options use “Single“
+ tab.
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import Highlight from '@/components/core/visualisation/highlight'
+import G4KillerDetail from './g4killer-detail'
+import Formatters from '@/formatters'
+import AppForm from '@/components/core/app-form'
+import { required, minValue, maxValue, decimal, maxLength } from 'vuelidate/lib/validators'
+import { chunkString } from '@/utils'
+
+const splitSequences = sequences =>
+ sequences.split('\n').reduce((acc, sequence) => [...acc, ...chunkString(sequence, 90)], [])
+
+export default {
+ components: {
+ Highlight,
+ G4KillerDetail,
+ AppForm,
+ },
+ data() {
+ return {
+ sequenceArray: [],
+ threshold: 1.0,
+ showRes: false,
+ results: null,
+ differences: '',
+ error: null,
+ }
+ },
+ validations: {
+ sequenceArray: {
+ required,
+ maxLength: maxLength(10),
+ },
+ threshold: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(2),
+ },
+ },
+ methods: {
+ handleSequenceChange(event) {
+ this.sequenceArray = splitSequences(event.target.value)
+ },
+ calculate() {
+ this.error = null
+ this.results = []
+ this.differences = []
+
+ this.sequenceArray.forEach(sequence => {
+ const item = sequence.trim()
+
+ if (item.length > 0) {
+ this.$http
+ .post('/analyse/g4killer', {
+ sequence: item,
+ threshold: this.threshold,
+ })
+ .then(response => {
+ let sequence = response.data
+ this.results.push(sequence)
+ sequence.showMutated = false
+ if (response.data.mutationSequences != null) {
+ sequence.mutationSequences = response.data.mutationSequences.map(ms => ({
+ origin: ms,
+ sequence: this.replaceMutationSequence(ms),
+ showDetail: false,
+ }))
+ }
+ })
+ .catch(error => {
+ if (error.response) {
+ this.error = error.response.data.errors
+ }
+ })
+ .finally(() => {
+ this.$refs.calculateForm.enable()
+ })
+ }
+ })
+ },
+ replaceMutationSequence(mutationSequence) {
+ const replacement = ['A', 'T']
+ return mutationSequence.replace(/W/g, () => {
+ return replacement[Math.floor(Math.random() * replacement.length)]
+ })
+ },
+ toggleShowDetail(mutationSequence) {
+ mutationSequence.showDetail = !mutationSequence.showDetail
+ },
+ },
+ filters: {
+ number: Formatters.number,
+ },
+}
+</script>
+
+<style scoped>
+.sequence {
+ max-width: 300px;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+pre {
+ font-size: 1.2rem;
+ white-space: pre-line;
+}
+</style>
diff --git a/src/components/g4killer/form-single.vue b/src/components/g4killer/form-single.vue
new file mode 100644
index 0000000..fa91d48
--- /dev/null
+++ b/src/components/g4killer/form-single.vue
@@ -0,0 +1,217 @@
+<template>
+ <div class="container">
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v">
+ <div class="row">
+ <div class="col-md-5">
+ <label class="mandatory">Sequence</label>
+ <input type="text" class="form-control" v-model="$v.sequence.$model" required />
+ <br />
+ </div>
+ <div class="col-md-3">
+ <label class="mandatory">Target G4 hunter score</label>
+ <input type="number" class="form-control" step="0.1" min="0" max="2" required v-model="$v.threshold.$model" />
+ <br />
+ </div>
+ <div class="col-md-4">
+ <label>On complementary sequence</label>
+ <b-form-checkbox class="form-control switch" name="check-button" v-model="onComplementary" switch>
+ <b>(Complementary: {{ onComplementary ? 'On' : 'Off' }})</b>
+ </b-form-checkbox>
+ <br />
+ </div>
+ </div>
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.sequence.required">Sequence is required.</div>
+ <div v-if="!$v.sequence.maxLength">Sequence max length is {{ $v.sequence.$params.maxLength.max }}.</div>
+ <div v-if="!$v.threshold.required">Threshold is required.</div>
+ <div v-if="!$v.threshold.decimal">
+ Threshold must be decimal number.
+ </div>
+ <div v-if="$v.threshold.$model <= 1.2">
+ The probability of G-quadruplex formation with G4Hunter score below 1.2 is low.
+ </div>
+ <div v-if="!$v.threshold.maxValue">Maximal value of threshold is {{ $v.threshold.$params.maxValue.max }}.</div>
+ </div>
+ <div class="alert alert-danger" v-if="analyse">Analyse failed: {{ analyse.errors[0].defaultMessage }}</div>
+ <button type="submit" class="btn btn-primary">Calculate</button>
+ </app-form>
+
+ <hr />
+
+ <div v-if="result">
+ <h2>Result</h2>
+ <table class="table table-striped">
+ <tbody>
+ <tr>
+ <th class="text-left">Original sequence</th>
+ <th class="text-left">Score</th>
+ <th class="text-center"></th>
+ </tr>
+ <tr>
+ <td class="sequence text-left text-bold">
+ <Highlight :sequence="result.originSequence" />
+ </td>
+ <td class="text-left">{{ result.originScore | number }}</td>
+ <td class="text-center"></td>
+ </tr>
+ <template v-if="result.mutationSequences">
+ <tr>
+ <th class="text-left" v-if="result.mutationSequences.length == 1">
+ A mutated sequence
+ </th>
+ <th class="text-left" v-else>List of mutated sequences</th>
+ <th class="text-left">Score</th>
+ <th class="text-center">Details</th>
+ </tr>
+ </template>
+ <template v-for="mutationSequence in result.mutationSequences">
+ <tr>
+ <td class="sequence text-monospace text-bold">
+ <Highlight :sequence="mutationSequence.sequence" :mask="mutationSequence.origin">
+ </Highlight>
+ </td>
+ <td class="text-left">{{ result.mutationScore | number }}</td>
+ <td class="text-center">
+ <b-button
+ variant="primary"
+ v-if="!mutationSequence.showDetail"
+ @click="toggleShowDetail(mutationSequence)"
+ >
+ Show detail
+ </b-button>
+ <b-button
+ variant="primary"
+ v-if="mutationSequence.showDetail"
+ @click="toggleShowDetail(mutationSequence)"
+ >
+ Hide detail
+ </b-button>
+ </td>
+ </tr>
+ <tr v-if="mutationSequence.showDetail">
+ <td class="text-center" colspan="3">
+ <G4KillerDetail :sequence="result.originSequence" :mutation="mutationSequence"> </G4KillerDetail>
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ <div class="alert alert-warning" v-if="result && !result.mutationSequences">
+ The target score {{ threshold }} is below the G4Hunter score of the sequence.
+ <b>No mutation is needed!</b>
+ </div>
+ <hr />
+ </div>
+ <div class="card bg-light">
+ <div class="card-body">
+ Please insert your nucleic acid sequence and choose desired G4 hunter score.
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import Highlight from '@/components/core/visualisation/highlight'
+import G4KillerDetail from './g4killer-detail'
+import Formatters from '@/formatters'
+import AppForm from '@/components/core/app-form'
+import { decimal, maxLength, maxValue, minValue, required } from 'vuelidate/lib/validators'
+
+export default {
+ components: {
+ Highlight,
+ G4KillerDetail,
+ AppForm,
+ },
+ data() {
+ return {
+ sequence: '',
+ threshold: 1.0,
+ result: null,
+ differences: '',
+ onComplementary: false,
+ analyse: null,
+ }
+ },
+ validations: {
+ sequence: {
+ required,
+ maxLength: maxLength(100),
+ },
+ threshold: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(2),
+ },
+ },
+ methods: {
+ calculate() {
+ this.result = null
+ this.differences = []
+
+ this.$http
+ .post('/analyse/g4killer', {
+ sequence: this.sequence,
+ threshold: this.threshold,
+ onComplementary: this.onComplementary,
+ })
+ .then(response => {
+ this.result = response.data
+ this.analyse = null
+
+ this.result.mutationSequences = response.data.mutationSequences.map(ms => ({
+ origin: ms,
+ sequence: this.replaceMutationSequence(ms),
+ showDetail: false,
+ }))
+ })
+ .catch(error => {
+ if (error.response) {
+ this.analyse = error.response.data
+ }
+ })
+ .finally(() => {
+ this.$refs.calculateForm.enable()
+ })
+ },
+ replaceMutationSequence(mutationSequence) {
+ const replacement = ['A', 'T']
+ return mutationSequence.replace(/W/g, () => {
+ return replacement[Math.floor(Math.random() * replacement.length)]
+ })
+ },
+ toggleShowDetail(mutationSequence) {
+ mutationSequence.showDetail = !mutationSequence.showDetail
+ },
+ },
+ mounted() {
+ if (this.$route.query.threshold) {
+ this.threshold = parseFloat(this.$route.query.threshold)
+ }
+ if (this.$route.query.sequence) {
+ this.sequence = this.$route.query.sequence
+ this.onComplementary = this.$route.query.onComplementary
+ this.calculate()
+ }
+ },
+ filters: {
+ number: Formatters.number,
+ difference: function(mutationSequence) {
+ return mutationSequence.origin.replace(/W/g, '-').replace(/\w/g, '|')
+ },
+ },
+}
+</script>
+
+<style scoped>
+.sequence {
+ max-width: 400px;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+.switch {
+ border: 0;
+}
+</style>
diff --git a/src/components/g4killer/g4killer-detail.vue b/src/components/g4killer/g4killer-detail.vue
new file mode 100644
index 0000000..e3e5d20
--- /dev/null
+++ b/src/components/g4killer/g4killer-detail.vue
@@ -0,0 +1,59 @@
+<template>
+ <b-container class="g4killer-detail container">
+ <b-row>
+ <b-col cols="8">
+ <pre>
+ {{ sequence }}
+ {{ mutation | difference }}
+ {{ selectedMutation }}
+ </pre
+ >
+ </b-col>
+ <b-col cols="4">
+ <b-form-group>
+ <b-form-radio-group v-model="selected">
+ Replace
+ <b-form-radio value="W">W</b-form-radio>
+ with:<br />
+ <b-form-radio value="R">non-G base,</b-form-radio>
+ <b-form-radio value="A">A,</b-form-radio>
+ <b-form-radio value="C">C,</b-form-radio>
+ <b-form-radio value="T">T.</b-form-radio>
+ <br />
+ </b-form-radio-group>
+ </b-form-group>
+ </b-col>
+ </b-row>
+ </b-container>
+</template>
+
+<script>
+export default {
+ props: ['mutation', 'sequence'],
+ data() {
+ return {
+ selected: 'W',
+ detail: '',
+ }
+ },
+ computed: {
+ selectedMutation: function() {
+ if (this.selected === 'W') return this.mutation.origin
+ if (this.selected === 'R') return this.mutation.sequence
+ else {
+ return this.mutation.origin.replace(/W/g, this.selected)
+ }
+ },
+ },
+ filters: {
+ difference: ms => ms.origin.replace(/W/g, '-').replace(/\w/g, '|'),
+ },
+}
+</script>
+
+<style scoped>
+pre {
+ font-size: 1.2rem;
+ white-space: pre-line;
+}
+</style>
diff --git a/src/components/g4killer/g4killer-tool.vue b/src/components/g4killer/g4killer-tool.vue
new file mode 100644
index 0000000..ebc6ad1
--- /dev/null
+++ b/src/components/g4killer/g4killer-tool.vue
@@ -0,0 +1,29 @@
+<template>
+ <div class="container">
+ <h1>G4 killer</h1>
+ <b-tabs>
+ <b-tab title="Single">
+ <br />
+ <form-single></form-single>
+ </b-tab>
+ <b-tab title="Multiple">
+ <br />
+ <form-multiple></form-multiple>
+ </b-tab>
+ </b-tabs>
+ </div>
+</template>
+
+<script>
+import FormSingle from './form-single'
+import FormMultiple from './form-multiple'
+
+export default {
+ components: {
+ FormSingle,
+ FormMultiple,
+ },
+}
+</script>
+
+<style></style>
diff --git a/src/components/help/about.vue b/src/components/help/about.vue
new file mode 100644
index 0000000..d88fc44
--- /dev/null
+++ b/src/components/help/about.vue
@@ -0,0 +1,37 @@
+<template>
+ <div class="container">
+ <h1>About DNA analyser</h1>
+
+ <h2>Credits</h2>
+ <p>
+ Václav Brázda: management, project design, data analyse.
+ <br />
+ Jiřà Šťastný: mentoring, testing.
+ <br />
+ Jan KolomaznÃk: coding, database design.
+ <br />
+ Jiřà Lýsek: graphic and interface design.
+ <br />
+ Jan KovaÅ™Ãk: testing, server maintenance.
+ </p>
+
+ <h2>Acknowledgements</h2>
+ <p>
+ Václav Brázda is supported by the Grant Agency of the Czech Republic (15-21855S).
+ </p>
+
+ <h2>Contact</h2>
+ <p>
+ <a href="mailto:palindrome@ibp.cz">palindrome@ibp.cz</a>
+ </p>
+
+ <h2>Download</h2>
+ <p>
+ <a target="_blank" href="http://git.pef.mendelu.cz/bioinformatics/dna-analyser/">Download this application</a>
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/faq.vue b/src/components/help/faq.vue
new file mode 100644
index 0000000..7a4ad84
--- /dev/null
+++ b/src/components/help/faq.vue
@@ -0,0 +1,65 @@
+<template>
+ <div class="container">
+ <h1>FAQ</h1>
+
+ <h2>What advantages does this software have?</h2>
+ <ul>
+ <li>
+ We support analyse of long sequences (technical limit is 2GiB, but longer sequences take long time - be
+ patient).
+ </li>
+ <li>
+ We allow you to store results of your analyse for comparison with others. This feature requires user account.
+ </li>
+ <li>
+ We support export of found features and/or summary of stored results in CSV format.
+ </li>
+ <li>Direct NCBI import using sequence ID.</li>
+ </ul>
+
+ <h2>What limitations does this software have?</h2>
+ <ul>
+ <li>
+ There are currently no hardcoded limitations, use this software wisely to preserve this policy for other users.
+ Thank you. We will delete inactive accounts or prune old results once we reach storage capacity on our server.
+ </li>
+ </ul>
+
+ <!-- TODO
+ <h2>How is ΔG calculated?</h2>
+ <p>
+
+ </p>
+ -->
+
+ <h2>Is there any development going on?</h2>
+ <p>
+ We are currently working on new features and bug fixes. You can join us - contact us by email.
+ </p>
+
+ <p>
+ In case of any questions or recommendations please contact us:
+ <a href="mailto:palindrome@ibp.cz">palindrome@ibp.cz</a>.
+ </p>
+
+ <h2>Can I download this app?</h2>
+ <p>
+ Yes, you can! You can use your own copy of this software (read enclosed licence). The link for download is in
+ <router-link :to="{ name: 'help.about' }">About</router-link> section.
+ </p>
+
+ <!--
+ <h2>How to cite?</h2>
+ <p>
+ Brazda, V., Kolomaznik, J., Lysek, J., Haronikova, L., Coufal, J. and Stastny, J. (2016)
+ Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide
+ sequences.
+ Biochem Bioph Res Co, 478, 1739-1745.
+ </p>
+ -->
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/help-cruciform.vue b/src/components/help/help-cruciform.vue
new file mode 100644
index 0000000..88d1f5b
--- /dev/null
+++ b/src/components/help/help-cruciform.vue
@@ -0,0 +1,63 @@
+<template>
+ <div class="container app-content" role="main">
+ <h1>Cruciform</h1>
+
+ <p>
+ Palindrome analyser is a web-based software that generates information about the presence of inverted repeats in
+ any DNA sequences. Inverted repeats are DNA sequences capable of forming cruciform structures that have an
+ important role in the regulation of natural processes involving DNA. Cruciforms are fundamentally critical for a
+ wide range of biological processes, including replication and regulation of gene expression, as well as nucleosome
+ structure and recombination. They have also been implicated in the evolution and development of diseases.
+ Palindrome analyser is a user-friendly application that provides many options for analysing inverted repeats in
+ various DNA sequences including oligonucleotides, plasmids and genomes. It allows users to search and retrieve
+ desired gene/nucleotide sequence entries from the NCBI databases, and provide data on length, sequence, locations
+ and energy required for palindromeModel formation. Moreover, it features an interactive graphical data
+ representation of the distribution of the inverted repeats, with options for sorting the length of
+ palindromeModel, length of loop, and number of mismatches. This open access web-based software is an invaluable
+ tool for searching and analysing inverted repeats in DNA sequences.
+ </p>
+
+ <h2>Usage - preparation</h2>
+ <p>
+ Select input - text/NCBI ID/uploaded sequence. Adjust parameters of analyse. In range inputs any number, range
+ (m-n) or individual numbers (a,b,c) can be inserted. When you are satisfied with parameters you can press Analyse
+ button and wait a while (or longer depending on the length of sequence) for results. If you ticked the "Store
+ results" checkbox you can find the results in Analysis overview module and view the results later. The checkbox
+ labelled circular modifies the treatment of sequence during analyse such that the sequence is analysed as infinite
+ (or cicluar) sequence.
+ </p>
+
+ <h2>Usage - analyse results</h2>
+ <p>
+ The results section is divided in two views - overview and similarity analyse. Common part is heatmap and sequence
+ browser. The heatmap divides sequence into given amount of data where each segment shows amount of palindromes in
+ that particular segment. By clicking on the heatmap segment the browser moves on the beginning of clicked segment,
+ the segment is highlighted with green border and palindromes in overview which do not belong into selected segment
+ are hidden. The browser shows various amount of base pairs depending on Internet browser window width. In the
+ bottom part of page we can find summary of sequence analyse with histograms.
+ </p>
+ <h3>Overview of palindromes</h3>
+ <p>
+ This part can be used to browse and filter individual palindromes. You can filter found sequences by length,
+ spacer length and mismatch count. There is also a filter which searches particular sequences. By clicking the
+ magnifier icon of palindromeModel, the sequence browser moves to given position. This is useful to analyse
+ surrounding base pairs of palindromeModel. The details button shows graphical representation of loop with
+ positions. All filters can be removed by clicking cancel filter button.
+ </p>
+ <h3>Analysis of similarity</h3>
+ <p>
+ This view is useful to group palindromes by the beginning of the sequence, the inverted part or even by spacer.
+ You can filter out grouped sequences by amount of their occurrences in analysed sequence. Highlight location
+ button will mark the heatmap data where grouped palindromes are located (yellow border). The highlight of
+ palindromeModel location can be removed from heatmap by clicking cancel highlight button.
+ </p>
+ <h2>Storing results and sequences</h2>
+ <p>
+ Only registered users can store results and upload/import sequences.
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/help-g4killer.vue b/src/components/help/help-g4killer.vue
new file mode 100644
index 0000000..1277390
--- /dev/null
+++ b/src/components/help/help-g4killer.vue
@@ -0,0 +1,62 @@
+<template>
+ <div class="container">
+ <h1>G4 killer help</h1>
+ <p>
+ This algorithm allows to generation of mutated DNA sequences with desired G4Hunter score with minimal mutation
+ steps. The algorithm gradually performs all possible changes and calculates a score for each. Then sorted results
+ according to their G4Hunter score from best to worst and lists the best and continue until the sequence reach
+ desired G4Hunter score.
+ </p>
+ <p>
+ Please be aware that for G4 hunter algorithm are important also surrounding sequences. Therefore could be useful
+ to put your nucleic acid sequence without any non-G bases on edges.
+ </p>
+ <img :src="'/static/img/g4killer.png'" />
+
+ <h2>Usage</h2>
+ <h3>G4 killer – single</h3>
+ <p>
+ Module for mutation of one G-prone sequence
+ </p>
+ <p>
+ Insert your G-prone sequence, select “target G4 hunter score“. In the case that you inserted complementary C-rich
+ sequence, please click “On complementary sequence“. Click “Calculate“. Results – original and mutated sequence
+ will be visualized in your browser with information about original G4Hunter score and G4 hunter score of mutated
+ sequence. The changes in sequence is in bold. By click “Show details“ the alignment of original and mutated
+ sequence is shown. You can choose desired nucleotide for W replacement.
+ </p>
+ <h3>G4 killer – multiple</h3>
+ <p>
+ Module for mutation of multiple G-prone sequence at ones (limit 10 sequences)
+ </p>
+ <p>
+ Insert your G-prone sequences separated by a paragraph character. Select you G4 hunter target score. Click
+ “Calculate“. One the best result for each sequence is shown. For more options use “Single“ tab.
+ </p>
+ <h2>G4 killer FAQ</h2>
+ <h3>It is possible to analyze C-rich sequences?</h3>
+ <p>
+ Yes, in the tab “Single†for analysis of one DNA sequence click “On complementary sequence“.
+ </p>
+ <h3>What W means in the mutated sequence?</h3>
+ <p>
+ W is IUPAC nucleotide code for “weak“ bases A or T.
+ </p>
+ <h3>What do brighter Gs and Cs mean?</h3>
+ <p>
+ Brighter tone is used for longer groups to underline the nature of the G4 hunter algorithm which favors longer
+ Gs/Cs sequences with higher score.
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
+
+<style scoped>
+pre {
+ font-size: 1.2rem;
+ display: inline;
+}
+</style>
diff --git a/src/components/help/help-import.vue b/src/components/help/help-import.vue
new file mode 100644
index 0000000..cfc754a
--- /dev/null
+++ b/src/components/help/help-import.vue
@@ -0,0 +1,29 @@
+<template>
+ <div class="container app-content" role="main">
+ <h1>Upload of sequences and NCBI import</h1>
+
+ <h2>Usage of upload</h2>
+ <p>
+ We support currently only 2 types of data inputs - plain text files with A, C, G and T characters encoding the
+ sequence and Fasta format.
+ <br />
+ When uploading a file, select a name for your sequence. Then select data type (plain or fasta). Choose a file from
+ your hard drive and press Upload button. After a while the file should be available in overview of
+ uploaded/imported sequences - My sequences.
+ </p>
+
+ <h2>Usage of NCBI</h2>
+ <p>
+ Simply type a NCBI ID (e.g. NC_001770) and press import button. After a while the file should be available in
+ overview of uploaded/imported sequences - My sequences.
+ </p>
+
+ <p class="alert alert-warning">
+ Only registered users can upload/import sequences.
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/help-p53.vue b/src/components/help/help-p53.vue
new file mode 100644
index 0000000..e5790ca
--- /dev/null
+++ b/src/components/help/help-p53.vue
@@ -0,0 +1,42 @@
+<template>
+ <div class="container app-content" role="main">
+ <h1>p53 predictor</h1>
+
+ <p>
+ This tools implements calculations of p53 binding predictor for 20 base pairs sequences.
+ </p>
+
+ <h2>Single mode</h2>
+
+ <p>
+ This tab calculates individual predictor for a single sequence.
+ </p>
+
+ <h2>Multiple mode</h2>
+
+ <p>
+ This tab provides calculation of multiple predictors for various sequences. Input is a multiline text where each
+ line is a 20 bp sequence.
+ </p>
+
+ <h2>Find best mode</h2>
+
+ <p>
+ In this mode a calculation is performed for every 20 bp sub-sequence of a long sequence. The sub-sequences are
+ extracted by moving a 20 bp window along the input sequence one character at a time. Selected amount of best
+ sequences is presented.
+ </p>
+
+ <p>
+ Implemented method of predictor calculation is explained in following article:
+ <br />
+ Veprintsev, D.B. and A.R. Fersht,
+ <em>Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA</em>. Nucleic acids
+ research, 2008. <strong>36</strong>(5): p. 1589-98.
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/help-quadruplex.vue b/src/components/help/help-quadruplex.vue
new file mode 100644
index 0000000..f86e9db
--- /dev/null
+++ b/src/components/help/help-quadruplex.vue
@@ -0,0 +1,150 @@
+<template>
+ <div class="container">
+ <h1>G4 hunter help</h1>
+ <p>
+ This algorithm is a re-implementation of the G4 hunter algorithm described in the article “Re-evaluation of
+ G-quadruplex propensity with G4Hunter†(<a href="https://academic.oup.com/nar/article/44/4/1746/1854457"
+ >https://academic.oup.com/nar/article/44/4/1746/1854457</a
+ >), original source code is available here
+ <a href="https://github.com/AnimaTardeb/G4-Hunter">https://github.com/AnimaTardeb/G4-Hunter</a>. G4Hunter is a
+ tool for prediction of G-quadruplex propensity in nucleic acids, this algorithm considers G-richness and
+ G-skewness of a tested sequence and shows a quadruplex propensity score. Mathematically, the algorithm searches
+ for Gs/Cs and sums scores for each such base or group of bases. G bases add positive score and C bases have a
+ negative effect on the resulting sum. For subsequent occurrences of Gs/Cs, the score rises/decreases by one point
+ per additional base up to the value of 4/-4. The sum of scores is than divided by the length of the window. The
+ highest resulting score possible is 4/-4.
+ </p>
+ <strong>Examples:</strong>
+ <ul>
+ <li>
+ <pre>CCC</pre>
+ => -3-3-3 = -9 => -9 / 3 = -3
+ </li>
+ <li>
+ <pre>GGGGGG</pre>
+ => 4+4+4+4+4+4 = 24 => 24 / 6 = 4
+ </li>
+ <li>
+ <pre>ATCCCAAGGGAA</pre>
+ => 0+0-3-3-3+0+0+3+3+3+0+0 = 0 => 0 / 12 = 0
+ </li>
+ <li>
+ <pre>ATGGATGGATGATGAT</pre>
+ => 0+0+2+2+0+0+2+2+0+0+1+0+0+1+0+0 = 10 => 10 / 16 = 0.625
+ </li>
+ </ul>
+ <p>
+ The algorithm automatically groups subsequent hits. When the algorithm finds two or more subsequent hits with
+ score higher than threshold occupying neighbouring positions in the analysed sequence, it concatenates those
+ results into one with starting position defined by the first hit, containing all bases from all grouped hits and
+ the score is recalculated. This leads to results longer than the defined window and can lead to lower resulting
+ score than threshold.
+ </p>
+ <strong>Example (window 25, threshold 1):</strong>
+ <table class="table table-bordered">
+ <tr>
+ <th>Position</th>
+ <th>Sequence</th>
+ <th>Score</th>
+ <th>Result</th>
+ </tr>
+ <tr>
+ <td>349</td>
+ <td>
+ <pre>GATCCACTTGGCTACATCCGCCCCC</pre>
+ </td>
+ <td class="text-right">-1</td>
+ <td rowspan="4">
+ <pre>GATCCACTTGGCTACATCCGCCCCCTTA</pre>
+ <br />
+ Length: 28 (25 bases from first hit + 3 bases from subsequent hits)
+ <br />
+ Score: -0.893
+ </td>
+ </tr>
+ <tr>
+ <td>350</td>
+ <td>
+ <pre>ATCCACTTGGCTACATCCGCCCCCT</pre>
+ </td>
+ <td class="text-right">-1.04</td>
+ </tr>
+ <tr>
+ <td>351</td>
+ <td>
+ <pre>TCCACTTGGCTACATCCGCCCCCTT</pre>
+ </td>
+ <td class="text-right">-1.04</td>
+ </tr>
+ <tr>
+ <td>352</td>
+ <td>
+ <pre>CCACTTGGCTACATCCGCCCCCTTA</pre>
+ </td>
+ <td class="text-right">-1.04</td>
+ </tr>
+ </table>
+
+ <h2>Usage – preparation</h2>
+ <p>
+ First, select sequences for analysis using the sequence selection tool. You can select one or more sequences for
+ analysis. Be aware that calculations will take longer for longer sequences. In the analysis settings form, select
+ a threshold value (meaningful values are from 0.9 and higher, recommended value 1.4) and window size (from 10 to
+ 100).
+ </p>
+
+ <h2>Usage – results</h2>
+ <p>
+ You will be presented with a heatmap and list of grouped results when the analysis is completed and results are
+ found. Results are automatically stored in the database and you can access them from the menu (create an account
+ first to preserve the results).
+ </p>
+ <p>
+ The heatmap shows the amount of hits in precalculated segments (up to 80 segments). The length of the segment is
+ variable. A hit is considered to occupy a given segment when it starts in that segment. The heatmap can be
+ switched into “percentage viewâ€, where you can observe the percent of that segment that is occupied by identified
+ hits.
+ </p>
+ <p>
+ The Results list always contains position, length, actual sequence and score. You can sort the list by position,
+ length and score. There is a mini-chart for grouped results which plots value of score from individual non-grouped
+ hits. You can expand each row by clicking the magnifying glass icon and inspect the surrounding bases of the
+ sequence and non-grouped hits (if presented).
+ </p>
+ <p>
+ Each sequence is coloured: red is used for Gs and blue for Cs. Brighter tone is used for longer groups to
+ underline the nature of the G4 hunter algorithm which favours longer Gs/Cs sequences with higher score.
+ </p>
+
+ <h2>G4 hunter FAQ</h2>
+
+ <h3>
+ Why do you show results longer than defined window and with lower score than threshold?
+ </h3>
+ <p>
+ Because the algorithm uses grouping of subsequent hits. The resulting sequence is longer and possibly has a worse
+ score. You can view grouped hits in details of particular result or download CSV export of non-grouped hits.
+ </p>
+ <h3>Why do percentages in the heatmap not add up to 100?</h3>
+ <p>
+ The percentage shows how many bases in that particular segment are occupied by hits. E.g.: for segment of length
+ 50 and one hit of length 25, the occupied length is 50%.
+ </p>
+ <h3>What do brighter Gs and Cs mean?</h3>
+ <p>
+ Brighter tone is used for longer groups to underline the nature of the G4 hunter algorithm which favours longer
+ Gs/Cs sequences with higher score.
+ </p>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
+
+<style scoped>
+pre {
+ font-size: 1.2rem;
+ display: inline;
+}
+</style>
diff --git a/src/components/help/help-rloopr.vue b/src/components/help/help-rloopr.vue
new file mode 100644
index 0000000..eebefa7
--- /dev/null
+++ b/src/components/help/help-rloopr.vue
@@ -0,0 +1,156 @@
+<template>
+ <div class="container">
+ <h1>R-loop tracker help</h1>
+ <p>
+ This algorithm is a re-implementation of algorithm based on R-loop detection algorithm called
+ <a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">QmRLFS finder</a>. R-loop tracker is a toll for prediction of
+ R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and
+ R-loop elongation zone containing at least 40% of Guanine density. Our tool offers integration with Genome
+ browser, enhanced visualization and export formats, as well on-line sorting, and statistical characteristic.
+ Thanks to new java-based architecture can process whole chromosomes as well as complete genomes by batch analyses.
+ </p>
+
+ <h2 id="input">Input data</h2>
+ <hr />
+ <p>
+ Sequence can be imported as a text, fasta file or directly from NCBI database, for details please check help part
+ for <a href="/#/help/import">Import</a>. The choices are described in
+ <a href="/adoc/sequence.html">documentation</a>.<br /><br />
+ If you want to integrate your analysis with Genome browser, you need to provide information about the location of
+ the sequence in the genome. The name of the sequence has to have the following format:
+ <br /><br />
+ <code>
+ <Organism>_chr<number-of-chromosome>:<sequence-start>-<sequence-end>
+ </code>
+ <br /><br />
+ example of such name is as follows:<br /><br />
+ <code>
+ Human_chr8:128748315-128753680
+ </code>
+ <br /><br />
+ The organism's first letter must be capital (upper-case). This is ideal format, which will result in smooth import
+ into Genome browser.
+ </p>
+
+ <h2>Model selection</h2>
+ <hr />
+ <p>On the analysis page, you can select one of 2 models.</p>
+ <ul>
+ <li>
+ <b>RIZ 3G-cluster</b> RIZ (R-loop initiation zone) consists of <b>three</b> consecutive G-clusters which have at
+ least <b>3</b> Guanines in them.
+ </li>
+ <li>
+ <b>RIZ 4G-cluster</b>RIZ (R-loop initiation zone) consists of <b>two</b> consecutive G-clusters which have at
+ least <b>4</b> Guanines in them.
+ </li>
+ </ul>
+ <p>
+ Both of the models are described in <a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">this article</a>.<br />
+ You can of course select both of the models at once.
+ </p>
+
+ <h2>Output formats</h2>
+ <hr />
+ <h3>Website</h3>
+ Website offers visualization of R-loop distribution in analyzed sequence. Each sequence is coloured: red is used for
+ Gs and blue for Cs. Brighter tone is used for longer Gs/Cs sequences. Results are shown as a table with following
+ sortable columns:
+ <ul>
+ <li><b>Position</b></li>
+ - start of the R-loop in given sequence
+ <li><b>Length</b></li>
+ - length of the R-loop
+ <li><b>Model</b></li>
+ - which model was used to detect the R-loop
+ <li><b>Strand</b></li>
+ - DNA strand (direction)
+ <li><b>RIZ</b></li>
+ - R-loop initiation zone sequence
+ <li><b>Linker length</b></li>
+ - length of a linker (0 if none is detected)
+ <li><b>REZ</b></li>
+ - R-loop elongation zone sequence. Altogether, RIZ+linker+REZ represents the whole R-loop
+ <li><b>RIZ Guanine richness</b></li>
+ - percentage of Guanine in RIZ area
+ <li><b>Rloop Guanine richness</b></li>
+ - percentage of Guanine in whole R-loop
+ <li><b>Number of 3G clusters</b></li>
+ <li><b>Number of 4G clusters</b></li>
+ <li><b>Number of 5G clusters and more</b></li>
+ </ul>
+
+ <h3 id="file-export">File export</h3>
+ All results can be exported into two possible file formats:
+ <ol>
+ <li>
+ <b>CSV</b> common file format with the following fields:
+ <ul>
+ <li>
+ position, length, RIZ, linker, REZ, model, strand (same as on website)
+ </li>
+ <li>
+ RIZGRICHNESS (percentage of Guanine nucleotides in RIZ sequence)
+ </li>
+ <li>
+ RLOOPGRICHNESS (percentage of Guanine nucleotides in whole R-loop)
+ </li>
+ <li>
+ G3 (count of 3G clusters in the sequence)
+ </li>
+ <li>
+ G4 (count of 4G clusters in the sequence)
+ </li>
+ <li>
+ GN (count of 5G and more clusters in the sequence)
+ </li>
+ </ul>
+ </li>
+ <li>
+ <b>bedGraph</b>
+ <br />
+ BedGraph is a special
+ <a href="https://genome.ucsc.edu/goldenPath/help/bedgraph.html">file format for Genome Browser integration</a>.
+ We have to improve our score rating for R-loops, which will result in better visualisation in Genome Browser.
+ <br />
+ In order to integrate your analysis into <a href="https://genome.ucsc.edu/">Genome Browser</a>, you have to
+ follow these steps:
+ <ol>
+ <li>
+ Navigate to the <a href="https://genome.ucsc.edu/cgi-bin/hgCustom">Custom tracks page</a> (Home -> My Data
+ -> Custom Tracks)
+ </li>
+ <li>Upload the bedGraph file downloaded from DNA analyser and hit the <code>Submit</code> button</li>
+ <li>
+ You should see the table with your track and now You can view it in Genome Browser (after hitting
+ <code>Go</code> button
+ </li>
+ <li>
+ The tracks will have green color shade according to their score and the track itself will be named
+ DNA-analyser
+ </li>
+ </ol>
+ </li>
+ </ol>
+ <h3>Example</h3>
+ The most basic example is to use the pre-imported sequence <code>Myc_chr8:128748315-128753680</code> available when
+ you are not logged in. You can find already imported sequences in the navigation by clicking on
+ <a href="/#/analyse/rloopr">Analyses -> R-loop tracker</a>. If you do not see the sequence, try logging out
+ beforehand. After this, just hit the green <b>Analyse</b> button, which starts the <em>RIZ 3G-cluster</em>
+ analysis for you.
+ <h4>Troubleshooting</h4>
+ If the track does not upload succesfully, try to follow the name specification described in
+ <a href="#input">Input section</a>.
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
+
+<style scoped>
+pre {
+ font-size: 1.2rem;
+ display: inline;
+}
+</style>
diff --git a/src/components/help/help-zdna.vue b/src/components/help/help-zdna.vue
new file mode 100644
index 0000000..7e63526
--- /dev/null
+++ b/src/components/help/help-zdna.vue
@@ -0,0 +1,156 @@
+<template>
+ <div class="container">
+ <h1>Z-DNA tracker help</h1>
+ <p>
+ This algorithm is a re-implementation of algorithm based on R-loop detection algorithm called
+ <a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">QmRLFS finder</a>. R-loop tracker is a toll for prediction of
+ R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and
+ R-loop elongation zone containing at least 40% of Guanine density. Our tool offers integration with Genome
+ browser, enhanced visualization and export formats, as well on-line sorting, and statistical characteristic.
+ Thanks to new java-based architecture can process whole chromosomes as well as complete genomes by batch analyses.
+ </p>
+
+ <h2 id="input">Input data</h2>
+ <hr />
+ <p>
+ Sequence can be imported as a text, fasta file or directly from NCBI database, for details please check help part
+ for <a href="/#/help/import">Import</a>. The choices are described in
+ <a href="/adoc/sequence.html">documentation</a>.<br /><br />
+ If you want to integrate your analysis with Genome browser, you need to provide information about the location of
+ the sequence in the genome. The name of the sequence has to have the following format:
+ <br /><br />
+ <code>
+ <Organism>_chr<number-of-chromosome>:<sequence-start>-<sequence-end>
+ </code>
+ <br /><br />
+ example of such name is as follows:<br /><br />
+ <code>
+ Human_chr8:128748315-128753680
+ </code>
+ <br /><br />
+ The organism's first letter must be capital (upper-case). This is ideal format, which will result in smooth import
+ into Genome browser.
+ </p>
+
+ <h2>Model selection</h2>
+ <hr />
+ <p>On the analysis page, you can select one of 2 models.</p>
+ <ul>
+ <li>
+ <b>RIZ 3G-cluster</b> RIZ (R-loop initiation zone) consists of <b>three</b> consecutive G-clusters which have at
+ least <b>3</b> Guanines in them.
+ </li>
+ <li>
+ <b>RIZ 4G-cluster</b>RIZ (R-loop initiation zone) consists of <b>two</b> consecutive G-clusters which have at
+ least <b>4</b> Guanines in them.
+ </li>
+ </ul>
+ <p>
+ Both of the models are described in <a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">this article</a>.<br />
+ You can of course select both of the models at once.
+ </p>
+
+ <h2>Output formats</h2>
+ <hr />
+ <h3>Website</h3>
+ Website offers visualization of R-loop distribution in analyzed sequence. Each sequence is coloured: red is used for
+ Gs and blue for Cs. Brighter tone is used for longer Gs/Cs sequences. Results are shown as a table with following
+ sortable columns:
+ <ul>
+ <li><b>Position</b></li>
+ - start of the R-loop in given sequence
+ <li><b>Length</b></li>
+ - length of the R-loop
+ <li><b>Model</b></li>
+ - which model was used to detect the R-loop
+ <li><b>Strand</b></li>
+ - DNA strand (direction)
+ <li><b>RIZ</b></li>
+ - R-loop initiation zone sequence
+ <li><b>Linker length</b></li>
+ - length of a linker (0 if none is detected)
+ <li><b>REZ</b></li>
+ - R-loop elongation zone sequence. Altogether, RIZ+linker+REZ represents the whole R-loop
+ <li><b>RIZ Guanine richness</b></li>
+ - percentage of Guanine in RIZ area
+ <li><b>Rloop Guanine richness</b></li>
+ - percentage of Guanine in whole R-loop
+ <li><b>Number of 3G clusters</b></li>
+ <li><b>Number of 4G clusters</b></li>
+ <li><b>Number of 5G clusters and more</b></li>
+ </ul>
+
+ <h3 id="file-export">File export</h3>
+ All results can be exported into two possible file formats:
+ <ol>
+ <li>
+ <b>CSV</b> common file format with the following fields:
+ <ul>
+ <li>
+ position, length, RIZ, linker, REZ, model, strand (same as on website)
+ </li>
+ <li>
+ RIZGRICHNESS (percentage of Guanine nucleotides in RIZ sequence)
+ </li>
+ <li>
+ RLOOPGRICHNESS (percentage of Guanine nucleotides in whole R-loop)
+ </li>
+ <li>
+ G3 (count of 3G clusters in the sequence)
+ </li>
+ <li>
+ G4 (count of 4G clusters in the sequence)
+ </li>
+ <li>
+ GN (count of 5G and more clusters in the sequence)
+ </li>
+ </ul>
+ </li>
+ <li>
+ <b>bedGraph</b>
+ <br />
+ BedGraph is a special
+ <a href="https://genome.ucsc.edu/goldenPath/help/bedgraph.html">file format for Genome Browser integration</a>.
+ We have to improve our score rating for R-loops, which will result in better visualisation in Genome Browser.
+ <br />
+ In order to integrate your analysis into <a href="https://genome.ucsc.edu/">Genome Browser</a>, you have to
+ follow these steps:
+ <ol>
+ <li>
+ Navigate to the <a href="https://genome.ucsc.edu/cgi-bin/hgCustom">Custom tracks page</a> (Home -> My Data
+ -> Custom Tracks)
+ </li>
+ <li>Upload the bedGraph file downloaded from DNA analyser and hit the <code>Submit</code> button</li>
+ <li>
+ You should see the table with your track and now You can view it in Genome Browser (after hitting
+ <code>Go</code> button
+ </li>
+ <li>
+ The tracks will have green color shade according to their score and the track itself will be named
+ DNA-analyser
+ </li>
+ </ol>
+ </li>
+ </ol>
+ <h3>Example</h3>
+ The most basic example is to use the pre-imported sequence <code>Myc_chr8:128748315-128753680</code> available when
+ you are not logged in. You can find already imported sequences in the navigation by clicking on
+ <a href="/#/analyse/rloopr">Analyses -> R-loop tracker</a>. If you do not see the sequence, try logging out
+ beforehand. After this, just hit the green <b>Analyse</b> button, which starts the <em>RIZ 3G-cluster</em>
+ analysis for you.
+ <h4>Troubleshooting</h4>
+ If the track does not upload succesfully, try to follow the name specification described in
+ <a href="#input">Input section</a>.
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
+
+<style scoped>
+pre {
+ font-size: 1.2rem;
+ display: inline;
+}
+</style>
diff --git a/src/components/help/help.vue b/src/components/help/help.vue
new file mode 100644
index 0000000..e02ce63
--- /dev/null
+++ b/src/components/help/help.vue
@@ -0,0 +1,9 @@
+<template>
+ <div class="container">
+ <router-view></router-view>
+ </div>
+</template>
+
+<script>
+export default {}
+</script>
diff --git a/src/components/help/status.vue b/src/components/help/status.vue
new file mode 100644
index 0000000..b2d646c
--- /dev/null
+++ b/src/components/help/status.vue
@@ -0,0 +1,42 @@
+<template>
+ <div class="container">
+ <h1>Status</h1>
+
+ <h2>Server backend</h2>
+ <p>Health: {{ healthStatus }}</p>
+ <p>Version: {{ version }}</p>
+ <p>Assembly date : {{ assemblyDate }}</p>
+ </div>
+</template>
+
+<script>
+export default {
+ data() {
+ return {
+ healthStatus: 'UNKNOWN',
+ version: 'UNKNOWN',
+ assemblyDate: 'UNKNOWN',
+ }
+ },
+
+ methods: {
+ downloadHealth() {
+ this.$http.get('management/health').then(response => {
+ this.healthStatus = response.data.status
+ })
+ },
+ downloadInfo() {
+ this.$http.get('management/info').then(response => {
+ this.version = response.data.app.version
+ let date = new Date(response.data.app.assemblyDate)
+ this.assemblyDate = date.toLocaleDateString()
+ })
+ },
+ },
+
+ mounted() {
+ this.downloadHealth()
+ this.downloadInfo()
+ },
+}
+</script>
diff --git a/src/components/p53predictor/form-best.vue b/src/components/p53predictor/form-best.vue
new file mode 100644
index 0000000..715b9ed
--- /dev/null
+++ b/src/components/p53predictor/form-best.vue
@@ -0,0 +1,135 @@
+<template>
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v">
+ <div class="form-group">
+ <textarea class="form-control" v-model="sequence"></textarea>
+ </div>
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.sequence.required">Sequence is required.</div>
+ <div v-if="!$v.sequence.minLength">
+ Sequence length has to be minimal
+ {{ $v.sequence.$params.minLength.min }}.
+ </div>
+ <div v-if="!$v.sequence.maxLength">
+ Sequence length has to be maximal
+ {{ $v.sequence.$params.maxLength.max }}.
+ </div>
+ </div>
+
+ <div class="form-group row">
+ <label for="limit" class="col-sm-2 col-form-label">Show matches (no.):</label>
+ <div class="col-sm-2">
+ <input id="limit" type="number" class="form-control" step="1" min="1" max="200" required v-model="limit" />
+ </div>
+
+ <button type="submit" class="btn btn-primary">
+ Calculate
+ </button>
+ </div>
+ <template v-if="calculated">
+ <div class="alert alert-warning" v-if="results.length == 0">
+ None of the subsequents has Δ log <em>K</em><sub>d</sub> goes from 0 (the best fully function p53 response
+ element) to about 2 (non functional p53 response element), the percent relative affinity: 0.02 Δ log <em>K</em
+ ><sub>d</sub> corresponds to 1% of reduced relative affinity.
+ </div>
+ <div v-if="results.length > 0">
+ <hr />
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>Position</th>
+ <th>Sequence</th>
+ <th class="text-center">log <em>K</em><sub>d</sub>(x)</th>
+ <th class="text-center">Δ log <em>K</em><sub>d</sub>(x)</th>
+ <th class="text-center">Relative affinity</th>
+ </tr>
+ <tr v-for="r in results.slice(0, limit)">
+ <td>{{ r.row + 1 }}</td>
+ <td>
+ <pre>{{ r.sequence }}</pre>
+ </td>
+ <td class="text-right">{{ r.difference | number }}</td>
+ <td class="text-right">{{ r.predictor | number }}</td>
+ <td class="text-right">{{ (r.affinity * 100) | number(0) }} %</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </template>
+ </app-form>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import { required, minLength, maxLength } from 'vuelidate/lib/validators'
+import AppForm from '@/components/core/app-form'
+
+export default {
+ data() {
+ return {
+ sequence: '',
+ ref: -7.61,
+ results: [],
+ limit: 10,
+ calculated: false,
+ }
+ },
+ validations: {
+ sequence: {
+ required,
+ minLength: minLength(20),
+ maxLength: maxLength(200),
+ },
+ },
+ methods: {
+ calculate() {
+ this.calculated = false
+ this.results = []
+ var promises = []
+ for (let i = 0; i < this.sequence.length - 20; i++) {
+ var seq = this.sequence.substr(i, 20)
+ var p = this.$http
+ .post('/analyse/p53predictor/tool', {
+ sequence: seq,
+ })
+ .then(
+ response => {
+ response.data.payload.row = i
+ if (response.data.payload.affinity > 0) {
+ this.results.push(response.data.payload)
+ }
+ },
+ () => {
+ //TODO
+ }
+ )
+ promises.push(p)
+ }
+ Promise.all(promises).finally(() => {
+ this.$refs.calculateForm.enable()
+ this.results.sort((a, b) => {
+ return a.predictor - b.predictor
+ })
+ this.calculated = true
+ })
+ },
+ },
+ mounted() {
+ if (this.$route.query.limit) {
+ this.limit = parseInt(this.$route.query.limit)
+ }
+ },
+ filters: {
+ number: Formatters.number,
+ },
+ components: {
+ AppForm,
+ },
+}
+</script>
+
+<style scoped>
+textarea {
+ font-family: monospace;
+}
+</style>
diff --git a/src/components/p53predictor/form-multiple.vue b/src/components/p53predictor/form-multiple.vue
new file mode 100644
index 0000000..ce268b9
--- /dev/null
+++ b/src/components/p53predictor/form-multiple.vue
@@ -0,0 +1,120 @@
+<template>
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v">
+ <label class="mandatory">Sequences (one sequence of length 20 per line)</label>
+ <textarea class="form-control" v-model="sequences" rows="10"></textarea>
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.sequences.required">Sequence is required.</div>
+ <div v-if="!$v.sequences.minLength">
+ Sequence length has to be at least
+ {{ $v.sequences.$params.maxLength.max }}.
+ </div>
+ <div v-if="!$v.sequences.numLines">The limit is {{ $v.sequences.$params.numLines.amount }} rows.</div>
+ </div>
+
+ <button type="submit" class="btn btn-primary">
+ Calculate
+ </button>
+
+ <div v-if="results.length">
+ <hr />
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>Row</th>
+ <th>Sequence</th>
+ <th class="text-center">log <em>K</em><sub>d</sub>(x)</th>
+ <th class="text-center">Δ log <em>K</em><sub>d</sub>(x)</th>
+ <th class="text-center">Relative affinity</th>
+ </tr>
+ <tr v-for="r in results">
+ <td>{{ r.row + 1 }}</td>
+ <td>
+ <pre>{{ r.sequence }}</pre>
+ </td>
+ <td class="text-right">{{ r.difference | number }}</td>
+ <td class="text-right">{{ r.predictor | number }}</td>
+ <td class="text-right">{{ (r.affinity * 100) | number(0) }} %</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </app-form>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import AppForm from '@/components/core/app-form'
+import { required, minLength, helpers } from 'vuelidate/lib/validators'
+
+const numLines = lines => {
+ return helpers.withParams({ type: 'numLines', amount: lines }, s => {
+ return (
+ s.split('\n').filter(r => {
+ return r.trim() != ''
+ }).length <= lines
+ )
+ })
+}
+
+export default {
+ data() {
+ return {
+ sequences: '',
+ ref: -7.61,
+ results: [],
+ }
+ },
+ validations: {
+ sequences: {
+ required,
+ minLength: minLength(20),
+ numLines: numLines(20),
+ },
+ },
+ methods: {
+ calculate() {
+ this.results = []
+ var promises = []
+ this.sequences.split('\n').forEach((row, i) => {
+ row = row.trim()
+ if (row.length == 20) {
+ var p = this.$http
+ .post('/analyse/p53predictor/tool', {
+ sequence: row,
+ })
+ .then(
+ response => {
+ response.data.payload.row = i
+ this.results.push(response.data.payload)
+ },
+ () => {
+ //TODO
+ }
+ )
+ promises.push(p)
+ }
+ })
+ Promise.all(promises).finally(() => {
+ this.$refs.calculateForm.enable()
+ this.results.sort((a, b) => {
+ return a.predictor - b.predictor
+ })
+ })
+ },
+ },
+ filters: {
+ number: Formatters.number,
+ },
+ components: {
+ AppForm,
+ },
+}
+</script>
+
+<style scoped>
+textarea {
+ font-family: monospace;
+}
+</style>
diff --git a/src/components/p53predictor/form-single.vue b/src/components/p53predictor/form-single.vue
new file mode 100644
index 0000000..d25d760
--- /dev/null
+++ b/src/components/p53predictor/form-single.vue
@@ -0,0 +1,99 @@
+<template>
+ <app-form @submit="calculate" ref="calculateForm" :validator="$v.sequence">
+ <label class="mandatory">Sequence</label>
+ <input type="text" class="form-control" v-model="$v.sequence.$model" required maxlength="20" />
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.sequence.$anyError">
+ <div v-if="!$v.sequence.required">Sequence is required.</div>
+ <div v-if="!$v.sequence.minLength || !$v.sequence.maxLength">
+ Sequence length has to be {{ $v.sequence.$params.maxLength.max }}.
+ </div>
+ </div>
+
+ <button type="submit" class="btn btn-primary">
+ Calculate
+ </button>
+
+ <div v-if="result">
+ <hr />
+
+ <h2>Result</h2>
+
+ log <em>K</em><sub>d</sub>(x) = log <em>K</em><sub>d</sub>(ref) + Σ Δ log <em>K</em><sub>d</sub>(i,N) =
+ {{ ref | number }} + {{ result.predictor | number }} = {{ result.difference | number }}
+ <br />
+ Σ Δ log <em>K</em><sub>d</sub>(i,N) = {{ result.predictor | number }}
+ <br />
+ <span v-if="!$v.result.predictor.$invalid">Relative affinity: {{ (result.affinity * 100) | number(0) }} %</span>
+ <br />
+ <div class="alert alert-danger" v-if="$v.result.predictor.$invalid">
+ Δ log <em>K</em><sub>d</sub> goes from 0 (the best fully function p53 response element) to about 2 (non
+ functional p53 response element), the percent relative affinity: 0.02 Δ log <em>K</em><sub>d</sub> corresponds
+ to 1% of reduced relative affinity.
+ </div>
+ </div>
+ </app-form>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import { required, minLength, maxLength, between } from 'vuelidate/lib/validators'
+import AppForm from '@/components/core/app-form'
+
+export default {
+ data() {
+ return {
+ sequence: '',
+ ref: -7.61,
+ result: null,
+ }
+ },
+ validations: {
+ sequence: {
+ required,
+ minLength: minLength(20),
+ maxLength: maxLength(20),
+ },
+ result: {
+ predictor: {
+ between: between(0, 2),
+ },
+ },
+ },
+ methods: {
+ calculate() {
+ this.result = null
+ this.$http
+ .post('/analyse/p53predictor/tool', {
+ sequence: this.sequence,
+ })
+ .then(
+ response => {
+ this.result = response.data.payload
+ },
+ () => {
+ //TODO
+ }
+ )
+ .finally(() => {
+ this.$refs.calculateForm.enable()
+ })
+ },
+ },
+ mounted() {
+ if (this.$route.query.sequence) {
+ this.sequence = this.$route.query.sequence
+ this.calculate()
+ }
+ },
+ filters: {
+ number: Formatters.number,
+ },
+ components: {
+ AppForm,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/p53predictor/p53-form.vue b/src/components/p53predictor/p53-form.vue
new file mode 100644
index 0000000..790fdea
--- /dev/null
+++ b/src/components/p53predictor/p53-form.vue
@@ -0,0 +1,57 @@
+<template>
+ <form @submit.prevent="startAnalysis()">
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Threshold</label>
+ <div class="col-md-8">
+ <input
+ type="number"
+ class="form-control"
+ step="0.1"
+ min="0.1"
+ max="4"
+ name="threshold"
+ v-model.number="threshold"
+ v-validate="{
+ required: true,
+ decimal: 1,
+ min_value: 0.1,
+ max_value: 4,
+ }"
+ />
+ </div>
+ </div>
+ <p v-if="threshold < 0.9" class="alert alert-warning">
+ Threshold recommended value is XXX or more.
+ </p>
+ <p v-for="e in formErrors.all()" class="alert alert-danger">
+ {{ e }}
+ </p>
+ <div class="text-right">
+ <slot name="additionalButtons"></slot>
+ <button type="submit" class="btn btn-success btn-block"><i class="fa fa-play"></i> Analyse</button>
+ </div>
+ </form>
+</template>
+
+<script>
+export default {
+ data() {
+ return {
+ threshold: 0.5,
+ }
+ },
+ methods: {
+ startAnalysis() {
+ this.$validator.validateAll().then(result => {
+ if (result) {
+ this.$emit('start', {
+ threshold: this.threshold,
+ })
+ }
+ })
+ },
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/p53predictor/p53-predictor-results.vue b/src/components/p53predictor/p53-predictor-results.vue
new file mode 100644
index 0000000..59a7a90
--- /dev/null
+++ b/src/components/p53predictor/p53-predictor-results.vue
@@ -0,0 +1,118 @@
+<template>
+ <div>
+ <h2 v-if="sequence">
+ {{ sequence.name }}
+ <span v-if="sequence.name != analysisInfo.title"> : {{ analysisInfo.title }} </span>
+ <!-- slot for back button -->
+ <slot></slot>
+ </h2>
+
+ <heatmap v-if="heatmapData" :data="heatmapData" @segmentClick="showSegment" :selected="selectedSegment"></heatmap>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import Heatmap from '@/components/core/visualisation/heatmap'
+import SequenceStats from '@/components/sequence/helpers/sequence-stats'
+
+export default {
+ props: ['analysisInfo', 'downloadToken'],
+ data() {
+ return {
+ currentSort: {
+ crit: 'position',
+ asc: true,
+ },
+ sequence: null,
+ heatmapData: null,
+ selectedSegment: undefined,
+ sequenceStart: undefined, //position of quadruplex list start
+ sequenceLength: undefined,
+ }
+ },
+ methods: {
+ getSequenceInfo() {
+ return this.$http.get('sequence/' + this.analysisInfo.sequenceId).then(response => {
+ this.sequence = response.data.payload
+ SequenceStats.getBasesCounts(this.$http, this.sequence).then()
+ })
+ },
+ reload() {},
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ downloadHeatmap() {
+ //adjust segment count to be larger than windowSize size, max 80 segments
+ var segmentsCount = Math.min(80, Math.max(1, Math.floor(this.sequence.length / 20)))
+ return this.$http
+ .get('analyse/p53predictor/' + this.analysisInfo.id + '/heatmap', {
+ params: {
+ segments: segmentsCount,
+ },
+ })
+ .then(response => {
+ this.heatmapData = response.data
+ })
+ },
+ /**
+ * click in heatmap
+ *
+ * @param seg
+ */
+ showSegment(pos, size) {
+ if (this.selectedSegment == pos) {
+ this.selectedSegment = undefined
+ this.sequenceStart = undefined
+ this.sequenceLength = undefined
+ } else {
+ this.selectedSegment = pos
+ this.sequenceStart = Math.floor(pos * size)
+ this.sequenceLength = Math.ceil(size)
+ }
+ this.reload()
+ },
+ toggleDetails(quadruplex) {
+ quadruplex.ui.showDetails = !quadruplex.ui.showDetails
+ },
+ downloadUrl(aggregate) {
+ if (this.downloadToken) {
+ return (
+ this.$http.defaults.baseURL +
+ 'analyse/g4hunter/' +
+ this.analysisInfo.id +
+ '/quadruplex.csv?aggregate=' +
+ (aggregate ? 'true' : 'false') +
+ '&token=' +
+ this.downloadToken
+ )
+ }
+ return ''
+ },
+ },
+ mounted() {
+ this.reload()
+ this.getSequenceInfo().then(() => {
+ this.downloadHeatmap()
+ })
+ },
+ computed: {
+ GCCount() {
+ return SequenceStats.calcGCCount(this.sequence)
+ },
+ GCRate() {
+ return SequenceStats.calcGCRate(this.sequence)
+ },
+ },
+ components: {
+ heatmap: Heatmap,
+ },
+ filters: {
+ number: Formatters.number,
+ genePos: Formatters.genePos,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/p53predictor/p53-predictor-tool.vue b/src/components/p53predictor/p53-predictor-tool.vue
new file mode 100644
index 0000000..259870e
--- /dev/null
+++ b/src/components/p53predictor/p53-predictor-tool.vue
@@ -0,0 +1,45 @@
+<template>
+ <div class="container">
+ <h1>P53 predictor</h1>
+
+ <b-tabs>
+ <b-tab title="Single">
+ <br />
+ <form-single></form-single>
+ </b-tab>
+ <b-tab title="Multiple">
+ <br />
+ <form-multiple></form-multiple>
+ </b-tab>
+ <b-tab title="Find best">
+ <br />
+ <form-best></form-best>
+ </b-tab>
+ </b-tabs>
+
+ <hr />
+
+ <p>
+ Ideal binding sequence for p53: GGACATGCCCGGGCATGTCC, log <em>K</em><sub>d</sub>(x) = - 7.61
+ <br />
+ Veprintsev, D.B. and A.R. Fersht, Algorithm for prediction of tumour suppressor p53 affinity for binding sites in
+ DNA. Nucleic acids research, 2008. 36(5): p. 1589-98.
+ </p>
+ </div>
+</template>
+
+<script>
+import FormSingle from './form-single'
+import FormMultiple from './form-multiple'
+import FormBest from './form-best'
+
+export default {
+ components: {
+ FormSingle,
+ FormMultiple,
+ FormBest,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/p53predictor/p53-predictor.vue b/src/components/p53predictor/p53-predictor.vue
new file mode 100644
index 0000000..1e62a2b
--- /dev/null
+++ b/src/components/p53predictor/p53-predictor.vue
@@ -0,0 +1,129 @@
+<template>
+ <div class="container-fluid">
+ <h1>p53 Predictor</h1>
+ <div class="row">
+ <div class="col-md-3">
+ <sequence-selector ref="sequenceSelector" @select="collectTags"></sequence-selector>
+ </div>
+ <div class="col-md-3 offset-md-6">
+ <p53-form @start="startAnalysis">
+ <template slot="additionalButtons">
+ <button type="button" class="btn btn-primary btn-block" @click="modifyTags">
+ <span class="fa fa-tag"></span> Modify tags
+ </button>
+ </template>
+ </p53-form>
+ </div>
+ </div>
+
+ <modal-alert ref="alertModal">Select a sequence first.</modal-alert>
+ <modal-confirm ref="tagsModal">
+ <label>Tags</label>
+ <input-tag class="form-control" :tags.sync="tagsToModify"></input-tag>
+ </modal-confirm>
+ </div>
+</template>
+
+<script>
+import SequenceSelector from '@/components/sequence/sequence-selector'
+import P53Form from './p53-form'
+import InputTag from 'vue-input-tag'
+import BatchWatcher from '@/services/batch-watcher'
+
+export default {
+ data() {
+ return {
+ selectedTags: [],
+ tagsToModify: [],
+ finishedAnalysis: [],
+ waiting: false,
+ waitError: false,
+ resultIDs: [],
+ }
+ },
+ methods: {
+ /**
+ * merge all tag arrays from all selected sequences
+ */
+ collectTags() {
+ var sequences = this.$refs.sequenceSelector.getSelected()
+ this.selectedTags = []
+ this.selectedTags = sequences.reduce((acc, seq) => {
+ seq.tags.forEach(tag => {
+ if (acc.indexOf(tag) == -1) {
+ acc.push(tag)
+ }
+ })
+ return acc
+ }, [])
+ },
+ startAnalysis(config) {
+ var sequences = this.$refs.sequenceSelector.getSelectedIds()
+ if (sequences.length == 0) {
+ this.$refs.alertModal.display()
+ return
+ }
+ this.$http
+ .post('analyse/p53predictor', {
+ threshold: config.threshold,
+ sequences: sequences,
+ tags: this.selectedTags,
+ })
+ .then(
+ response => {
+ this.resultIDs = response.data.items.map(info => {
+ this.$store.commit('addWork', {
+ key: info.id,
+ title: 'Quadruplex analysis',
+ })
+ return info.id
+ })
+ this.waitForResults()
+ },
+ () => {
+ //TODO batch creation failed
+ }
+ )
+ },
+ waitForResults() {
+ this.waitError = false
+ this.waiting = true
+ var bw = new BatchWatcher(this.$http)
+ for (let resultId of this.resultIDs) {
+ bw.wait('analyse/p53predictor/' + resultId)
+ .then(
+ response => {
+ this.finishedAnalysis.push(response.data)
+ },
+ () => {
+ this.waitError = true
+ }
+ )
+ .finally(() => {
+ this.$store.commit('workDone', resultId)
+ this.waiting = false
+ })
+ }
+ },
+ modifyTags() {
+ this.tagsToModify = this.selectedTags.slice() //copy array
+ var sequences = this.$refs.sequenceSelector.getSelected()
+ if (sequences.length == 0) {
+ this.$refs.alertModal.display()
+ return
+ }
+ this.$refs.tagsModal.display().then(
+ () => {
+ this.selectedTags = this.tagsToModify
+ },
+ () => {}
+ )
+ },
+ },
+ components: {
+ SequenceSelector,
+ P53Form,
+ InputTag,
+ },
+}
+</script>
diff --git a/src/components/p53predictor/stored-results-detail.vue b/src/components/p53predictor/stored-results-detail.vue
new file mode 100644
index 0000000..7523c47
--- /dev/null
+++ b/src/components/p53predictor/stored-results-detail.vue
@@ -0,0 +1,54 @@
+<template>
+ <div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-10">
+ <h1>p53 predictor stored results</h1>
+ </div>
+ <div class="col-sm-2">
+ <br />
+ <router-link class="btn btn-primary btn-block" :to="{ name: 'results.p53predictor' }">Back</router-link>
+ </div>
+ </div>
+
+ <results v-if="analysis" :analysis-info="analysis" :download-token="downloadToken"></results>
+
+ <http-error :info="httpError"></http-error>
+ </div>
+</template>
+
+<script>
+import HttpError from '@/components/core/http-error'
+import Results from './p53-predictor-results'
+
+export default {
+ data() {
+ return {
+ analysis: null,
+ downloadToken: '',
+ httpError: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http.get('analyse/p53predictor/' + this.$route.params.id).then(
+ response => {
+ this.analysis = response.data.payload
+ this.downloadToken = response.data.downloadToken
+ },
+ err => {
+ this.httpError = err
+ }
+ )
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ HttpError,
+ Results,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/p53predictor/stored-results.vue b/src/components/p53predictor/stored-results.vue
new file mode 100644
index 0000000..316ce28
--- /dev/null
+++ b/src/components/p53predictor/stored-results.vue
@@ -0,0 +1,196 @@
+<template>
+ <div class="container">
+ <h1>p53 predictor results</h1>
+
+ <pagination ref="pagination" @pageChange="downloadResults">
+ <checkable-list ref="resultsList">
+ <th slot="header">Sequence/Analyse name</th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="finished" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="resultCount" :current="currentSort">Results count</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">Tags</th>
+ <th class="text-center" slot="header">Details</th>
+ <th class="text-center" slot="header">Edit</th>
+ <th class="text-center" slot="header">Delete</th>
+
+ <span slot="item-name" slot-scope="props">
+ {{ props.item.title }}
+ </span>
+
+ <template slot-scope="props">
+ <td class="text-right">
+ <span v-if="props.item.finished">{{ props.item.finished | dateTime }}</span>
+ <span v-else class="fa fa-spinner animate"></span>
+ </td>
+ <td class="text-right">
+ <span v-if="props.item.finished">
+ {{ props.item.resultCount | number(0) }}
+ </span>
+ </td>
+ <td>
+ <b-badge v-for="tag in props.item.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <td class="text-center">
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{
+ name: 'results.p53predictor.detail',
+ params: { id: props.item.id },
+ }"
+ >
+ <span class="fa fa-search"></span>
+ </router-link>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-primary btn-sm" @click.stop="editResult(props.item)">
+ <span class="fa fa-edit"></span>
+ </button>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-danger btn-sm" @click.stop="deleteResult(props.item)">
+ <span class="fa fa-trash"></span>
+ </button>
+ </td>
+ </template>
+
+ <p slot="no-items" class="alert alert-warning">
+ No results found.
+ </p>
+ </checkable-list>
+ </pagination>
+
+ <button type="button" class="btn btn-default" @click="toggleSelection">
+ <i class="fa fa-refresh"></i> Invert selection
+ </button>
+ <button class="btn btn-danger" @click="deleteResults"><i class="fa fa-trash"></i> Delete selected</button>
+
+ <modal-confirm ref="confirmModal">Really delete results?</modal-confirm>
+ <modal-confirm ref="confirmModalMulti">Really delete selected results?</modal-confirm>
+
+ <modal-confirm ref="editModal">
+ <template slot="header">
+ Modify result
+ </template>
+
+ <result-editor v-if="selectedResult" :result="selectedResult" ref="resultEditor"></result-editor>
+
+ <template slot="buttonConfirm">
+ Save changes
+ </template>
+ </modal-confirm>
+ </div>
+</template>
+
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import CheckableList from '@/components/core/checkable-list'
+import Pagination from '@/components/core/pagination'
+import ResultEditor from '@/components/core/result-editor'
+
+/**
+ * list of stored result groups
+ */
+export default {
+ data() {
+ return {
+ selectedResult: null,
+ currentSort: {
+ crit: 'finished',
+ asc: true,
+ },
+ downloadToken: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http
+ .get('analyse/p53predictor', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.$refs.resultsList.setItems(response.data.items)
+ this.downloadToken = response.data.downloadToken
+ })
+ },
+ performDelete(result) {
+ return this.$http.delete('analyse/p53predictor/' + result.id)
+ },
+ deleteResult(result) {
+ this.$refs.confirmModal
+ .display()
+ .then(() => {
+ return this.performDelete(result)
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ },
+ deleteResults() {
+ this.$refs.confirmModalMulti.display().then(() => {
+ var checked = this.$refs.resultsList.getCheckedItems()
+ var promises = []
+ checked.forEach(result => {
+ if (result.ui.checked) {
+ promises.push(this.performDelete(result))
+ }
+ })
+ Promise.all(promises).then(() => {
+ this.downloadResults()
+ })
+ })
+ },
+ editResult(result) {
+ this.selectedResult = result
+ this.$refs.editModal
+ .display()
+ .then(() => {
+ this.$http
+ .put('analyse/p53predictor/' + result.id + '/tags', {
+ tags: this.$refs.resultEditor.getTags(),
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ })
+ .finally(() => {
+ this.selectedResult = null
+ })
+ },
+ sortResults(info) {
+ this.currentSort = info
+ this.downloadResults()
+ },
+ toggleSelection() {
+ this.$refs.resultsList.toggleSelection()
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ 'checkable-list': CheckableList,
+ pagination: Pagination,
+ 'result-editor': ResultEditor,
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ sequenceName: Formatters.sequenceName,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/quadruplex/quadruplex-details.vue b/src/components/quadruplex/quadruplex-details.vue
new file mode 100644
index 0000000..a3ff3e7
--- /dev/null
+++ b/src/components/quadruplex/quadruplex-details.vue
@@ -0,0 +1,66 @@
+<template>
+ <table class="table table-bordered">
+ <tr>
+ <th>Position</th>
+ <th>Sequence</th>
+ <th>Score</th>
+ <th>G4 killer</th>
+ </tr>
+ <tr v-for="part in parts">
+ <td class="text-right">{{ part.position | number(0) }}</td>
+ <td class="text-monospace text-bold">
+ <highlight :sequence="part.sequence"></highlight>
+ </td>
+ <td class="text-right">{{ part.score | number(2) }}</td>
+ <td class="text-center">
+ <router-link
+ class="btn btn-primary btn-sm"
+ target="_blank"
+ :to="{ name: 'analyse.g4killer', query: { sequence: part.sequence } }"
+ >
+ Kill
+ </router-link>
+ </td>
+ </tr>
+ </table>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import Highlight from '@/components/core/visualisation/highlight'
+
+/**
+ * display quadruplexes before grouping
+ */
+export default {
+ props: ['quadruplex', 'length'],
+ computed: {
+ parts() {
+ var ret = []
+ var seq = this.quadruplex.sequence
+ for (var i = 0; i < seq.length - this.length + 1; i++) {
+ ret.push({
+ position: this.quadruplex.position + i,
+ sequence: seq.substr(i, this.length),
+ score: this.quadruplex.subScoreList[i],
+ })
+ }
+ return ret
+ },
+ },
+ components: {
+ highlight: Highlight,
+ },
+ filters: {
+ number: Formatters.number,
+ genePos: Formatters.genePos,
+ },
+}
+</script>
+
+<style scoped>
+td,
+th {
+ padding: 0.3rem;
+}
+</style>
diff --git a/src/components/quadruplex/quadruplex-form.vue b/src/components/quadruplex/quadruplex-form.vue
new file mode 100644
index 0000000..419a2a5
--- /dev/null
+++ b/src/components/quadruplex/quadruplex-form.vue
@@ -0,0 +1,166 @@
+<template>
+ <div class="row">
+ <div class="col-md-12" v-show="ui.advanced">
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Search mode</label>
+ <div class="col-md-8">
+ <select class="form-control" v-model="searchMode">
+ <option value="GC" selected>G and C</option>
+ <option value="G">G only (positive)</option>
+ <option value="C">C only (negative)</option>
+ </select>
+ </div>
+ </div>
+ <div class="form-group row">
+ <label class="col-3 col-form-label">G/C score per bp</label>
+ <label class="col-3 col-form-label">GG/CC score per bp</label>
+ <label class="col-3 col-form-label">GGG/CCC score per bp</label>
+ <label class="col-3 col-form-label">GGGG/CCCC score per bp</label>
+ </div>
+ <div class="form-group row">
+ <div class="col-3">
+ <input type="number" class="form-control" step="0.1" min="0" max="10" v-model.number="$v.seqScore1.$model" />
+ </div>
+ <div class="col-3">
+ <input type="number" class="form-control" step="0.1" min="0" max="10" v-model.number="$v.seqScore2.$model" />
+ </div>
+ <div class="col-3">
+ <input type="number" class="form-control" step="0.1" min="0" max="10" v-model.number="$v.seqScore3.$model" />
+ </div>
+ <div class="col-3">
+ <input type="number" class="form-control" step="0.1" min="0" max="10" v-model.number="$v.seqScore4.$model" />
+ </div>
+ </div>
+ </div>
+ <div class="col-md-12">
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Window</label>
+ <div class="col-md-8">
+ <input
+ type="number"
+ class="form-control"
+ step="1"
+ min="10"
+ max="100"
+ v-bind:value="windowSize"
+ v-on:input="updateValue($event.target.value, 'windowSize')"
+ />
+ </div>
+ </div>
+ <p v-if="windowSize < 20 || windowSize > 30" class="alert alert-warning">
+ Window size recommended value is between 20 and 30.
+ </p>
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Threshold</label>
+ <div class="col-md-8">
+ <input
+ type="number"
+ class="form-control"
+ step="0.1"
+ min="0.1"
+ max="4"
+ v-bind:value="threshold"
+ v-on:input="updateValue($event.target.value, 'threshold')"
+ />
+ </div>
+ </div>
+ <p v-if="threshold < 0.9" class="alert alert-warning">
+ Threshold recommended value is 0.9 or more.
+ </p>
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.windowSize.required">Window size is required.</div>
+ <div v-if="!$v.windowSize.numeric">Window size must be numeric.</div>
+ <div v-if="!$v.windowSize.minValue">Minimal length of window is {{ $v.windowSize.$params.minValue.min }}.</div>
+ <div v-if="!$v.windowSize.maxValue">Maximal length of window is {{ $v.windowSize.$params.maxValue.max }}.</div>
+ <div v-if="!$v.threshold.required">Threshold is required.</div>
+ <div v-if="!$v.threshold.decimal">
+ Threshold must be decimal number.
+ </div>
+ <div v-if="!$v.threshold.minValue">Minimal value of threshold is {{ $v.threshold.$params.minValue.min }}.</div>
+ <div v-if="!$v.threshold.maxValue">Maximal value of threshold is {{ $v.threshold.$params.maxValue.max }}.</div>
+ <div v-if="!$v.seqScore1.required">Score is required.</div>
+ <div v-if="!$v.seqScore1.decimal">Score must be decimal number.</div>
+ <div v-if="!$v.seqScore1.minValue">Minimal value of score is {{ $v.threshold.$params.seqScore1.min }}.</div>
+ <div v-if="!$v.seqScore1.maxValue">Maximal value of score is {{ $v.threshold.$params.seqScore1.max }}.</div>
+ <div v-if="!$v.seqScore2.required">Score is required.</div>
+ <div v-if="!$v.seqScore2.decimal">Score must be decimal number.</div>
+ <div v-if="!$v.seqScore2.minValue">Minimal value of score is {{ $v.threshold.$params.seqScore2.min }}.</div>
+ <div v-if="!$v.seqScore2.maxValue">Maximal value of score is {{ $v.threshold.$params.seqScore2.max }}.</div>
+ <div v-if="!$v.seqScore3.required">Score is required.</div>
+ <div v-if="!$v.seqScore3.decimal">Score must be decimal number.</div>
+ <div v-if="!$v.seqScore3.minValue">Minimal value of score is {{ $v.threshold.$params.seqScore3.min }}.</div>
+ <div v-if="!$v.seqScore3.maxValue">Maximal value of score is {{ $v.threshold.$params.seqScore3.max }}.</div>
+ <div v-if="!$v.seqScore4.required">Score is required.</div>
+ <div v-if="!$v.seqScore4.decimal">Score must be decimal number.</div>
+ <div v-if="!$v.seqScore4.minValue">Minimal value of score is {{ $v.threshold.$params.seqScore4.min }}.</div>
+ <div v-if="!$v.seqScore4.maxValue">Maximal value of score is {{ $v.threshold.$params.seqScore4.max }}.</div>
+ </div>
+
+ <div class="text-right">
+ <!--
+ <button type="button" class="btn btn-primary btn-block" @click="toggleAdvanced">
+ <i class="fa fa-cog"></i> Show advanced settings
+ </button>
+ -->
+ <slot name="additionalButtons"></slot>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, numeric, minValue, maxValue, decimal } from 'vuelidate/lib/validators'
+
+export default {
+ props: ['windowSize', 'threshold'],
+ validations: {
+ windowSize: {
+ required,
+ numeric,
+ minValue: minValue(10),
+ maxValue: maxValue(100),
+ },
+ threshold: {
+ required,
+ decimal,
+ minValue: minValue(0.1),
+ maxValue: maxValue(4),
+ },
+ seqScore1: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(10),
+ },
+ seqScore2: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(10),
+ },
+ seqScore3: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(10),
+ },
+ seqScore4: {
+ required,
+ decimal,
+ minValue: minValue(0),
+ maxValue: maxValue(10),
+ },
+ },
+ methods: {
+ toggleAdvanced() {
+ this.ui.advanced = !this.ui.advanced
+ },
+ updateValue: function(value, type) {
+ this.$emit('input', value, type)
+ },
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/quadruplex/quadruplex-results.vue b/src/components/quadruplex/quadruplex-results.vue
new file mode 100644
index 0000000..f9a629f
--- /dev/null
+++ b/src/components/quadruplex/quadruplex-results.vue
@@ -0,0 +1,344 @@
+<template>
+ <div>
+ <h2 v-if="sequence">
+ {{ sequence.name }}
+ <span v-if="sequence.name != analysisInfo.title"> : {{ analysisInfo.title }} </span>
+ <!-- slot for back button -->
+ <slot></slot>
+ </h2>
+
+ <!-- overview -->
+ <div v-show="quadruplexList">
+ <heatchart
+ v-if="heatmapData"
+ :data="heatmapData"
+ @dataPointClick="showSegment"
+ @onZoom="zoomHeatchart"
+ ></heatchart>
+ <heatmap v-if="heatmapData" :data="heatmapData" @segmentClick="showSegment" :selected="selectedSegment">
+ </heatmap>
+
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>Analysis settings</th>
+ <th>Analysis results</th>
+ <th class="text-center">Export</th>
+ <th v-if="sequence">Sequence info</th>
+ </tr>
+ <tr>
+ <td>
+ Window size: {{ analysisInfo.windowSize | number(0) }}
+ <br />
+ Threshold: {{ analysisInfo.threshold | number(2) }}
+ </td>
+ <td>
+ Quadruplexes found: {{ analysisInfo.resultCount | number(0) }}
+ <br />
+ <span v-if="sequence">Frequency: {{ analysisInfo.frequency | number(1) }} / 1000 bp</span>
+ </td>
+ <td class="text-center">
+ <a v-if="downloadToken" :href="downloadUrl(false)" class="btn btn-primary btn-sm">
+ <span class="fa fa-cubes"></span> CSV Individual
+ </a>
+ <a v-if="downloadToken" :href="downloadUrl(true)" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span> CSV Grouped
+ </a>
+ <a v-if="downloadToken" :href="downloadBED()" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span> Bedgraph
+ </a>
+ </td>
+ <td v-if="sequence">
+ {{ sequence.name }}
+ <br />
+ {{ sequence.length | number(0) }} bp
+ <br />
+ GC: {{ GCCount }} ({{ GCRate | number(1) }}%)
+ </td>
+ </tr>
+ </tbody>
+ </table>
+
+ <!-- list of results -->
+ <pagination ref="pagination" @pageChange="reload" :page-size="20">
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="position" :current="currentSort">Position</sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="length" :current="currentSort">Length</sort-toggle>
+ </th>
+ <th class="text-center"> </th>
+ <th>Sequence</th>
+ <th>Score chart</th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="score" :current="currentSort">G4Hunter score</sort-toggle>
+ <sort-toggle @sort="sortSequences" crit="absScore" :current="currentSort">(abs)</sort-toggle>
+ </th>
+ <th class="text-center"></th>
+ </tr>
+ <template v-for="quadruplex in quadruplexList">
+ <tr>
+ <td class="text-right">
+ {{ quadruplex.position | number(0) }}
+ </td>
+ <td class="text-right">
+ {{ quadruplex.length }}
+ </td>
+ <td class="text-center">
+ <span class="toggle fa fa-search" @click="toggleDetails(quadruplex)" title="Toggle details"></span>
+ </td>
+ <td class="sequence text-monospace text-bold">
+ <highlight :sequence="quadruplex.sequence"></highlight>
+ </td>
+ <td @click="toggleDetails(quadruplex)">
+ <mini-chart
+ v-if="quadruplex.subScoreList && quadruplex.subScoreList.length > 0"
+ :w="100"
+ :h="21"
+ :data="quadruplex.subScoreList"
+ ></mini-chart>
+ </td>
+ <td class="text-right">
+ {{ quadruplex.score | number }}
+ </td>
+ <td class="text-center">
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{
+ name: 'analyse.g4killer',
+ query: {
+ sequence: quadruplex.sequence,
+ onComplementary: quadruplex.score < 0,
+ },
+ }"
+ >
+ Kill
+ <!--target="_blank"-->
+ </router-link>
+ </td>
+ </tr>
+ <tr v-if="quadruplex.ui.showDetails">
+ <td colspan="7" class="details">
+ <div class="row">
+ <div class="col-10">
+ Sequence with surrounding bases:
+ <br />
+ <sequence-view
+ :sequence="sequence"
+ :feature-pos="quadruplex.position"
+ :feature-len="quadruplex.length"
+ >
+ <template slot-scope="slotProps">
+ <highlight :sequence="slotProps.left"></highlight
+ ><highlight :sequence="slotProps.feature" class="feature"></highlight
+ ><highlight :sequence="slotProps.right"></highlight>
+ </template>
+ </sequence-view>
+ </div>
+ <div class="col-2">
+ <button class="btn btn-primary btn-block btn-sm" @click="toggleDetails(quadruplex)">
+ Close
+ </button>
+ </div>
+ </div>
+ <div v-if="quadruplex.subScoreList && quadruplex.subScoreList.length > 0">
+ Before grouping:
+ <quadruplex-details :quadruplex="quadruplex" :length="analysisInfo.windowSize"></quadruplex-details>
+ </div>
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ </pagination>
+ </div>
+ <div v-show="quadruplexList && quadruplexList.length == 0">
+ <p class="alert alert-warning">
+ No quadruplexes found.
+ </p>
+ </div>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import SortToggle from '@/components/core/sort-toggle'
+import Heatchart from '@/components/core/visualisation/heatchart'
+import Heatmap from '@/components/core/visualisation/heatmap'
+import Pagination from '@/components/core/pagination'
+import SequenceStats from '@/components/sequence/helpers/sequence-stats'
+import Helpers from '@/helpers'
+import SequenceView from '@/components/core/visualisation/sequence-view'
+import QuadruplexDetails from './quadruplex-details'
+import Details from './quadruplex-details'
+import MiniChart from '@/components/core/visualisation/mini-chart'
+import Highlight from '@/components/core/visualisation/highlight'
+
+/**
+ * list of results for sequence analysis
+ */
+export default {
+ props: ['analysisInfo', 'downloadToken'],
+ data() {
+ return {
+ currentSort: {
+ crit: 'position',
+ asc: true,
+ },
+ sequence: null,
+ sequenceFrom: undefined,
+ sequenceTo: undefined,
+ quadruplexList: null,
+ heatmapData: null,
+ selectedSegment: undefined,
+ sequenceStart: undefined, //position of quadruplex list start
+ sequenceLength: undefined,
+ }
+ },
+ methods: {
+ getSequenceInfo() {
+ return this.$http.get('sequence/' + this.analysisInfo.sequenceId).then(response => {
+ this.sequence = response.data.payload
+ this.sequenceTo = this.sequence.length
+ })
+ },
+ reload() {
+ return this.$http
+ .get('analyse/g4hunter/' + this.analysisInfo.id + '/quadruplex', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ sequenceStart: this.sequenceStart,
+ sequenceLength: this.sequenceLength,
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ Helpers.setUIState(response.data.items, 'showDetails', false)
+ this.quadruplexList = response.data.items
+ })
+ },
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ async downloadHeatmap() {
+ const total = this.sequence.length
+ const { sequenceFrom: from = 0, sequenceTo: to = total, analysisInfo } = this
+ //adjust segment count to be larger than windowSize size, max 80 segments
+ const segments = Math.min(80, Math.max(1, Math.floor((to - from) / analysisInfo.windowSize)) * (to - from))
+ const { data } = await this.$http.get(`analyse/g4hunter/${analysisInfo.id}/heatmap`, {
+ params: { segments, from, to },
+ })
+
+ this.heatmapData = { ...data, from, to, total }
+ },
+ /**
+ * click in heatmap
+ *
+ * @param seg
+ */
+ showSegment(pos, size) {
+ if (this.selectedSegment == pos) {
+ this.selectedSegment = undefined
+ this.sequenceStart = undefined
+ this.sequenceLength = undefined
+ } else {
+ this.selectedSegment = pos
+ this.sequenceStart = Math.floor(pos * size)
+ this.sequenceLength = Math.ceil(size)
+ }
+ this.reload()
+ },
+ async zoomHeatchart(from, to, onSuccess) {
+ this.sequenceFrom = from
+ this.sequenceTo = to
+ await this.downloadHeatmap()
+ onSuccess()
+ },
+ toggleDetails(quadruplex) {
+ quadruplex.ui.showDetails = !quadruplex.ui.showDetails
+ },
+ downloadUrl(aggregate) {
+ if (this.downloadToken) {
+ return (
+ this.$http.defaults.baseURL +
+ 'analyse/g4hunter/' +
+ this.analysisInfo.id +
+ '/quadruplex.csv?aggregate=' +
+ (aggregate ? 'true' : 'false') +
+ '&token=' +
+ this.downloadToken
+ )
+ }
+ return ''
+ },
+ downloadBED() {
+ if (this.downloadToken) {
+ return (
+ this.$http.defaults.baseURL +
+ 'analyse/g4hunter/' +
+ this.analysisInfo.id +
+ '/quadruplex.bedgraph?token=' +
+ this.downloadToken
+ )
+ }
+ return ''
+ },
+ },
+ mounted() {
+ this.reload()
+ this.getSequenceInfo().then(() => {
+ this.downloadHeatmap()
+ })
+ },
+ computed: {
+ GCCount() {
+ return SequenceStats.calcGCCount(this.sequence)
+ },
+ GCRate() {
+ return SequenceStats.calcGCRate(this.sequence)
+ },
+ },
+ components: {
+ MiniChart,
+ QuadruplexDetails,
+ 'sort-toggle': SortToggle,
+ heatmap: Heatmap,
+ pagination: Pagination,
+ highlight: Highlight,
+ 'sequence-view': SequenceView,
+ 'quadruplex-details': Details,
+ 'mini-chart': MiniChart,
+ heatchart: Heatchart,
+ },
+ filters: {
+ number: Formatters.number,
+ genePos: Formatters.genePos,
+ },
+}
+</script>
+
+<style scoped>
+td,
+th {
+ padding: 0.5rem;
+}
+td.sequence {
+ max-width: 400px;
+}
+td.details {
+ max-width: 600px;
+}
+td.details .feature {
+ border: 1px solid red;
+}
+td .toggle {
+ cursor: pointer;
+}
+</style>
diff --git a/src/components/quadruplex/quadruplex.vue b/src/components/quadruplex/quadruplex.vue
new file mode 100644
index 0000000..b797146
--- /dev/null
+++ b/src/components/quadruplex/quadruplex.vue
@@ -0,0 +1,132 @@
+<template>
+ <div class="container-fluid">
+ <h1>G4 hunter</h1>
+ <div class="row">
+ <div class="col-md-4">
+ <h2>Analysis setting</h2>
+ <quadruplex-form :threshold="threshold" :windowSize="windowSize" @input="modifyFormValue" />
+ </div>
+ <div class="col-md-8">
+ <h2>Sequences</h2>
+ <sequence-selector ref="sequenceSelector" @analyse="startAnalysis" />
+ </div>
+ </div>
+
+ <div class="alert alert-danger" v-if="serverError">{{ serverError }}</div>
+
+ <div v-if="waitError">
+ <hr />
+ <div class="alert alert-danger">
+ <div class="row">
+ <p class="col-10">
+ Waiting for results took too long.
+ </p>
+ <div class="col-2">
+ <button class="btn btn-primary btn-block" @click="waitForResults()">
+ <span class="fa fa-refresh"></span> Keep waiting
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <b-tabs v-if="finishedAnalysis.length > 0">
+ <b-tab v-for="(analysis, i) of finishedAnalysis" :key="analysis.payload.id" :title="'Results ' + (i + 1)">
+ <br />
+ <results :analysis-info="analysis.payload" :download-token="analysis.downloadToken">
+ <b-btn variant="danger" class="float-right" @click="closeResults(analysis.payload)">
+ Close tab
+ </b-btn>
+ </results>
+ </b-tab>
+ </b-tabs>
+
+ <hr />
+ <div class="card bg-light">
+ <div class="card-body">
+ This algorithm is a rewrite of
+ <a href="https://github.com/AnimaTardeb/G4-Hunter"
+ >G4 hunter Python implementation by Jean-Louis Mergny and Amina Bedrat</a
+ >.
+ </div>
+ </div>
+ </div>
+</template>
+
+<script type="text/javascript">
+import SequenceSelector from '@/components/sequence/sequence-selector'
+import BatchWatcher from '@/services/batch-watcher'
+import QuadruplexForm from './quadruplex-form'
+import Results from './quadruplex-results'
+
+/**
+ * quadruplex analysis
+ */
+export default {
+ data() {
+ return {
+ windowSize: 25,
+ threshold: 1.2,
+ config: {},
+ finishedAnalysis: [],
+ waiting: false,
+ waitError: false,
+ serverError: null,
+ }
+ },
+ methods: {
+ closeResults(analysis) {
+ this.finishedAnalysis = this.finishedAnalysis.filter(info => {
+ return info.payload.id != analysis.id
+ })
+ },
+ waitForResult(resultId) {
+ this.waitError = false
+ this.waiting = true
+ var bw = new BatchWatcher(this.$http)
+ return bw
+ .wait('analyse/g4hunter/' + resultId)
+ .then(response => {
+ this.finishedAnalysis.push(response.data)
+ })
+ .finally(() => {
+ this.$store.commit('workDone', resultId)
+ this.waiting = false
+ })
+ },
+ modifyFormValue(value, type) {
+ this[type] = value
+ },
+ startAnalysis(sequence, callback) {
+ this.$http
+ .post('analyse/g4hunter', {
+ windowSize: this.windowSize,
+ threshold: this.threshold,
+ sequence: sequence.id,
+ tags: sequence.tags,
+ })
+ .then(response => {
+ const item = response.data.payload
+ this.serverError = null
+ this.$store.commit('addWork', {
+ key: item.id,
+ title: 'Quadruplex analysis',
+ })
+ return this.waitForResult(item.id)
+ })
+ .then(() => {
+ callback()
+ })
+ .catch(error => {
+ this.serverError = error?.response?.data?.message
+ callback('FAILED')
+ })
+ },
+ },
+ components: {
+ 'sequence-selector': SequenceSelector,
+ results: Results,
+ 'quadruplex-form': QuadruplexForm,
+ },
+}
+</script>
diff --git a/src/components/quadruplex/stored-results-details.vue b/src/components/quadruplex/stored-results-details.vue
new file mode 100644
index 0000000..d75a21d
--- /dev/null
+++ b/src/components/quadruplex/stored-results-details.vue
@@ -0,0 +1,57 @@
+<template>
+ <div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-10">
+ <h1>G4 hunter stored results</h1>
+ </div>
+ <div class="col-sm-2">
+ <br />
+ <router-link class="btn btn-primary btn-block" :to="{ name: 'results.quadruplex' }">Back</router-link>
+ </div>
+ </div>
+
+ <results v-if="analysis" :analysis-info="analysis" :download-token="downloadToken"></results>
+
+ <http-error :info="httpError"></http-error>
+ </div>
+</template>
+
+<script>
+import Results from './quadruplex-results'
+import HttpError from '@/components/core/http-error'
+
+/**
+ * display previously stored results
+ */
+export default {
+ data() {
+ return {
+ analysis: null,
+ downloadToken: '',
+ httpError: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http.get('analyse/g4hunter/' + this.$route.params.id).then(
+ response => {
+ this.analysis = response.data.payload
+ this.downloadToken = response.data.downloadToken
+ },
+ err => {
+ this.httpError = err
+ }
+ )
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ results: Results,
+ 'http-error': HttpError,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/quadruplex/stored-results.vue b/src/components/quadruplex/stored-results.vue
new file mode 100644
index 0000000..41b9272
--- /dev/null
+++ b/src/components/quadruplex/stored-results.vue
@@ -0,0 +1,243 @@
+<template>
+ <div class="container">
+ <h1>G4 hunter results</h1>
+
+ <pagination ref="pagination" @pageChange="downloadResults">
+ <checkable-list ref="resultsList">
+ <th slot="header">Sequence/Analyse name</th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="finished" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="resultCount" :current="currentSort">Results count</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">Export</th>
+ <th class="text-center" slot="header">Tags</th>
+ <th class="text-center" slot="header">Details</th>
+ <th class="text-center" slot="header">Edit</th>
+ <th class="text-center" slot="header">Delete</th>
+
+ <span slot="item-name" slot-scope="props">
+ {{ props.item.title }}
+ </span>
+
+ <template slot-scope="props">
+ <td class="text-right">
+ <span v-if="props.item.finished">{{ props.item.finished | dateTime }}</span>
+ <span v-else class="fa fa-spinner animate"></span>
+ </td>
+ <td class="text-right">
+ <span v-if="props.item.finished">
+ {{ props.item.resultCount | number(0) }}
+ </span>
+ </td>
+ <td class="text-center">
+ <a :href="downloadUrl(props.item, false)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-cubes"></span>
+ </a>
+ <a :href="downloadUrl(props.item, true)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span>
+ </a>
+ <a :href="downloadBED(props.item)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span>
+ </a>
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{
+ name: 'results.quadruplex.detail',
+ params: { id: props.item.id },
+ }"
+ >
+ <span class="fa fa-search"></span>
+ </router-link>
+ </td>
+ <td>
+ <b-badge v-for="tag in props.item.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <td class="text-center">
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{
+ name: 'results.quadruplex.detail',
+ params: { id: props.item.id },
+ }"
+ >
+ <span class="fa fa-search"></span>
+ </router-link>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-primary btn-sm" @click.stop="editResult(props.item)">
+ <span class="fa fa-edit"></span>
+ </button>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-danger btn-sm" @click.stop="deleteResult(props.item)">
+ <span class="fa fa-trash"></span>
+ </button>
+ </td>
+ </template>
+
+ <p slot="no-items" class="alert alert-warning">
+ No results found.
+ </p>
+ </checkable-list>
+ </pagination>
+
+ <button type="button" class="btn btn-default" @click="toggleSelection">
+ <i class="fa fa-refresh"></i> Invert selection
+ </button>
+ <button class="btn btn-danger" @click="deleteResults"><i class="fa fa-trash"></i> Delete selected</button>
+
+ <modal-confirm ref="confirmModal">Really delete results?</modal-confirm>
+ <modal-confirm ref="confirmModalMulti">Really delete selected results?</modal-confirm>
+
+ <modal-confirm ref="editModal">
+ <template slot="header">
+ Modify result
+ </template>
+
+ <result-editor v-if="selectedResult" :result="selectedResult" ref="resultEditor"></result-editor>
+
+ <template slot="buttonConfirm">
+ Save changes
+ </template>
+ </modal-confirm>
+ </div>
+</template>
+
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import CheckableList from '@/components/core/checkable-list'
+import Pagination from '@/components/core/pagination'
+import ResultEditor from '@/components/core/result-editor'
+
+/**
+ * list of stored result groups
+ */
+export default {
+ data() {
+ return {
+ selectedResult: null,
+ currentSort: {
+ crit: 'finished',
+ asc: true,
+ },
+ downloadToken: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http
+ .get('analyse/g4hunter', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.$refs.resultsList.setItems(response.data.items)
+ this.downloadToken = response.data.downloadToken
+ })
+ },
+ performDelete(result) {
+ return this.$http.delete('analyse/g4hunter/' + result.id)
+ },
+ deleteResult(result) {
+ this.$refs.confirmModal
+ .display()
+ .then(() => {
+ return this.performDelete(result)
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ },
+ deleteResults() {
+ this.$refs.confirmModalMulti.display().then(() => {
+ var checked = this.$refs.resultsList.getCheckedItems()
+ var promises = []
+ checked.forEach(result => {
+ if (result.ui.checked) {
+ promises.push(this.performDelete(result))
+ }
+ })
+ Promise.all(promises).then(() => {
+ this.downloadResults()
+ })
+ })
+ },
+ editResult(result) {
+ this.selectedResult = result
+ this.$refs.editModal
+ .display()
+ .then(() => {
+ this.$http
+ .put('analyse/g4hunter/' + result.id + '/tags', {
+ tags: this.$refs.resultEditor.getTags(),
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ })
+ .finally(() => {
+ this.selectedResult = null
+ })
+ },
+ sortResults(info) {
+ this.currentSort = info
+ this.downloadResults()
+ },
+ toggleSelection() {
+ this.$refs.resultsList.toggleSelection()
+ },
+ downloadUrl(analysisInfo, aggregate) {
+ if (this.downloadToken) {
+ return (
+ this.$http.defaults.baseURL +
+ 'analyse/g4hunter/' +
+ analysisInfo.id +
+ '/quadruplex.csv?aggregate=' +
+ (aggregate ? 'true' : 'false') +
+ '&token=' +
+ this.downloadToken
+ )
+ }
+ return ''
+ },
+ downloadBED(analysisInfo) {
+ if (this.downloadToken) {
+ return (
+ this.$http.defaults.baseURL +
+ 'analyse/g4hunter/' +
+ analysisInfo.id +
+ '/quadruplex.bedgraph?token=' +
+ this.downloadToken
+ )
+ }
+ return ''
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ 'checkable-list': CheckableList,
+ pagination: Pagination,
+ 'result-editor': ResultEditor,
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ sequenceName: Formatters.sequenceName,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/rloopr/rloopr-form.vue b/src/components/rloopr/rloopr-form.vue
new file mode 100644
index 0000000..2a9637c
--- /dev/null
+++ b/src/components/rloopr/rloopr-form.vue
@@ -0,0 +1,63 @@
+<template>
+ <div class="row">
+ <div class="col-md-12">
+ <div class="col-md-6" style="margin-bottom: 20px;margin-top: 20px">
+ <div class="custom-control custom-checkbox custom-control-inline">
+ <input
+ type="checkbox"
+ class="custom-control-input"
+ id="rloop-model-1"
+ value="0"
+ v-model.number="rizModel"
+ @change="updateValue"
+ />
+ <label
+ class="custom-control-label"
+ for="rloop-model-1"
+ v-b-tooltip.hover
+ title="Detecting three G-clusters between nucleotides, with at least 3 conseutive guanines"
+ >
+ RIZ 3G-cluster
+ </label>
+ </div>
+ </div>
+
+ <div class="col-md-6">
+ <div class="custom-control custom-checkbox custom-control-inline">
+ <input
+ type="checkbox"
+ class="custom-control-input"
+ id="rloop-model-2"
+ value="1"
+ v-model.number="rizModel"
+ @change="updateValue"
+ />
+ <label
+ class="custom-control-label"
+ for="rloop-model-2"
+ v-b-tooltip.hover
+ v-b-tooltip.placement.bottom
+ title="Detecting two G-clusters between nucleotides, with at least 4 conseutive guanines"
+ >
+ RIZ 4G-cluster
+ </label>
+ </div>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+export default {
+ data() {
+ return {
+ rizModel: [0],
+ }
+ },
+ methods: {
+ updateValue() {
+ this.$emit('checkModel', this.rizModel)
+ },
+ },
+}
+</script>
diff --git a/src/components/rloopr/rloopr-results.vue b/src/components/rloopr/rloopr-results.vue
new file mode 100644
index 0000000..62b52d6
--- /dev/null
+++ b/src/components/rloopr/rloopr-results.vue
@@ -0,0 +1,339 @@
+<template>
+ <div>
+ <h2 v-if="sequence">
+ {{ sequence.name }}
+ <span v-if="sequence.name != analysisInfo.title">: {{ analysisInfo.title }}</span>
+ <!-- slot for back button -->
+ <slot></slot>
+ </h2>
+
+ <div v-show="rloopList">
+ <heatchart
+ v-if="heatmapData"
+ :data="heatmapData"
+ @dataPointClick="showSegment"
+ @onZoom="zoomHeatchart"
+ ></heatchart>
+ <heatmap v-if="heatmapData" :data="heatmapData" @segmentClick="showSegment" :selected="selectedSegment">
+ </heatmap>
+
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>Analysis results</th>
+ <th class="text-center">Export</th>
+ <th v-if="sequence">Sequence info</th>
+ </tr>
+ <tr>
+ <td>
+ Rloops found: {{ analysisInfo.resultCount | number(0) }}
+ <br />
+ <span v-if="sequence">
+ (Overall R-loop length / Sequence length) for <em>RIZ 3G cluster (m1)</em>:
+ <b>{{ ((totalRloopLenM1 / sequence.length) * 100) | number(2) }} %</b>
+ </span>
+ <br />
+ <span v-if="sequence">
+ (Overall R-loop length / Sequence length) for <em>RIZ 4G cluster (m2)</em>:
+ <b>{{ ((totalRloopLenM2 / sequence.length) * 100) | number(2) }} %</b>
+ </span>
+ </td>
+ <td class="text-center">
+ <a v-if="downloadToken" :href="downloadCSV()" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span> CSV
+ </a>
+ <a v-if="downloadToken" :href="downloadBED()" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span> BedGraph
+ </a>
+ </td>
+ <td v-if="sequence">
+ {{ sequence.name }}
+ <br />
+ {{ sequence.length | number(0) }} bp
+ <br />
+ GC: {{ GCCount }} ({{ GCRate | number(1) }}%)
+ </td>
+ </tr>
+ </tbody>
+ </table>
+
+ <pagination ref="pagination" @pageChange="reload" :page-size="10">
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="position" :current="currentSort">Position</sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="length" :current="currentSort">Length</sort-toggle>
+ </th>
+ <th>
+ Model
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="strand" :current="currentSort">Strand</sort-toggle>
+ </th>
+ <th>RIZ</th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="rizGRichness" :current="currentSort">
+ RIZ Guanine richness
+ </sort-toggle>
+ </th>
+ <th>linker</th>
+ <th>REZ</th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="rloopGRichness" :current="currentSort">
+ R-loop Guanine richness
+ </sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="g3" :current="currentSort">3G clusters</sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="g4" :current="currentSort">4G clusters</sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="gn" :current="currentSort">
+ 5G clusters and larger
+ </sort-toggle>
+ </th>
+ </tr>
+ <template v-for="rloop in rloopList">
+ <tr>
+ <td>
+ {{ rloop.position | number(0) }}
+ </td>
+ <td>
+ {{ rloop.length }}
+ </td>
+ <td>
+ {{ rloop.model }}
+ </td>
+ <td>
+ {{ rloop.strand }}
+ </td>
+ <td class="sequence text-monospace text-bold">
+ <highlight :sequence="rloop.riz"></highlight>
+ </td>
+ <td class="sequence text-monospace">{{ (rloop.rizGRichness * 100) | number(2) }} %</td>
+ <td class="sequence text-monospace">
+ {{ rloop.linker.length | number(0) }}
+ </td>
+ <td class="text-center">
+ <span class="toggle fa fa-search" @click="toggleDetails(rloop)" title="Toggle details"></span>
+ </td>
+ <td class="sequence text-monospace">{{ (rloop.rloopGRichness * 100) | number(2) }} %</td>
+ <td class="sequence text-monospace">
+ {{ rloop.g3cnt | number(0) }}
+ </td>
+ <td class="sequence text-monospace">
+ {{ rloop.g4cnt | number(0) }}
+ </td>
+ <td class="sequence text-monospace">
+ {{ rloop.gncnt | number(0) }}
+ </td>
+ </tr>
+ <tr v-if="rloop.ui.showRez">
+ <td colspan="8" class="details">
+ <div class="row">
+ <div class="col-10">
+ REZ sequence:
+ <br />
+ <highlight class="sequence text-monospace text-bold" :sequence="rloop.rez"></highlight>
+ </div>
+ <div class="col-2">
+ <button class="btn btn-primary btn-block btn-sm" @click="toggleDetails(rloop)">
+ Close
+ </button>
+ </div>
+ </div>
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ </pagination>
+
+ <div v-show="rloopList && rloopList.length == 0">
+ <p class="alert alert-warning">
+ No R-loops found.
+ </p>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import SortToggle from '@/components/core/sort-toggle'
+import Pagination from '@/components/core/pagination'
+import SequenceStats from '@/components/sequence/helpers/sequence-stats'
+import Helpers from '@/helpers'
+import Heatchart from '@/components/core/visualisation/heatchart'
+import Heatmap from '@/components/core/visualisation/heatmap'
+import Highlight from '@/components/core/visualisation/highlight'
+
+/**
+ * list of results for sequence analysis
+ */
+export default {
+ props: ['analysisInfo', 'downloadToken'],
+ data() {
+ return {
+ sequence: null,
+ rloopList: null,
+ avgRloopLen: null,
+ totalRloopLenM1: null,
+ totalRloopLenM2: null,
+ heatmapData: null,
+ selectedSegment: undefined,
+ sequenceStart: undefined,
+ sequenceLength: undefined,
+ currentSort: {
+ crit: 'position',
+ asc: true,
+ },
+ }
+ },
+ methods: {
+ getSequenceInfo() {
+ return this.$http.get('sequence/' + this.analysisInfo.sequenceId).then(response => {
+ this.sequence = response.data.payload
+ })
+ },
+ countNucleic() {
+ this.$http.patch('sequence/' + this.analysisInfo.sequenceId + '/nucleic-counts').catch(err => {
+ this.httpError = err
+ })
+ },
+ reload() {
+ return this.$http
+ .get('analyse/rloopr/' + this.analysisInfo.id + '/rloops', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ sequenceStart: this.sequenceStart,
+ sequenceLength: this.sequenceLength,
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ Helpers.setUIState(response.data.items, 'showRez', false)
+ this.rloopList = response.data.items
+ this.countNucleic()
+ })
+ },
+ toggleDetails(rloop) {
+ rloop.ui.showRez = !rloop.ui.showRez
+ },
+ getAvgRizLen() {
+ return this.$http.get('analyse/rloopr/' + this.analysisInfo.id + '/average/length').then(response => {
+ this.avgRloopLen = response.data
+ })
+ },
+ getTotalRloopLenM1() {
+ return this.$http.get('analyse/rloopr/' + this.analysisInfo.id + '/total/length/m1').then(response => {
+ this.totalRloopLenM1 = response.data
+ })
+ },
+ getTotalRloopLenM2() {
+ return this.$http.get('analyse/rloopr/' + this.analysisInfo.id + '/total/length/m2').then(response => {
+ this.totalRloopLenM2 = response.data
+ })
+ },
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ async downloadHeatmap() {
+ const total = this.sequence.length
+ const { sequenceFrom: from = 0, sequenceTo: to = total, analysisInfo } = this
+ const segments = 80
+ const { data } = await this.$http.get(`analyse/rloopr/${analysisInfo.id}/heatmap`, {
+ params: { segments, from, to },
+ })
+
+ this.heatmapData = { ...data, from, to, total }
+ },
+ /**
+ * click in heatmap
+ *
+ * @param seg
+ */
+ showSegment(pos, size) {
+ if (this.selectedSegment == pos) {
+ this.selectedSegment = undefined
+ this.sequenceStart = undefined
+ this.sequenceLength = undefined
+ } else {
+ this.selectedSegment = pos
+ this.sequenceStart = Math.floor(pos * size)
+ this.sequenceLength = Math.ceil(size)
+ }
+ this.reload()
+ },
+ async zoomHeatchart(from, to, onSuccess) {
+ this.sequenceFrom = from
+ this.sequenceTo = to
+ await this.downloadHeatmap()
+ onSuccess()
+ },
+ downloadCSV() {
+ return `${this.$http.defaults.baseURL}analyse/rloopr/${this.analysisInfo.id}/rloopr.csv`
+ },
+ downloadBED() {
+ return `${this.$http.defaults.baseURL}analyse/rloopr/${this.analysisInfo.id}/rloopr.bedgraph`
+ },
+ },
+ mounted() {
+ this.reload()
+ this.getTotalRloopLenM1()
+ this.getTotalRloopLenM2()
+ this.getSequenceInfo().then(() => {
+ this.getAvgRizLen().then(() => {
+ this.downloadHeatmap()
+ })
+ })
+ },
+ computed: {
+ GCCount() {
+ return SequenceStats.calcGCCount(this.sequence)
+ },
+ GCRate() {
+ return SequenceStats.calcGCRate(this.sequence)
+ },
+ },
+ components: {
+ highlight: Highlight,
+ 'sort-toggle': SortToggle,
+ pagination: Pagination,
+ heatmap: Heatmap,
+ heatchart: Heatchart,
+ },
+ filters: {
+ number: Formatters.number,
+ genePos: Formatters.genePos,
+ },
+}
+</script>
+
+<style scoped>
+td,
+th {
+ padding: 0.5rem;
+}
+td.sequence {
+ max-width: 400px;
+}
+td.details {
+ max-width: 600px;
+}
+td.details .feature {
+ border: 1px solid red;
+}
+td .toggle {
+ cursor: pointer;
+}
+</style>
diff --git a/src/components/rloopr/rloopr.vue b/src/components/rloopr/rloopr.vue
new file mode 100644
index 0000000..9d64e7f
--- /dev/null
+++ b/src/components/rloopr/rloopr.vue
@@ -0,0 +1,132 @@
+<template>
+ <div class="container-fluid">
+ <h1>R-loop tracker</h1>
+ <div class="row">
+ <div class="col-md-4">
+ <h2>Prediction models</h2>
+ <rloopr-form @checkModel="updateModel" />
+ </div>
+ <div class="col-md-8">
+ <h2>Sequences</h2>
+ <sequence-selector ref="sequenceSelector" @analyse="startAnalysis" />
+ </div>
+ </div>
+
+ <div class="alert alert-danger" v-if="serverError">{{ serverError }}</div>
+
+ <div v-if="waitError">
+ <hr />
+ <div class="alert alert-danger">
+ <div class="row">
+ <p class="col-10">
+ Waiting for results took too long.
+ </p>
+ <div class="col-2">
+ <button class="btn btn-primary btn-block" @click="waitForResult(analysisId)">
+ <span class="fa fa-refresh"></span> Keep waiting
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <b-tabs v-if="finishedAnalysis.length > 0">
+ <b-tab v-for="(analysis, i) of finishedAnalysis" :key="analysis.payload.id" :title="'Results ' + (i + 1)">
+ <br />
+ <results :analysis-info="analysis.payload" :download-token="analysis.downloadToken">
+ <b-btn variant="danger" class="float-right" @click="closeResults(analysis.payload)">
+ Close tab
+ </b-btn>
+ </results>
+ </b-tab>
+ </b-tabs>
+
+ <hr />
+ <div class="card bg-light">
+ <div class="card-body">
+ R-loop tracker algorithm is based on
+ <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489302/">QmRLFS-finder tool</a>.
+ </div>
+ </div>
+ </div>
+</template>
+
+<script type="text/javascript">
+import SequenceSelector from '@/components/sequence/sequence-selector'
+import BatchWatcher from '@/services/batch-watcher'
+import RlooprForm from './rloopr-form'
+import Results from './rloopr-results'
+
+const RIZ_MODEL = Object.freeze({ m1: 0, m2: 1, both: 2 }) // enum for clear view on models
+
+/**
+ * R-loop analysis
+ */
+export default {
+ data() {
+ return {
+ rizModel: [RIZ_MODEL.m1],
+ config: {},
+ finishedAnalysis: [],
+ analysisId: null,
+ waiting: false,
+ waitError: false,
+ serverError: null,
+ }
+ },
+ methods: {
+ closeResults(analysis) {
+ this.finishedAnalysis = this.finishedAnalysis.filter(info => {
+ return info.payload.id != analysis.id
+ })
+ },
+ waitForResult(analysisId) {
+ this.waitError = false
+ this.waiting = true
+ var bw = new BatchWatcher(this.$http)
+ this.$store.commit('addWork', { key: analysisId, title: 'R-loop-R analysis' })
+ return bw
+ .wait('analyse/rloopr/' + analysisId + '/analysis')
+ .then(response => {
+ this.finishedAnalysis.push(response.data)
+ })
+ .finally(() => {
+ this.$store.commit('workDone', analysisId)
+ this.waiting = false
+ })
+ },
+ updateModel(value) {
+ this.rizModel = value
+ },
+ startAnalysis(sequence, callback) {
+ this.$http
+ .post('analyse/rloopr', {
+ rizModel: this.rizModel,
+ sequence: sequence.id,
+ tags: sequence.tags,
+ })
+ .then(response => {
+ const item = response.data.payload
+ this.serverError = null
+ this.analysisId = item.id
+ return this.waitForResult(item.id)
+ })
+ .then(() => {
+ callback()
+ })
+ .catch(error => {
+ this.serverError = error?.response?.data?.message
+ callback('FAILED')
+ })
+ },
+ clearAnalysis() {
+ this.rloopAnalysis = []
+ },
+ },
+ components: {
+ 'sequence-selector': SequenceSelector,
+ results: Results,
+ 'rloopr-form': RlooprForm,
+ },
+}
+</script>
diff --git a/src/components/rloopr/stored-results-details.vue b/src/components/rloopr/stored-results-details.vue
new file mode 100644
index 0000000..15da495
--- /dev/null
+++ b/src/components/rloopr/stored-results-details.vue
@@ -0,0 +1,55 @@
+<template>
+ <div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-10">
+ <h1>R-loop tracker stored results</h1>
+ </div>
+ <div class="col-sm-2">
+ <br />
+ <router-link class="btn btn-primary btn-block" :to="{ name: 'results.rloopr' }">Back</router-link>
+ </div>
+ </div>
+
+ <results v-if="analysis" :analysis-info="analysis" :download-token="downloadToken"></results>
+
+ <http-error :info="httpError"></http-error>
+ </div>
+</template>
+
+<script>
+import Results from './rloopr-results'
+import HttpError from '@/components/core/http-error'
+
+/**
+ * display previously stored results
+ */
+export default {
+ data() {
+ return {
+ analysis: null,
+ downloadToken: '',
+ httpError: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http.get('analyse/rloopr/' + this.$route.params.id + '/analysis').then(
+ response => {
+ this.analysis = response.data.payload
+ this.downloadToken = response.data.downloadToken
+ },
+ err => {
+ this.httpError = err
+ }
+ )
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ results: Results,
+ 'http-error': HttpError,
+ },
+}
+</script>
diff --git a/src/components/rloopr/stored-results.vue b/src/components/rloopr/stored-results.vue
new file mode 100644
index 0000000..f84171d
--- /dev/null
+++ b/src/components/rloopr/stored-results.vue
@@ -0,0 +1,202 @@
+<template>
+ <div class="container">
+ <h1>R-loop tracker results</h1>
+
+ <pagination ref="pagination" @pageChange="downloadResults">
+ <checkable-list ref="resultsList">
+ <th slot="header">Sequence/Analyse name</th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="finished" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="resultCount" :current="currentSort">Results count</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">Tags</th>
+ <th class="text-center" slot="header">Details</th>
+ <th class="text-center" slot="header">Edit</th>
+ <th class="text-center" slot="header">Delete</th>
+
+ <span slot="item-name" slot-scope="props">
+ {{ props.item.title }}
+ </span>
+
+ <template slot-scope="props">
+ <td class="text-right">
+ <span v-if="props.item.finished">{{ props.item.finished | dateTime }}</span>
+ <span v-else class="fa fa-spinner animate"></span>
+ </td>
+ <td class="text-right">
+ <span v-if="props.item.finished">
+ {{ props.item.resultCount | number(0) }}
+ </span>
+ </td>
+ <td>
+ <b-badge v-for="tag in props.item.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <td class="text-center">
+ <a :href="downloadCSV(props.item)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span>
+ </a>
+ <a :href="downloadBED(props.item)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span>
+ </a>
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{ name: 'results.rloopr.detail', params: { id: props.item.id } }"
+ >
+ <span class="fa fa-search"></span>
+ </router-link>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-primary btn-sm" @click.stop="editResult(props.item)">
+ <span class="fa fa-edit"></span>
+ </button>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-danger btn-sm" @click.stop="deleteResult(props.item)">
+ <span class="fa fa-trash"></span>
+ </button>
+ </td>
+ </template>
+
+ <p slot="no-items" class="alert alert-warning">
+ No results found.
+ </p>
+ </checkable-list>
+ </pagination>
+
+ <button type="button" class="btn btn-default" @click="toggleSelection">
+ <i class="fa fa-refresh"></i> Invert selection
+ </button>
+ <button class="btn btn-danger" @click="deleteResults"><i class="fa fa-trash"></i> Delete selected</button>
+
+ <modal-confirm ref="confirmModal">Really delete results?</modal-confirm>
+ <modal-confirm ref="confirmModalMulti">Really delete selected results?</modal-confirm>
+
+ <modal-confirm ref="editModal">
+ <template slot="header">
+ Modify result
+ </template>
+
+ <result-editor v-if="selectedResult" :result="selectedResult" ref="resultEditor"></result-editor>
+
+ <template slot="buttonConfirm">
+ Save changes
+ </template>
+ </modal-confirm>
+ </div>
+</template>
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import CheckableList from '@/components/core/checkable-list'
+import Pagination from '@/components/core/pagination'
+import ResultEditor from '@/components/core/result-editor'
+
+/**
+ * list of stored result groups
+ */
+export default {
+ data() {
+ return {
+ selectedResult: null,
+ currentSort: {
+ crit: 'finished',
+ asc: true,
+ },
+ downloadToken: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http
+ .get('analyse/rloopr', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.$refs.resultsList.setItems(response.data.items)
+ this.downloadToken = response.data.downloadToken
+ })
+ },
+ performDelete(result) {
+ return this.$http.delete('analyse/rloopr/' + result.id)
+ },
+ deleteResult(result) {
+ this.$refs.confirmModal
+ .display()
+ .then(() => {
+ return this.performDelete(result)
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ },
+ deleteResults() {
+ this.$refs.confirmModalMulti.display().then(() => {
+ var checked = this.$refs.resultsList.getCheckedItems()
+ var promises = []
+ checked.forEach(result => {
+ if (result.ui.checked) {
+ promises.push(this.performDelete(result))
+ }
+ })
+ Promise.all(promises).then(() => {
+ this.downloadResults()
+ })
+ })
+ },
+ editResult(result) {
+ this.selectedResult = result
+ this.$refs.editModal
+ .display()
+ .then(() => {
+ this.$http
+ .put('analyse/rloopr/' + result.id + '/tags', {
+ tags: this.$refs.resultEditor.getTags(),
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ })
+ .finally(() => {
+ this.selectedResult = null
+ })
+ },
+ sortResults(info) {
+ this.currentSort = info
+ this.downloadResults()
+ },
+ toggleSelection() {
+ this.$refs.resultsList.toggleSelection()
+ },
+ downloadCSV(analysisInfo) {
+ return `${this.$http.defaults.baseURL}analyse/rloopr/${analysisInfo.id}/rloopr.csv`
+ },
+ downloadBED(analysisInfo) {
+ return `${this.$http.defaults.baseURL}analyse/rloopr/${analysisInfo.id}/rloopr.bedgraph`
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ 'checkable-list': CheckableList,
+ pagination: Pagination,
+ 'result-editor': ResultEditor,
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ sequenceName: Formatters.sequenceName,
+ },
+}
+</script>
diff --git a/src/components/sequence/helpers/sequence-stats.js b/src/components/sequence/helpers/sequence-stats.js
new file mode 100644
index 0000000..ed36c69
--- /dev/null
+++ b/src/components/sequence/helpers/sequence-stats.js
@@ -0,0 +1,46 @@
+export default {
+ /**
+ * calculate amount of Gs and Cs in sequence
+ *
+ * @param sequence
+ * @returns {*}
+ */
+ calcGCCount(sequence) {
+ if (sequence.nucleicCounts) {
+ var c = sequence.nucleicCounts.C || 0
+ var g = sequence.nucleicCounts.G || 0
+ return c + g
+ }
+ return 0
+ },
+
+ calcNucleicCount(sequence, letters) {
+ if (sequence.nucleicCounts) {
+ var cnt = 0
+ for (var l of letters) {
+ if (sequence.nucleicCounts[l]) {
+ cnt += sequence.nucleicCounts[l]
+ }
+ }
+ return cnt
+ }
+ return 0
+ },
+
+ /**
+ * calculate rate of Gs and Cs in sequence
+ *
+ * @param sequence
+ * @returns {number}
+ */
+ calcGCRate(sequence) {
+ if (sequence.length) {
+ var a = this.calcGCCount(sequence)
+ var b = this.calcNucleicCount(sequence, ['A', 'C', 'T', 'G'])
+ if (b != 0) {
+ return (a / b) * 100
+ }
+ }
+ return 0
+ },
+}
diff --git a/src/components/sequence/list-with-action.vue b/src/components/sequence/list-with-action.vue
new file mode 100644
index 0000000..f21c65c
--- /dev/null
+++ b/src/components/sequence/list-with-action.vue
@@ -0,0 +1,258 @@
+<template>
+ <div>
+ <div class="row">
+ <div class="col-4">
+ <input class="form-control" type="text" v-model="filterTags" placeholder="Search by tag" />
+ </div>
+ <div class="col-1">
+ <button @click="loadSequences" class="btn btn-primary">
+ Search
+ </button>
+ </div>
+ </div>
+ <br />
+
+ <div v-show="sequences.length > 0">
+ <pagination ref="pagination" :pageSize="pageSize" @pageChange="loadSequences">
+ <table class="table table-striped table-hover">
+ <tbody>
+ <!-- HEADER -->
+ <tr>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="name" :current="currentSort">Title</sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="length" :current="currentSort">Length</sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="created" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center">Tags</th>
+ <th class="text-center">
+ <button type="button" class="btn btn-default" @click="reload">
+ <i class="fa fa-refresh"></i>
+ </button>
+ </th>
+ <slot name="list-header-right"></slot>
+ </tr>
+ <!-- LISTING -->
+ <tr v-for="s in sequences" :key="s.id">
+ <td>
+ <label class="font-italic" v-if="sequenceError(s)">Sequence import error</label>
+ <label class="font-italic" v-else-if="sequenceDownloading(s)">Sequence import in progress</label>
+ <label v-else-if="sequenceDownloaded(s)">{{ s.name }}</label>
+ </td>
+ <td class="text-right">
+ <span v-if="sequenceDownloaded(s)"> {{ s.length | number(0) }} bp </span>
+ <span v-else-if="sequenceDownloading(s)" class="fa fa-spinner animate"></span>
+ <span v-else-if="sequenceError(s)" class="fa fa-exclamation-circle"></span>
+ </td>
+ <td class="text-right">{{ s.created | dateTime }}</td>
+ <td>
+ <b-badge v-for="tag in s.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <td :set="(isLoading = loadingSequenceIds.includes(s.id))">
+ <button class="btn btn-success btn-block" :disabled="isLoading" @click="analyse(s)">
+ <i v-if="failedSequenceIds.includes(s.id)" class="fa fa-exclamation-circle"></i>
+ <i v-else-if="!isLoading" class="fa fa-play"></i>
+ <i v-else-if="isLoading" class="spinner-border spinner-border-sm"></i>
+ Analyse
+ </button>
+ </td>
+ <slot
+ :sequence="s"
+ :downloaded="sequenceDownloaded(s)"
+ :downloading="sequenceDownloading(s)"
+ :error="sequenceError(s)"
+ ></slot>
+ </tr>
+ </tbody>
+ </table>
+ </pagination>
+ </div>
+ <div v-show="sequences.length == 0">
+ <button type="button" class="btn btn-default" @click="reload">
+ <i class="fa fa-refresh"></i>
+ </button>
+ <br />
+ <br />
+ <p class="alert alert-info">
+ There are no sequences here, upload some sequences first or click reload.
+ </p>
+ </div>
+ </div>
+</template>
+
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import Pagination from '@/components/core/pagination'
+import { BatchStates } from '@/services/batch-watcher'
+
+/**
+ * List of user's sequences with button for action
+ *
+ * Use slots to add more table column
+ *
+ * Usage:
+ * <sequence-list ref="sequenceList">
+ * <th class="text-center" slot="list-header-right">
+ * Delete
+ * </th>
+ * <template slot-scope="props">
+ * <td class="text-center" slot="list-right">
+ * <button class="btn btn-danger" @click="deleteSequence(props.sequence)">
+ * <i class="fa fa-trash"></i>
+ * </button>
+ * </td>
+ * </template>
+ * <button class="btn btn-danger" @click="deleteSequences()" slot="buttons-bottom">
+ * <i class="fa fa-trash"></i> Delete selected
+ * </button>
+ * </sequence-list>
+ */
+export default {
+ inject: ['EventBus'],
+ props: {
+ pageSize: {
+ default: 5,
+ type: Number,
+ },
+ },
+ data() {
+ return {
+ currentSort: {
+ crit: 'name',
+ asc: true,
+ },
+ batches: {},
+ sequences: [],
+ pageCount: 0,
+ filterTags: '',
+ loadingSequenceIds: [],
+ failedSequenceIds: [],
+ }
+ },
+ methods: {
+ loadSequences() {
+ var params = {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ }
+ if (this.filterTags) {
+ params.tags = this.filterTags
+ }
+ this.$http
+ .get('sequence', {
+ params: params,
+ })
+ .then(response => {
+ this.pageCount = response.data.page.totalElements
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.batches = response.data.batches
+ this.sequences = response.data.items
+
+ this.$emit('load')
+ })
+ },
+ reload() {
+ this.loadSequences()
+ },
+ analyse(data) {
+ this.loadingSequenceIds.push(data.id)
+ this.failedSequenceIds = this.failedSequenceIds.filter(id => id !== data.id)
+
+ this.$emit('analyse', data, status => {
+ if (status === 'FAILED') {
+ this.failedSequenceIds.push(data.id)
+ }
+
+ this.loadingSequenceIds = this.loadingSequenceIds.filter(id => id !== data.id)
+ })
+ },
+ /**
+ * sort toggle click
+ * @param Object info
+ */
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ /**
+ * return amount of sequences
+ *
+ * @returns {number}
+ */
+ getAllCount() {
+ return this.pageCount
+ },
+ /**
+ * return true, when sequence was successfully downloaded
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceDownloaded(sequence) {
+ if (this.batches[sequence.id]) {
+ return this.batches[sequence.id].status == BatchStates.FINISHED
+ }
+ if (sequence.length) {
+ return true
+ }
+ return false
+ },
+ /**
+ * returns true, when sequence import/upload is in progress
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceDownloading(sequence) {
+ if (this.batches[sequence.id]) {
+ return (
+ this.batches[sequence.id].status == BatchStates.CREATED ||
+ this.batches[sequence.id].status == BatchStates.WAITING ||
+ this.batches[sequence.id].status == BatchStates.RUNNING
+ )
+ }
+ return false
+ },
+ /**
+ * returns true, when sequence import/upload failed
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceError(sequence) {
+ if (this.batches[sequence.id]) {
+ return this.batches[sequence.id].status == BatchStates.FAILED
+ }
+ return false
+ },
+ },
+ mounted() {
+ this.reload()
+ this.EventBus.$on('reloadSequences', () => {
+ this.reload()
+ })
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ pagination: Pagination,
+ },
+}
+</script>
+
+<style scoped>
+.tags {
+ width: 15rem;
+}
+</style>
diff --git a/src/components/sequence/list.vue b/src/components/sequence/list.vue
new file mode 100644
index 0000000..6fc605c
--- /dev/null
+++ b/src/components/sequence/list.vue
@@ -0,0 +1,317 @@
+<template>
+ <div>
+ <div class="row">
+ <div class="col-4">
+ <input class="form-control" type="text" v-model="filterTags" placeholder="Search by tag" />
+ </div>
+ <div class="col-1">
+ <button @click="loadSequences" class="btn btn-primary">
+ Search
+ </button>
+ </div>
+ </div>
+ <br />
+
+ <div v-show="sequences.length > 0">
+ <pagination ref="pagination" @pageChange="loadSequences">
+ <table class="table table-striped table-hover">
+ <tbody>
+ <!-- HEADER -->
+ <tr>
+ <th>
+ <button type="button" class="btn btn-default" @click="reload">
+ <i class="fa fa-refresh"></i>
+ </button>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="name" :current="currentSort">Title</sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="length" :current="currentSort">Length</sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="created" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center">Tags</th>
+ <slot name="list-header-right"></slot>
+ </tr>
+ <!-- LISTING -->
+ <tr v-for="s in sequences" :key="s.id" @click="toggleSelection(s)" class="pointer">
+ <td colspan="2">
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" v-model="selections[s.id]" />
+ <label class="custom-control-label font-italic" v-if="sequenceError(s)">Sequence import error</label>
+ <label class="custom-control-label font-italic" v-else-if="sequenceDownloading(s)"
+ >Sequence import in progress</label
+ >
+ <label class="custom-control-label" v-else-if="sequenceDownloaded(s)">{{ s.name }}</label>
+ </div>
+ </td>
+ <td class="text-right">
+ <span v-if="sequenceDownloaded(s)"> {{ s.length | number(0) }} bp </span>
+ <span v-else-if="sequenceDownloading(s)" class="fa fa-spinner animate"></span>
+ <span v-else-if="sequenceError(s)" class="fa fa-exclamation-circle"></span>
+ </td>
+ <td class="text-right">{{ s.created | dateTime }}</td>
+ <td>
+ <b-badge v-for="tag in s.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <slot
+ :sequence="s"
+ :downloaded="sequenceDownloaded(s)"
+ :downloading="sequenceDownloading(s)"
+ :error="sequenceError(s)"
+ ></slot>
+ </tr>
+ </tbody>
+ </table>
+ </pagination>
+
+ <button type="button" class="btn btn-default" @click="inverseSelection" v-if="multiple">
+ <i class="fa fa-refresh"></i> Invert selection
+ </button>
+ <button type="button" class="btn btn-default" @click="selectNone" v-if="multiple">
+ <i class="fa fa-remove"></i> Clear selection
+ </button>
+ <slot name="buttons-bottom"></slot>
+ </div>
+ <div v-show="sequences.length == 0">
+ <button type="button" class="btn btn-default" @click="reload">
+ <i class="fa fa-refresh"></i>
+ </button>
+ <br />
+ <br />
+ <p class="alert alert-info">
+ There are no sequences here, upload some sequences first or click reload.
+ </p>
+ </div>
+ </div>
+</template>
+
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import Vue from 'vue'
+import Pagination from '@/components/core/pagination'
+import { BatchStates } from '@/services/batch-watcher'
+
+/**
+ * List of user's sequences with checkboxes for selection
+ *
+ * Use slots to add more table column
+ *
+ * Usage:
+ * <sequence-list ref="sequenceList">
+ * <th class="text-center" slot="list-header-right">
+ * Delete
+ * </th>
+ * <template slot-scope="props">
+ * <td class="text-center" slot="list-right">
+ * <button class="btn btn-danger" @click="deleteSequence(props.sequence)">
+ * <i class="fa fa-trash"></i>
+ * </button>
+ * </td>
+ * </template>
+ * <button class="btn btn-danger" @click="deleteSequences()" slot="buttons-bottom">
+ * <i class="fa fa-trash"></i> Delete selected
+ * </button>
+ * </sequence-list>
+ */
+export default {
+ inject: ['EventBus'],
+ props: {
+ pageSize: {
+ default: 10,
+ type: Number,
+ },
+ multiple: {
+ default: true,
+ type: Boolean,
+ },
+ },
+ data() {
+ return {
+ selections: {}, //state of checkboxes: id of sequence -> boolean
+ selected: [], //selected sequences
+ currentSort: {
+ crit: 'name',
+ asc: true,
+ },
+ batches: {},
+ sequences: [],
+ pageCount: 0,
+ filterTags: '',
+ }
+ },
+ methods: {
+ /**
+ * invert selection of sequences
+ */
+ inverseSelection() {
+ this.sequences.forEach(sequence => {
+ this.toggleSelection(sequence)
+ })
+ },
+ /**
+ * deselect all sequences
+ */
+ selectNone() {
+ this.selected.forEach(sequence => {
+ Vue.set(this.selections, sequence.id, false)
+ })
+ this.selected = []
+ },
+ loadSequences() {
+ var params = {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ }
+ if (this.filterTags) {
+ params.tags = this.filterTags
+ }
+ this.$http
+ .get('sequence', {
+ params: params,
+ })
+ .then(response => {
+ response.data.items.forEach(s => {
+ if (!this.selections[s.id]) {
+ Vue.set(this.selections, s.id, false)
+ }
+ })
+ this.pageCount = response.data.page.totalElements
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.batches = response.data.batches
+ this.sequences = response.data.items
+
+ this.$emit('load')
+ })
+ },
+ reload() {
+ this.selectNone()
+ this.loadSequences()
+ },
+ /**
+ * return selected sequences
+ */
+ getSelected() {
+ return this.selected
+ },
+ /**
+ * return only IDs of selected sequences
+ */
+ getSelectedIds() {
+ return this.selected.map(s => {
+ return s.id
+ })
+ },
+ /**
+ * sort toggle click
+ * @param Object info
+ */
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ /**
+ * return amount of sequences
+ *
+ * @returns {number}
+ */
+ getAllCount() {
+ return this.pageCount
+ },
+ /**
+ * select or unselect one sequence
+ *
+ * @param sequence
+ */
+ toggleSelection(sequence) {
+ if (!this.selections[sequence.id]) {
+ if (!this.multiple) {
+ this.selectNone()
+ }
+ //selecting the sequence
+ Vue.set(this.selections, sequence.id, true)
+ this.selected.push(sequence)
+ } else {
+ //unselecting the sequence
+ Vue.set(this.selections, sequence.id, false)
+ this.selected = this.selected.filter(s => {
+ return sequence.id != s.id
+ })
+ }
+ },
+ /**
+ * return true, when sequence was successfully downloaded
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceDownloaded(sequence) {
+ if (this.batches[sequence.id]) {
+ return this.batches[sequence.id].status == BatchStates.FINISHED
+ }
+ if (sequence.length) {
+ return true
+ }
+ return false
+ },
+ /**
+ * returns true, when sequence import/upload is in progress
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceDownloading(sequence) {
+ if (this.batches[sequence.id]) {
+ return (
+ this.batches[sequence.id].status == BatchStates.CREATED ||
+ this.batches[sequence.id].status == BatchStates.WAITING ||
+ this.batches[sequence.id].status == BatchStates.RUNNING
+ )
+ }
+ return false
+ },
+ /**
+ * returns true, when sequence import/upload failed
+ *
+ * @param sequence
+ * @returns {boolean}
+ */
+ sequenceError(sequence) {
+ if (this.batches[sequence.id]) {
+ return this.batches[sequence.id].status == BatchStates.FAILED
+ }
+ return false
+ },
+ },
+ mounted() {
+ this.reload()
+ this.EventBus.$on('reloadSequences', () => {
+ this.reload()
+ })
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ pagination: Pagination,
+ },
+}
+</script>
+
+<style scoped>
+.tags {
+ width: 15rem;
+}
+.pointer {
+ cursor: pointer;
+}
+</style>
diff --git a/src/components/sequence/ncbi-import-multi.vue b/src/components/sequence/ncbi-import-multi.vue
new file mode 100644
index 0000000..889da98
--- /dev/null
+++ b/src/components/sequence/ncbi-import-multi.vue
@@ -0,0 +1,118 @@
+<template>
+ <div>
+ <br />
+
+ <app-form @submit="uploadSequence" ref="importForm" :validator="$v">
+ <label>Tags (confirm using enter)</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+
+ <label class="mandatory">NCBI IDs (separate by spaces or newlines)</label>
+ <textarea v-model="ncbiIdStr" name="ncbiID" class="form-control" cols="80" rows="5"></textarea>
+ <br />
+
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" id="circularCheckNCBI" />
+ <label class="custom-control-label" for="circularCheckNCBI">Circular</label>
+ </div>
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.ncbiIdStr.required">NCBI IDs are required.</div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-check"></i> Import</button>
+ </app-form>
+ </div>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+import BatchWatcher from '@/services/batch-watcher'
+import { required } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ inject: ['EventBus'],
+ data() {
+ return {
+ title: '',
+ ncbiIdStr: '',
+ circular: false,
+ tags: [],
+ }
+ },
+ validations: {
+ ncbiIdStr: {
+ required,
+ },
+ },
+ methods: {
+ uploadSequence() {
+ var data = {
+ circular: this.circular,
+ tags: this.tags,
+ type: 'DNA',
+ ncbis: [],
+ }
+
+ this.ncbiIdStr.split(/\s/).forEach(id => {
+ var trimmed = id.trim()
+ if (trimmed) {
+ data.ncbis.push({
+ ncbiId: id,
+ })
+ }
+ })
+
+ this.$http
+ .post('sequence/import/ncbi', data)
+ .then(
+ response => {
+ this.EventBus.$emit('newSequence')
+
+ this.ncbiIdStr = ''
+ this.title = ''
+ this.circular = false
+ this.tags = []
+
+ for (let sequence of response.data.items) {
+ this.$store.commit('addWork', {
+ key: sequence.id,
+ title: 'NCBI import',
+ })
+
+ var bw = new BatchWatcher(this.$http)
+ bw.wait('sequence/' + sequence.id)
+ .then(
+ () => {
+ this.EventBus.$emit('newSequence')
+ },
+ () => {
+ this.EventBus.$emit('reloadSequences')
+ }
+ )
+ .finally(() => {
+ this.$store.commit('workDone', sequence.id)
+ })
+ }
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ .finally(() => {
+ this.$refs.importForm.enable()
+ })
+ },
+ },
+ components: {
+ InputTag,
+ FormResult,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/sequence/ncbi-import.vue b/src/components/sequence/ncbi-import.vue
new file mode 100644
index 0000000..79eb60e
--- /dev/null
+++ b/src/components/sequence/ncbi-import.vue
@@ -0,0 +1,118 @@
+<template>
+ <div>
+ <br />
+
+ <app-form @submit="uploadSequence" ref="importForm" :validator="$v">
+ <label>Title</label>
+ <input v-model="title" name="title" class="form-control" />
+ <br />
+
+ <label>Tags (confirm using enter)</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+
+ <label class="mandatory">NCBI ID</label>
+ <input v-model="$v.ncbiId.$model" name="ncbiId" class="form-control" />
+ <br />
+
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" id="circularCheckNCBI" />
+ <label class="custom-control-label" for="circularCheckNCBI">Circular</label>
+ </div>
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.ncbiId.required">NCBI ID is required.</div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-check"></i> Import</button>
+ </app-form>
+ </div>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+import BatchWatcher from '@/services/batch-watcher'
+import { required } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ inject: ['EventBus'],
+ data() {
+ return {
+ title: '',
+ ncbiId: '',
+ circular: false,
+ tags: [],
+ }
+ },
+ validations: {
+ ncbiId: {
+ required,
+ },
+ },
+ methods: {
+ uploadSequence() {
+ let data = {
+ circular: this.circular,
+ tags: this.tags,
+ type: 'DNA',
+ ncbis: [
+ {
+ name: this.title,
+ ncbiId: this.ncbiId,
+ },
+ ],
+ }
+
+ this.$http
+ .post('sequence/import/ncbi', data)
+ .then(
+ response => {
+ this.EventBus.$emit('newSequence')
+
+ this.ncbiId = ''
+ this.title = ''
+ this.circular = false
+ this.tags = []
+
+ for (let sequence of response.data.items) {
+ this.$store.commit('addWork', {
+ key: sequence.id,
+ title: 'NCBI import',
+ })
+
+ var bw = new BatchWatcher(this.$http)
+ bw.wait('sequence/' + sequence.id)
+ .then(
+ () => {
+ this.EventBus.$emit('newSequence')
+ },
+ () => {
+ this.EventBus.$emit('reloadSequences')
+ }
+ )
+ .finally(() => {
+ this.$store.commit('workDone', sequence.id)
+ })
+ }
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ .finally(() => {
+ this.$refs.importForm.enable()
+ })
+ },
+ },
+ components: {
+ InputTag,
+ FormResult,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/sequence/overview.vue b/src/components/sequence/overview.vue
new file mode 100644
index 0000000..0e2b1d8
--- /dev/null
+++ b/src/components/sequence/overview.vue
@@ -0,0 +1,159 @@
+<template>
+ <div>
+ <br />
+
+ <sequence-list @load="sequencesLoaded" ref="sequenceList">
+ <th class="text-center" slot="list-header-right">
+ Details
+ </th>
+ <th class="text-center" slot="list-header-right">
+ Edit
+ </th>
+ <th class="text-center" slot="list-header-right">
+ Delete
+ </th>
+ <template slot-scope="props">
+ <td class="text-center" slot="list-right">
+ <button class="btn btn-primary btn-sm" @click.stop="showDetails(props.sequence)" v-if="props.downloaded">
+ <i class="fa fa-search"></i>
+ </button>
+ </td>
+ <td class="text-center" slot="list-right">
+ <button class="btn btn-primary btn-sm" @click.stop="editSequence(props.sequence)" v-if="props.downloaded">
+ <i class="fa fa-edit"></i>
+ </button>
+ </td>
+ <td class="text-center" slot="list-right">
+ <button class="btn btn-danger btn-sm" @click.stop="deleteSequence(props.sequence)" v-if="!props.downloading">
+ <i class="fa fa-trash"></i>
+ </button>
+ </td>
+ </template>
+ <button class="btn btn-danger" @click="deleteSequences" slot="buttons-bottom">
+ <i class="fa fa-trash"></i> Delete selected
+ </button>
+ </sequence-list>
+
+ <hr />
+
+ All sequence count: {{ allSequenceCount }}
+
+ <modal-confirm ref="confirmModal">Really delete sequence?</modal-confirm>
+ <modal-confirm ref="confirmModalMulti">Really delete selected sequences?</modal-confirm>
+
+ <modal-alert ref="infoModal" size="lg">
+ <template slot="header" v-if="selectedSequence">
+ Details of sequence
+ </template>
+
+ <sequence-info v-if="selectedSequence" :sequence="selectedSequence"></sequence-info>
+ </modal-alert>
+
+ <modal-confirm ref="editModal">
+ <template slot="header">
+ Modify sequence
+ </template>
+
+ <sequence-editor v-if="selectedSequence" :sequence="selectedSequence" ref="sequenceEditor"></sequence-editor>
+
+ <template slot="buttonConfirm">
+ Save changes
+ </template>
+ </modal-confirm>
+ </div>
+</template>
+
+<script>
+import SequenceList from './list'
+import Formatters from '@/formatters'
+import SequenceInfo from './sequence-info'
+import SequenceEditor from './sequence-editor'
+
+export default {
+ inject: ['EventBus'],
+ data() {
+ return {
+ allSequenceCount: 0,
+ selectedSequence: null,
+ }
+ },
+ methods: {
+ showDetails(sequence) {
+ this.selectedSequence = sequence
+ this.$refs.infoModal
+ .display()
+ .then(
+ () => {},
+ () => {}
+ )
+ .finally(() => {
+ this.selectedSequence = null
+ })
+ },
+ editSequence(sequence) {
+ this.selectedSequence = sequence
+ this.$refs.editModal
+ .display()
+ .then(() => {
+ return this.$http.put('sequence/' + sequence.id + '/tags', {
+ tags: this.$refs.sequenceEditor.getTags(),
+ })
+ })
+ .then(
+ () => {
+ this.$refs.sequenceList.reload()
+ },
+ () => {}
+ )
+ .finally(() => {
+ this.selectedSequence = null
+ })
+ },
+ performDelete(sequence) {
+ return this.$http.delete('sequence/' + sequence.id)
+ },
+ deleteSequence(sequence) {
+ this.$refs.confirmModal
+ .display()
+ .then(() => {
+ return this.performDelete(sequence)
+ })
+ .then(() => {
+ this.$refs.sequenceList.reload()
+ })
+ },
+ deleteSequences() {
+ this.$refs.confirmModalMulti.display().then(
+ () => {
+ var promises = []
+ this.$refs.sequenceList.getSelected().forEach(sequence => {
+ promises.push(this.performDelete(sequence))
+ })
+ Promise.all(promises).then(() => {
+ this.$refs.sequenceList.reload()
+ })
+ },
+ () => {}
+ )
+ },
+ sequencesLoaded() {
+ this.allSequenceCount = this.$refs.sequenceList.getAllCount()
+ },
+ },
+ mounted() {
+ this.EventBus.$on('newSequence', () => {
+ if (this.$refs.sequenceList) {
+ this.$refs.sequenceList.reload()
+ }
+ })
+ },
+ components: {
+ 'sequence-list': SequenceList,
+ 'sequence-info': SequenceInfo,
+ 'sequence-editor': SequenceEditor,
+ },
+ filters: {
+ number: Formatters.number,
+ },
+}
+</script>
diff --git a/src/components/sequence/paste.vue b/src/components/sequence/paste.vue
new file mode 100644
index 0000000..31fe0d8
--- /dev/null
+++ b/src/components/sequence/paste.vue
@@ -0,0 +1,92 @@
+<template>
+ <div>
+ <br />
+
+ <app-form @submit="uploadSequence" ref="pasteForm" :validator="$v">
+ <label class="mandatory">Title</label>
+ <input v-model="$v.title.$model" name="title" class="form-control" />
+ <br />
+
+ <label>Tags (confirm using enter)</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+
+ <label class="mandatory">Paste sequence</label>
+ <textarea v-model="$v.sequence.$model" name="sequence" class="form-control" cols="80" rows="6"></textarea>
+ <br />
+
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" id="circularCheckPaste" />
+ <label class="custom-control-label" for="circularCheckPaste">Circular</label>
+ </div>
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.title.required">Title is required.</div>
+ <div v-if="!$v.sequence.required">Sequence is required.</div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-check"></i> Import</button>
+ </app-form>
+ </div>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+import { required } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ inject: ['EventBus'],
+ data() {
+ return {
+ sequence: '',
+ title: '',
+ circular: false,
+ tags: [],
+ }
+ },
+ validations: {
+ title: {
+ required,
+ },
+ sequence: {
+ required,
+ },
+ },
+ methods: {
+ uploadSequence() {
+ this.$http
+ .post('sequence/import/text', {
+ circular: this.circular,
+ data: this.sequence,
+ format: 'PLAIN',
+ name: this.title,
+ tags: this.tags,
+ type: 'DNA',
+ })
+ .then(
+ () => {
+ this.EventBus.$emit('newSequence')
+
+ this.sequence = ''
+ this.title = ''
+ this.tags = []
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ .finally(() => {
+ this.$refs.pasteForm.enable()
+ })
+ },
+ },
+ components: {
+ InputTag,
+ FormResult,
+ },
+}
+</script>
diff --git a/src/components/sequence/sequence-editor.vue b/src/components/sequence/sequence-editor.vue
new file mode 100644
index 0000000..a917472
--- /dev/null
+++ b/src/components/sequence/sequence-editor.vue
@@ -0,0 +1,49 @@
+<template>
+ <form v-if="sequence">
+ <label>Title</label>
+ <input v-model="name" class="form-control" disabled />
+ <br />
+ <label>Tags</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+ <button type="button" class="btn btn-danger" @click="clearTags">
+ <span class="fa fa-trash"></span> Remove all tags
+ </button>
+ </form>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+
+export default {
+ props: ['sequence'],
+ data() {
+ return {
+ tags: [],
+ name: '',
+ }
+ },
+ methods: {
+ getTags() {
+ return this.tags
+ },
+ clearTags() {
+ this.tags = []
+ },
+ copySourceInfo() {
+ if (this.sequence) {
+ this.tags = this.sequence.tags
+ this.name = this.sequence.name
+ }
+ },
+ },
+ mounted() {
+ this.copySourceInfo()
+ },
+ components: {
+ 'input-tag': InputTag,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/sequence/sequence-info.vue b/src/components/sequence/sequence-info.vue
new file mode 100644
index 0000000..61de45e
--- /dev/null
+++ b/src/components/sequence/sequence-info.vue
@@ -0,0 +1,83 @@
+<template>
+ <div v-if="detail">
+ <table class="table table-striped">
+ <tbody>
+ <tr>
+ <th>Title</th>
+ <td>{{ detail.name }}</td>
+ </tr>
+ <tr>
+ <th>Length</th>
+ <td>{{ detail.length }}</td>
+ </tr>
+ <tr>
+ <th>CG count</th>
+ <td v-if="detail.nucleicCounts">{{ GCCount }} / {{ ACTGCount }} ({{ GCRate | number(1) }}%)</td>
+ <td v-if="!detail.nucleicCounts">
+ <div class="spinner-border spinner-border-sm"></div>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ <table class="table table-striped">
+ <tbody>
+ <tr>
+ <th v-for="(v, k) in detail.nucleicCounts">{{ k }}</th>
+ </tr>
+ <tr>
+ <td v-for="v in detail.nucleicCounts">{{ v }}</td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+</template>
+
+<script>
+import SequenceStats from './helpers/sequence-stats'
+import Formatters from '@/formatters'
+
+export default {
+ props: ['sequence'],
+ data() {
+ return {
+ detail: null,
+ httpError: '',
+ }
+ },
+ methods: {
+ countNucleic() {
+ this.$http
+ .patch('sequence/' + this.detail.id + '/nucleic-counts')
+ .then(response => {
+ this.detail = response.data.payload
+ })
+ .catch(err => {
+ this.httpError = err
+ })
+ },
+ },
+ mounted() {
+ this.detail = this.sequence
+
+ if (!this.detail.nucleicCounts) {
+ this.countNucleic()
+ }
+ },
+ computed: {
+ GCCount() {
+ return SequenceStats.calcGCCount(this.detail)
+ },
+ ACTGCount() {
+ return SequenceStats.calcNucleicCount(this.detail, ['A', 'C', 'T', 'G'])
+ },
+ GCRate() {
+ return SequenceStats.calcGCRate(this.detail)
+ },
+ },
+ filters: {
+ number: Formatters.number,
+ },
+}
+</script>
+
+<style scoped></style>
diff --git a/src/components/sequence/sequence-selector.vue b/src/components/sequence/sequence-selector.vue
new file mode 100644
index 0000000..44d213d
--- /dev/null
+++ b/src/components/sequence/sequence-selector.vue
@@ -0,0 +1,42 @@
+<template>
+ <div>
+ <sequence-list ref="sequenceList" :page-size="pageSize" @analyse="analyse"> </sequence-list>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import SequenceList from './list-with-action'
+
+/**
+ * a component to select sequences
+ *
+ * usage:
+ * <sequence-selector ref="sequenceSelector" :page-size="5"></sequence-selector>
+ */
+export default {
+ props: {
+ pageSize: {
+ default: 5,
+ type: Number,
+ },
+ },
+ data() {
+ return {
+ sequences: [],
+ format: Formatters,
+ }
+ },
+ methods: {
+ analyse(data, callback) {
+ this.$emit('analyse', data, callback)
+ },
+ },
+ components: {
+ 'sequence-list': SequenceList,
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ },
+}
+</script>
diff --git a/src/components/sequence/sequence.vue b/src/components/sequence/sequence.vue
new file mode 100644
index 0000000..76a8e79
--- /dev/null
+++ b/src/components/sequence/sequence.vue
@@ -0,0 +1,44 @@
+<template>
+ <div class="container">
+ <h1>Sequences</h1>
+ <b-tabs>
+ <b-tab title="My sequences">
+ <sequence-overview></sequence-overview>
+ </b-tab>
+ <b-tab title="NCBI import">
+ <sequence-import></sequence-import>
+ </b-tab>
+ <b-tab title="NCBI multiple import">
+ <sequence-import-multi></sequence-import-multi>
+ </b-tab>
+ <b-tab title="Upload file">
+ <sequence-upload></sequence-upload>
+ </b-tab>
+ <b-tab title="Paste text">
+ <sequence-paste></sequence-paste>
+ </b-tab>
+ </b-tabs>
+ </div>
+</template>
+
+<script>
+import Overview from './overview'
+import Upload from './upload'
+import Paste from './paste'
+import Import from './ncbi-import'
+import ImportMulti from './ncbi-import-multi'
+
+export default {
+ data: function() {
+ return {}
+ },
+ computed: {},
+ components: {
+ 'sequence-overview': Overview,
+ 'sequence-upload': Upload,
+ 'sequence-paste': Paste,
+ 'sequence-import': Import,
+ 'sequence-import-multi': ImportMulti,
+ },
+}
+</script>
diff --git a/src/components/sequence/upload.vue b/src/components/sequence/upload.vue
new file mode 100644
index 0000000..fca3c8b
--- /dev/null
+++ b/src/components/sequence/upload.vue
@@ -0,0 +1,165 @@
+<template>
+ <div>
+ <br />
+
+ <app-form @submit="uploadSequence" ref="uploadForm" :validator="$v">
+ <label class="mandatory">Title</label>
+ <input v-model="$v.title.$model" name="title" class="form-control" />
+ <br />
+
+ <label>Tags (confirm using enter)</label>
+ <input-tag class="form-control" :tags.sync="tags"></input-tag>
+ <br />
+
+ <label class="mandatory">Format</label>
+ <select class="form-control" v-model="fileType">
+ <option :value="detector.typePlain">Plain</option>
+ <option :value="detector.typeFasta">Fasta</option>
+ </select>
+ <br />
+
+ <label class="mandatory">File (max {{ (maxUploadSize / 1024 / 1024) | number(0) }} MiB)</label>
+ <input
+ type="file"
+ name="file"
+ class="form-control"
+ @change="filesChange($event.target.name, $event.target.files)"
+ ref="fileInput"
+ />
+ <br />
+
+ <div class="custom-control custom-checkbox">
+ <input type="checkbox" class="custom-control-input" id="circularCheckUpload" />
+ <label class="custom-control-label" for="circularCheckUpload">Circular</label>
+ </div>
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.title.required">Title is required.</div>
+ <div v-if="!$v.fileInfo.required">File is required.</div>
+ <div v-if="!$v.fileInfo.maxFileSize">
+ File size cannot be more than
+ {{ (maxUploadSize / 1024 / 1024) | number(0) }} MiB.
+ </div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-check"></i> Upload</button>
+ </app-form>
+ </div>
+</template>
+
+<script>
+import InputTag from 'vue-input-tag'
+import Formatters from '@/formatters'
+import FiletypeDetector from '@/services/filetype-detector'
+import BatchWatcher from '@/services/batch-watcher'
+import FormResult from '@/components/core/form-result'
+import { required } from 'vuelidate/lib/validators'
+
+export default {
+ inject: ['EventBus', 'config'],
+ data: function() {
+ return {
+ title: '',
+ fileType: FiletypeDetector.typePlain,
+ circular: false,
+ tags: [],
+ maxUploadSize: this.config.maxUploadSize,
+ detector: FiletypeDetector,
+ fileInfo: null,
+ }
+ },
+ validations: {
+ title: {
+ required,
+ },
+ fileInfo: {
+ required,
+ maxFileSize: (fileInfo, vm) => {
+ if (fileInfo) {
+ return fileInfo.size <= vm.maxUploadSize
+ }
+ return true
+ },
+ },
+ },
+ methods: {
+ filesChange(fieldName, fileList) {
+ if (fileList.length) {
+ this.fileInfo = fileList[0]
+ this.$v.fileInfo.$touch()
+ if (!this.title) {
+ this.title = this.fileInfo.name
+ }
+ FiletypeDetector.detectType(this.fileInfo).then(type => {
+ this.fileType = type
+ })
+ } else {
+ this.fileInfo = null
+ }
+ },
+ uploadSequence() {
+ var formData = new FormData()
+ formData.append(
+ 'json',
+ JSON.stringify({
+ circular: this.circular,
+ format: this.fileType,
+ name: this.title,
+ tags: this.tags,
+ type: 'DNA',
+ })
+ )
+ formData.append('file', this.fileInfo, this.fileInfo.name)
+
+ this.$http
+ .post('sequence/import/file', formData)
+ .then(
+ response => {
+ this.EventBus.$emit('newSequence')
+
+ this.title = ''
+ this.tags = []
+ this.$refs.fileInput.value = ''
+ this.fileInfo = null
+
+ this.$store.commit('addWork', {
+ key: response.data.payload.id,
+ title: 'File upload',
+ })
+
+ var bw = new BatchWatcher(this.$http)
+ bw.wait('sequence/' + response.data.payload.id)
+ .then(
+ () => {
+ this.EventBus.$emit('newSequence')
+ },
+ () => {
+ this.EventBus.$emit('reloadSequences')
+ }
+ )
+ .finally(() => {
+ this.$store.commit('workDone', response.data.payload.id)
+ })
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ .finally(() => {
+ this.$refs.uploadForm.enable()
+ })
+ },
+ },
+ mounted() {},
+ components: {
+ InputTag,
+ FormResult,
+ },
+ filters: {
+ number: Formatters.number,
+ },
+}
+</script>
diff --git a/src/components/test/test.vue b/src/components/test/test.vue
new file mode 100644
index 0000000..bb4cfaa
--- /dev/null
+++ b/src/components/test/test.vue
@@ -0,0 +1,73 @@
+<template>
+ <div class="container-fluid">
+ <h1>GUI Test</h1>
+ <heatmap :data="heatmapData"></heatmap>
+ </div>
+</template>
+
+<script>
+import Heatmap from '@/components/core/visualisation/heatmap'
+
+export default {
+ data() {
+ return {
+ heatmapData: {
+ data: [
+ [
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ 0,
+ 5,
+ 10,
+ 15,
+ 20,
+ ],
+ ],
+ metaData: {
+ avg: 10,
+ min: 0,
+ max: 20,
+ segmentCount: 40,
+ segmentSize: 1234,
+ },
+ },
+ }
+ },
+ components: {
+ heatmap: Heatmap,
+ },
+}
+</script>
diff --git a/src/components/user/change-password.vue b/src/components/user/change-password.vue
new file mode 100644
index 0000000..5cd3269
--- /dev/null
+++ b/src/components/user/change-password.vue
@@ -0,0 +1,97 @@
+<template>
+ <div class="container">
+ <h1>Change password</h1>
+ <div class="row">
+ <div class="col-sm-4 col-sm-offset-4">
+ <form @submit.prevent="changePassword" v-if="!done" novalidate>
+ <label>Old password</label>
+ <input class="form-control" type="password" v-model="$v.oldPassword.$model" />
+ <br />
+
+ <label>Password</label>
+ <input class="form-control" type="password" v-model="$v.password1.$model" />
+ <br />
+
+ <label>Password confirm</label>
+ <input class="form-control" type="password" v-model="$v.password2.$model" />
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.oldPassword.required">Old password is required.</div>
+ <div v-if="!$v.password1.required">Password is required.</div>
+ <div v-if="!$v.password1.minLength">
+ Password must have at least
+ {{ $v.password1.$params.minLength.min }} letters.
+ </div>
+ <div v-if="!$v.password2.sameAsPassword">
+ Passwords must be identical.
+ </div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-user"></i> Change password</button>
+ </form>
+ <p class="alert alert-success" v-if="done">
+ Password was changed.
+ </p>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, minLength, sameAs } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ data() {
+ return {
+ oldPassword: '',
+ password1: '',
+ password2: '',
+ done: false,
+ }
+ },
+ validations: {
+ oldPassword: {
+ required,
+ },
+ password1: {
+ required,
+ minLength: minLength(4),
+ },
+ password2: {
+ sameAsPassword: sameAs('password1'),
+ },
+ },
+ methods: {
+ changePassword: function() {
+ this.done = false
+ this.$v.$touch()
+ if (!this.$v.$invalid) {
+ this.$http
+ .put('user/change-password', {
+ oldPassword: this.oldPassword,
+ newPassword: this.password1,
+ })
+ .then(
+ () => {
+ this.oldPassword = ''
+ this.password1 = ''
+ this.password2 = ''
+
+ this.done = true
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ }
+ },
+ },
+ components: {
+ FormResult,
+ },
+}
+</script>
diff --git a/src/components/user/login.vue b/src/components/user/login.vue
new file mode 100644
index 0000000..f5a0698
--- /dev/null
+++ b/src/components/user/login.vue
@@ -0,0 +1,83 @@
+<template>
+ <div class="container">
+ <div class="row">
+ <div class="col-sm-4 col-sm-offset-4">
+ <h1>Login</h1>
+ <form @submit.prevent="loginUser" novalidate>
+ <label>Email (used as login)</label>
+ <input class="form-control" type="email" v-model="$v.email.$model" />
+ <br />
+
+ <label>Password</label>
+ <input class="form-control" type="password" v-model="$v.password.$model" />
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.email.required">Email is required.</div>
+ <div v-if="!$v.email.email">Email is in wrong format.</div>
+ <div v-if="!$v.password.required">Password is required.</div>
+ <div v-if="!$v.password.minLength">
+ Password must have at least
+ {{ $v.password.$params.minLength.min }} letters.
+ </div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-user"></i> Login</button>
+ </form>
+ <hr />
+ <router-link :to="{ name: 'register' }">Register</router-link>
+ <br />
+ <router-link :to="{ name: 'reset-password' }">Reset password</router-link>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, email, minLength } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ inject: ['UserAuth'],
+ data() {
+ return {
+ email: '',
+ password: '',
+ }
+ },
+ validations: {
+ email: {
+ required,
+ email,
+ },
+ password: {
+ required,
+ minLength: minLength(4),
+ },
+ },
+ methods: {
+ loginUser: function() {
+ this.$v.$touch()
+ if (!this.$v.$invalid) {
+ this.UserAuth.login(this.email, this.password).then(
+ () => {
+ this.email = ''
+ this.password = ''
+
+ this.$router.push({ name: 'index' })
+ },
+ reason => {
+ this.$refs.formResult.failure(reason)
+ }
+ )
+ }
+ },
+ },
+ mounted: function() {},
+ components: {
+ FormResult,
+ },
+}
+</script>
diff --git a/src/components/user/register.vue b/src/components/user/register.vue
new file mode 100644
index 0000000..28b03f7
--- /dev/null
+++ b/src/components/user/register.vue
@@ -0,0 +1,99 @@
+<template>
+ <div class="container">
+ <div class="row">
+ <div class="col-sm-4 col-sm-offset-4">
+ <h1>Register</h1>
+ <form @submit.prevent="registerUser" novalidate>
+ <label>Email (used as login)</label>
+ <input class="form-control" type="email" v-model="$v.email.$model" />
+ <br />
+
+ <label>Password</label>
+ <input class="form-control" type="password" v-model="$v.password1.$model" />
+ <br />
+
+ <label>Password confirm</label>
+ <input class="form-control" type="password" v-model="$v.password2.$model" />
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.email.required">Email is required.</div>
+ <div v-if="!$v.email.email">Email is in wrong format.</div>
+ <div v-if="!$v.password1.required">Password is required.</div>
+ <div v-if="!$v.password1.minLength">
+ Password must have at least
+ {{ $v.password1.$params.minLength.min }} letters.
+ </div>
+ <div v-if="!$v.password2.sameAsPassword">
+ Passwords must be identical.
+ </div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-user"></i> Register</button>
+ </form>
+ <hr />
+ <router-link :to="{ name: 'login' }">Login</router-link>
+ <br />
+ <router-link :to="{ name: 'reset-password' }">Reset password</router-link>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, minLength, sameAs, email } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ data() {
+ return {
+ email: '',
+ password1: '',
+ password2: '',
+ }
+ },
+ validations: {
+ email: {
+ required,
+ email,
+ },
+ password1: {
+ required,
+ minLength: minLength(4),
+ },
+ password2: {
+ sameAsPassword: sameAs('password1'),
+ },
+ },
+ methods: {
+ registerUser() {
+ this.$v.$touch()
+ if (!this.$v.$invalid) {
+ var formData = {
+ login: this.email,
+ password: this.password1,
+ }
+
+ this.$http.post('user', formData).then(
+ () => {
+ this.email = ''
+ this.password1 = ''
+ this.password2 = ''
+
+ this.$router.push({ name: 'login' })
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ }
+ },
+ },
+ mounted() {},
+ components: {
+ FormResult,
+ },
+}
+</script>
diff --git a/src/components/user/reset-password.vue b/src/components/user/reset-password.vue
new file mode 100644
index 0000000..c12f256
--- /dev/null
+++ b/src/components/user/reset-password.vue
@@ -0,0 +1,77 @@
+<template>
+ <div class="container">
+ <div class="row">
+ <div class="col-sm-4 col-sm-offset-4">
+ <h1>Reset password</h1>
+ <form @submit.prevent="sendResetRequest" v-if="!done" novalidate>
+ <p class="alert alert-info">
+ We will send a new password to your email.
+ </p>
+
+ <label>Email</label>
+ <input class="form-control" type="email" v-model="$v.email.$model" />
+ <br />
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.email.required">Email is required.</div>
+ <div v-if="!$v.email.email">Email is in wrong format.</div>
+ </div>
+
+ <form-result ref="formResult"></form-result>
+
+ <button class="btn btn-success" type="submit"><i class="fa fa-user"></i> Reset password</button>
+ </form>
+ <p class="alert alert-success" v-if="done">
+ Password reset requested. Check your email for reset notification.
+ </p>
+ <hr />
+ <router-link :to="{ name: 'login' }">Login</router-link>
+ <br />
+ <router-link :to="{ name: 'register' }">Register</router-link>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, email } from 'vuelidate/lib/validators'
+import FormResult from '@/components/core/form-result'
+
+export default {
+ data() {
+ return {
+ email: '',
+ done: false,
+ }
+ },
+ validations: {
+ email: {
+ required,
+ email,
+ },
+ },
+ methods: {
+ sendResetRequest() {
+ this.done = false
+ this.$v.$touch()
+ if (!this.$v.$invalid) {
+ this.$http
+ .put('user/reset-password', {
+ login: this.email,
+ })
+ .then(
+ () => {
+ this.done = true
+ },
+ err => {
+ this.$refs.formResult.failure(err.response.data.message)
+ }
+ )
+ }
+ },
+ },
+ components: {
+ FormResult,
+ },
+}
+</script>
diff --git a/src/components/zdna/stored-results-details.vue b/src/components/zdna/stored-results-details.vue
new file mode 100644
index 0000000..87d9bb4
--- /dev/null
+++ b/src/components/zdna/stored-results-details.vue
@@ -0,0 +1,55 @@
+<template>
+ <div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-10">
+ <h1>Z-DNA stored results</h1>
+ </div>
+ <div class="col-sm-2">
+ <br />
+ <router-link class="btn btn-primary btn-block" :to="{ name: 'results.zdna' }">Back</router-link>
+ </div>
+ </div>
+
+ <results v-if="analysis" :analysis-info="analysis" :download-token="downloadToken"></results>
+
+ <http-error :info="httpError"></http-error>
+ </div>
+</template>
+
+<script>
+import Results from './zdna-results'
+import HttpError from '@/components/core/http-error'
+
+/**
+ * display previously stored results
+ */
+export default {
+ data() {
+ return {
+ analysis: null,
+ downloadToken: '',
+ httpError: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http.get('analyse/zdna/' + this.$route.params.id + '/analysis').then(
+ response => {
+ this.analysis = response.data.payload
+ this.downloadToken = response.data.downloadToken
+ },
+ err => {
+ this.httpError = err
+ }
+ )
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ results: Results,
+ 'http-error': HttpError,
+ },
+}
+</script>
diff --git a/src/components/zdna/stored-results.vue b/src/components/zdna/stored-results.vue
new file mode 100644
index 0000000..e6bf337
--- /dev/null
+++ b/src/components/zdna/stored-results.vue
@@ -0,0 +1,205 @@
+<template>
+ <div class="container">
+ <h1>Z-DNA results</h1>
+
+ <pagination ref="pagination" @pageChange="downloadResults">
+ <checkable-list ref="resultsList">
+ <th slot="header">Sequence/Analyse name</th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="finished" :current="currentSort">Created</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">
+ <sort-toggle @sort="sortResults" crit="resultCount" :current="currentSort">Results count</sort-toggle>
+ </th>
+ <th class="text-center" slot="header">Tags</th>
+ <th class="text-center" slot="header">Export</th>
+ <th class="text-center" slot="header">Details</th>
+ <th class="text-center" slot="header">Edit</th>
+ <th class="text-center" slot="header">Delete</th>
+
+ <span slot="item-name" slot-scope="props">
+ {{ props.item.title }}
+ </span>
+
+ <template slot-scope="props">
+ <td class="text-right">
+ <span v-if="props.item.finished">{{ props.item.finished | dateTime }}</span>
+ <span v-else class="fa fa-spinner animate"></span>
+ </td>
+ <td class="text-right">
+ <span v-if="props.item.finished">
+ {{ props.item.resultCount | number(0) }}
+ </span>
+ </td>
+ <td>
+ <b-badge v-for="tag in props.item.tags" :key="tag" pill variant="primary">
+ {{ tag }}
+ </b-badge>
+ </td>
+ <td class="text-center">
+ <a :href="downloadCSV(props.item)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span>
+ </a>
+ <a :href="downloadBED(props.item)" v-if="downloadToken" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span>
+ </a>
+ </td>
+ <td>
+ <router-link
+ class="btn btn-primary btn-sm"
+ :to="{ name: 'results.zdna.detail', params: { id: props.item.id } }"
+ >
+ <span class="fa fa-search"></span>
+ </router-link>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-primary btn-sm" @click.stop="editResult(props.item)">
+ <span class="fa fa-edit"></span>
+ </button>
+ </td>
+ <td class="text-center">
+ <button class="btn btn-danger btn-sm" @click.stop="deleteResult(props.item)">
+ <span class="fa fa-trash"></span>
+ </button>
+ </td>
+ </template>
+
+ <p slot="no-items" class="alert alert-warning">
+ No results found.
+ </p>
+ </checkable-list>
+ </pagination>
+
+ <button type="button" class="btn btn-default" @click="toggleSelection">
+ <i class="fa fa-refresh"></i> Invert selection
+ </button>
+ <button class="btn btn-danger" @click="deleteResults"><i class="fa fa-trash"></i> Delete selected</button>
+
+ <modal-confirm ref="confirmModal">Really delete results?</modal-confirm>
+ <modal-confirm ref="confirmModalMulti">Really delete selected results?</modal-confirm>
+
+ <modal-confirm ref="editModal">
+ <template slot="header">
+ Modify result
+ </template>
+
+ <result-editor v-if="selectedResult" :result="selectedResult" ref="resultEditor"></result-editor>
+
+ <template slot="buttonConfirm">
+ Save changes
+ </template>
+ </modal-confirm>
+ </div>
+</template>
+<script>
+import SortToggle from '@/components/core/sort-toggle'
+import Formatters from '@/formatters'
+import CheckableList from '@/components/core/checkable-list'
+import Pagination from '@/components/core/pagination'
+import ResultEditor from '@/components/core/result-editor'
+
+/**
+ * list of stored result groups
+ */
+export default {
+ data() {
+ return {
+ selectedResult: null,
+ currentSort: {
+ crit: 'finished',
+ asc: true,
+ },
+ downloadToken: '',
+ }
+ },
+ methods: {
+ downloadResults() {
+ this.$http
+ .get('analyse/zdna', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ this.$refs.resultsList.setItems(response.data.items)
+ this.downloadToken = response.data.downloadToken
+ })
+ },
+ performDelete(result) {
+ return this.$http.delete('analyse/zdna/' + result.id)
+ },
+ deleteResult(result) {
+ this.$refs.confirmModal
+ .display()
+ .then(() => {
+ return this.performDelete(result)
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ },
+ deleteResults() {
+ this.$refs.confirmModalMulti.display().then(() => {
+ var checked = this.$refs.resultsList.getCheckedItems()
+ var promises = []
+ checked.forEach(result => {
+ if (result.ui.checked) {
+ promises.push(this.performDelete(result))
+ }
+ })
+ Promise.all(promises).then(() => {
+ this.downloadResults()
+ })
+ })
+ },
+ editResult(result) {
+ this.selectedResult = result
+ this.$refs.editModal
+ .display()
+ .then(() => {
+ this.$http
+ .put('analyse/zdna/' + result.id + '/tags', {
+ tags: this.$refs.resultEditor.getTags(),
+ })
+ .then(() => {
+ this.downloadResults()
+ })
+ })
+ .finally(() => {
+ this.selectedResult = null
+ })
+ },
+ sortResults(info) {
+ this.currentSort = info
+ this.downloadResults()
+ },
+ toggleSelection() {
+ this.$refs.resultsList.toggleSelection()
+ },
+ downloadCSV(analysisInfo) {
+ return `${this.$http.defaults.baseURL}analyse/zdna/${analysisInfo.id}/zdna.csv`
+ },
+ downloadBED(analysisInfo) {
+ return `${this.$http.defaults.baseURL}analyse/zdna/${analysisInfo.id}/zdna.bedgraph`
+ },
+ },
+ mounted() {
+ this.downloadResults()
+ },
+ components: {
+ 'sort-toggle': SortToggle,
+ 'checkable-list': CheckableList,
+ pagination: Pagination,
+ 'result-editor': ResultEditor,
+ },
+ filters: {
+ dateTime: Formatters.dateTime,
+ number: Formatters.number,
+ sequenceName: Formatters.sequenceName,
+ },
+}
+</script>
diff --git a/src/components/zdna/zdna-form.vue b/src/components/zdna/zdna-form.vue
new file mode 100644
index 0000000..b29d85f
--- /dev/null
+++ b/src/components/zdna/zdna-form.vue
@@ -0,0 +1,75 @@
+<template>
+ <div class="row">
+ <div class="col-md-12">
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Minimal sequence size</label>
+ <div class="col-md-8">
+ <input
+ type="number"
+ class="form-control"
+ step="1"
+ min="10"
+ max="100"
+ v-bind:value="minSequenceSize"
+ v-on:input="updateValue($event.target.value, 'minSequenceSize')"
+ />
+ </div>
+ </div>
+ <p v-if="minSequenceSize > 20" class="alert alert-warning">
+ Minimal sequence size recommended value is between 10 and 20.
+ </p>
+ <div class="form-group row">
+ <label class="col-md-4 col-form-label">Threshold</label>
+ <div class="col-md-8">
+ <input
+ type="number"
+ class="form-control"
+ step="0.1"
+ min="0.1"
+ max="4"
+ v-bind:value="threshold"
+ v-on:input="updateValue($event.target.value, 'threshold')"
+ />
+ </div>
+ </div>
+
+ <div class="alert alert-danger" v-if="$v.$anyError">
+ <div v-if="!$v.minSequenceSize.required">Minimal sequence size is required.</div>
+ <div v-if="!$v.minSequenceSize.numeric">Minimal sequence size must be numeric.</div>
+ <div v-if="!$v.minSequenceSize.minValue">Minimal length of sequence is {{ $v.minSequenceSize.$params.minValue.min }}.</div>
+ <div v-if="!$v.threshold.required">Threshold is required.</div>
+ <div v-if="!$v.threshold.decimal">Threshold must be decimal number.</div>
+ <div v-if="!$v.threshold.minValue">Minimal value of threshold is {{ $v.threshold.$params.minValue.min }}.</div>
+ </div>
+
+ <div class="text-right">
+ <slot name="additionalButtons"></slot>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import { required, numeric, minValue, decimal } from 'vuelidate/lib/validators'
+
+export default {
+ props: ['minSequenceSize', 'threshold'],
+ validations: {
+ minSequenceSize: {
+ required,
+ numeric,
+ minValue: minValue(10),
+ },
+ threshold: {
+ required,
+ decimal,
+ minValue: minValue(15),
+ },
+ },
+ methods: {
+ updateValue: function(value, type) {
+ this.$emit('input', value, type)
+ },
+ },
+}
+</script>
diff --git a/src/components/zdna/zdna-results.vue b/src/components/zdna/zdna-results.vue
new file mode 100644
index 0000000..9742260
--- /dev/null
+++ b/src/components/zdna/zdna-results.vue
@@ -0,0 +1,287 @@
+<template>
+ <div>
+ <h2 v-if="sequence">
+ {{ sequence.name }}
+ <span v-if="sequence.name !== analysisInfo.title">: {{ analysisInfo.title }}</span>
+ <!-- slot for back button -->
+ <slot></slot>
+ </h2>
+
+ <!-- overview -->
+ <div v-show="zdnaList">
+ <heatchart
+ v-if="heatmapData"
+ :data="heatmapData"
+ @dataPointClick="showSegment"
+ @onZoom="zoomHeatchart"
+ ></heatchart>
+ <heatmap v-if="heatmapData" :data="heatmapData" @segmentClick="showSegment" :selected="selectedSegment">
+ </heatmap>
+
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>Analysis results</th>
+ <th class="text-center">Export</th>
+ <th v-if="sequence">Sequence info</th>
+ </tr>
+ <tr>
+ <td>
+ Window size: {{ analysisInfo.windowSize | number(0) }}
+ </td>
+ <td>
+ Z-DNAs found: {{ analysisInfo.resultCount | number(0) }}
+ <br />
+ <span v-if="sequence">Frequency: {{ analysisInfo.frequency | number(1) }} / 1000 bp</span>
+ </td>
+ <td class="text-center">
+ <a v-if="downloadToken" :href="downloadCSV()" class="btn btn-primary btn-sm">
+ <span class="fa fa-cube"></span> CSV
+ </a>
+ <a v-if="downloadToken" :href="downloadBED()" class="btn btn-primary btn-sm">
+ <span class="fa fa-bed"></span> BedGraph
+ </a>
+ </td>
+ <td v-if="sequence">
+ {{ sequence.name }}
+ <br />
+ {{ sequence.length | number(0) }} bp
+ <br />
+ GC: {{ GCCount }} ({{ GCRate | number(1) }}%)
+ </td>
+ </tr>
+ </tbody>
+ </table>
+
+ <!-- list of results -->
+ <pagination ref="pagination" @pageChange="reload" :page-size="10">
+ <table class="table table-striped table-hover">
+ <tbody>
+ <tr>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="position" :current="currentSort">Position</sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="length" :current="currentSort">Length</sort-toggle>
+ </th>
+ <th>Sequence</th>
+ <th>Wider sequence</th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="zdnaGCRichness" :current="currentSort">
+ Z-DNA GC richness
+ </sort-toggle>
+ </th>
+ <th>
+ <sort-toggle @sort="sortSequences" crit="zdnaGTRichness" :current="currentSort">
+ Z-DNA GT richness
+ </sort-toggle>
+ </th>
+ <th class="text-center">
+ <sort-toggle @sort="sortSequences" crit="score" :current="currentSort">Z-DNA score</sort-toggle>
+ </th>
+ </tr>
+ <template v-for="zdna in zdnaList">
+ <tr>
+ <td>
+ {{ zdna.position | number(0) }}
+ </td>
+ <td>
+ {{ zdna.length }}
+ </td>
+ <td class="sequence text-monospace text-bold">
+ <highlight :sequence="zdna.riz"></highlight>
+ </td>
+ <td class="sequence text-monospace">{{ (zdna.zdnaGCRichness * 100) | number(2) }} %</td>
+ <td class="sequence text-monospace">{{ (zdna.zdnaGTRichness * 100) | number(2) }} %</td>
+ <td class="text-right">
+ {{ zdna.score | number }}
+ </td>
+ </tr>
+ </template>
+ </tbody>
+ </table>
+ </pagination>
+
+ <div v-show="zdnaList && zdnaList.length === 0">
+ <p class="alert alert-warning">
+ No Z-DNAs found.
+ </p>
+ </div>
+ </div>
+ </div>
+</template>
+
+<script>
+import Formatters from '@/formatters'
+import SortToggle from '@/components/core/sort-toggle'
+import Pagination from '@/components/core/pagination'
+import SequenceStats from '@/components/sequence/helpers/sequence-stats'
+import Helpers from '@/helpers'
+import Heatchart from '@/components/core/visualisation/heatchart'
+import Heatmap from '@/components/core/visualisation/heatmap'
+import Highlight from '@/components/core/visualisation/highlight'
+
+/**
+ * list of results for sequence analysis
+ */
+export default {
+ props: ['analysisInfo', 'downloadToken'],
+ data() {
+ return {
+ sequence: null,
+ zdnaList: null,
+ avgZdnaLen: null,
+ totalZdnaLenM1: null,
+ totalZdnaLenM2: null,
+ heatmapData: null,
+ selectedSegment: undefined,
+ sequenceStart: undefined,
+ sequenceLength: undefined,
+ currentSort: {
+ crit: 'position',
+ asc: true,
+ },
+ }
+ },
+ methods: {
+ getSequenceInfo() {
+ return this.$http.get('sequence/' + this.analysisInfo.sequenceId).then(response => {
+ this.sequence = response.data.payload
+ })
+ },
+ countNucleic() {
+ this.$http.patch('sequence/' + this.analysisInfo.sequenceId + '/nucleic-counts').catch(err => {
+ this.httpError = err
+ })
+ },
+ reload() {
+ return this.$http
+ .get('analyse/zdna/' + this.analysisInfo.id + '/zdnas', {
+ params: {
+ sort: this.currentSort.crit,
+ order: this.currentSort.asc ? 'ASC' : 'DESC',
+ sequenceStart: this.sequenceStart,
+ sequenceLength: this.sequenceLength,
+ pageSize: this.$refs.pagination.getPageSize(),
+ pageNumber: this.$refs.pagination.getPageCurrent() - 1,
+ },
+ })
+ .then(response => {
+ this.$refs.pagination.setPageCount(response.data.page.totalElements)
+ Helpers.setUIState(response.data.items, 'showDetails', false)
+ this.zdnaList = response.data.items
+ this.countNucleic()
+ })
+ },
+ toggleDetails(zdna) {
+ zdna.ui.showDetails = !zdna.ui.showDetails
+ },
+ getAvgRizLen() {
+ return this.$http.get('analyse/zdna/' + this.analysisInfo.id + '/average/length').then(response => {
+ this.avgZdnaLen = response.data
+ })
+ },
+ getTotalZdnaLenM1() {
+ return this.$http.get('analyse/zdna/' + this.analysisInfo.id + '/total/length/m1').then(response => {
+ this.totalZdnaLenM1 = response.data
+ })
+ },
+ getTotalZdnaLenM2() {
+ return this.$http.get('analyse/zdna/' + this.analysisInfo.id + '/total/length/m2').then(response => {
+ this.totalZdnaLenM2 = response.data
+ })
+ },
+ sortSequences(info) {
+ this.currentSort = info
+ this.reload()
+ },
+ async downloadHeatmap() {
+ const total = this.sequence.length
+ const { sequenceFrom: from = 0, sequenceTo: to = total, analysisInfo } = this
+ const segments = 80
+ const { data } = await this.$http.get(`analyse/zdna/${analysisInfo.id}/heatmap`, {
+ params: { segments, from, to },
+ })
+
+ this.heatmapData = { ...data, from, to, total }
+ },
+ /**
+ * click in heatmap
+ *
+ * @param seg
+ */
+ showSegment(pos, size) {
+ if (this.selectedSegment === pos) {
+ this.selectedSegment = undefined
+ this.sequenceStart = undefined
+ this.sequenceLength = undefined
+ } else {
+ this.selectedSegment = pos
+ this.sequenceStart = Math.floor(pos * size)
+ this.sequenceLength = Math.ceil(size)
+ }
+ this.reload()
+ },
+ async zoomHeatchart(from, to, onSuccess) {
+ this.sequenceFrom = from
+ this.sequenceTo = to
+ await this.downloadHeatmap()
+ onSuccess()
+ },
+ downloadCSV() {
+ return `${this.$http.defaults.baseURL}analyse/zdna/${this.analysisInfo.id}/zdna.csv`
+ },
+ downloadBED() {
+ return `${this.$http.defaults.baseURL}analyse/zdna/${this.analysisInfo.id}/zdna.bedgraph`
+ },
+ },
+ mounted() {
+ this.reload()
+ this.getTotalZdnaLenM1()
+ this.getTotalZdnaLenM2()
+ this.getSequenceInfo().then(() => {
+ this.getAvgRizLen().then(() => {
+ this.downloadHeatmap()
+ })
+ })
+ },
+ computed: {
+ GCCount() {
+ return SequenceStats.calcGCCount(this.sequence)
+ },
+ GCRate() {
+ return SequenceStats.calcGCRate(this.sequence)
+ },
+ },
+ components: {
+ highlight: Highlight,
+ 'sort-toggle': SortToggle,
+ pagination: Pagination,
+ heatmap: Heatmap,
+ heatchart: Heatchart,
+ },
+ filters: {
+ number: Formatters.number,
+ genePos: Formatters.genePos,
+ },
+}
+</script>
+
+<style scoped>
+td,
+th {
+ padding: 0.5rem;
+}
+td.sequence {
+ max-width: 400px;
+}
+td.details {
+ max-width: 600px;
+}
+td.details .feature {
+ border: 1px solid red;
+}
+td .toggle {
+ cursor: pointer;
+}
+</style>
diff --git a/src/components/zdna/zdna.vue b/src/components/zdna/zdna.vue
new file mode 100644
index 0000000..5069cd2
--- /dev/null
+++ b/src/components/zdna/zdna.vue
@@ -0,0 +1,130 @@
+<template>
+ <div class="container-fluid">
+ <h1>Z-DNA tracker</h1>
+ <div class="row">
+ <div class="col-md-4">
+ <h2>Prediction models</h2>
+ <zdna-form @checkModel="updateModel" />
+ </div>
+ <div class="col-md-8">
+ <h2>Sequences</h2>
+ <sequence-selector ref="sequenceSelector" @analyse="startAnalysis" />
+ </div>
+ </div>
+
+ <div class="alert alert-danger" v-if="serverError">{{ serverError }}</div>
+
+ <div v-if="waitError">
+ <hr />
+ <div class="alert alert-danger">
+ <div class="row">
+ <p class="col-10">
+ Waiting for results took too long.
+ </p>
+ <div class="col-2">
+ <button class="btn btn-primary btn-block" @click="waitForResult(analysisId)">
+ <span class="fa fa-refresh"></span> Keep waiting
+ </button>
+ </div>
+ </div>
+ </div>
+ </div>
+
+ <b-tabs v-if="finishedAnalysis.length > 0">
+ <b-tab v-for="(analysis, i) of finishedAnalysis" :key="analysis.payload.id" :title="'Results ' + (i + 1)">
+ <br />
+ <results :analysis-info="analysis.payload" :download-token="analysis.downloadToken">
+ <b-btn variant="danger" class="float-right" @click="closeResults(analysis.payload)">
+ Close tab
+ </b-btn>
+ </results>
+ </b-tab>
+ </b-tabs>
+
+ <hr />
+ <div class="card bg-light">
+ <div class="card-body">
+ Z-DNA tracker algorithm is based on
+ <a href="https://nonb-abcc.ncifcrf.gov/apps/nBMST/default/">non-B DNA Motif Search Tool</a>.
+ </div>
+ </div>
+ </div>
+</template>
+
+<script type="text/javascript">
+import SequenceSelector from '@/components/sequence/sequence-selector'
+import BatchWatcher from '@/services/batch-watcher'
+import ZdnaForm from './zdna-form'
+import Results from './zdna-results'
+
+/**
+ * Z-DNA analysis
+ */
+export default {
+ data() {
+ return {
+ windowSize: 12,
+ config: {},
+ finishedAnalysis: [],
+ analysisId: null,
+ waiting: false,
+ waitError: false,
+ serverError: null,
+ }
+ },
+ methods: {
+ closeResults(analysis) {
+ this.finishedAnalysis = this.finishedAnalysis.filter(info => {
+ return info.payload.id !== analysis.id
+ })
+ },
+ waitForResult(analysisId) {
+ this.waitError = false
+ this.waiting = true
+ var bw = new BatchWatcher(this.$http)
+ this.$store.commit('addWork', { key: analysisId, title: 'Z-DNA analysis' })
+ return bw
+ .wait('analyse/zdna/' + analysisId + '/analysis')
+ .then(response => {
+ this.finishedAnalysis.push(response.data)
+ })
+ .finally(() => {
+ this.$store.commit('workDone', analysisId)
+ this.waiting = false
+ })
+ },
+ updateModel(value) {
+ this.windowSize = value
+ },
+ startAnalysis(sequence, callback) {
+ this.$http
+ .post('analyse/zdna', {
+ windowSize: this.windowSize,
+ sequence: sequence.id,
+ tags: sequence.tags,
+ })
+ .then(response => {
+ const item = response.data.payload
+ this.serverError = null
+ this.analysisId = item.id
+ return this.waitForResult(item.id)
+ })
+ .then(() => {
+ callback()
+ })
+ .catch(error => {
+ this.serverError = error?.response?.data?.message
+ callback('FAILED')
+ })
+ },
+ clearAnalysis() {
+ this.zdnaAnalysis = []
+ },
+ },
+ components: {
+ 'sequence-selector': SequenceSelector,
+ results: Results,
+ 'zdna-form': ZdnaForm,
+ },
+}
+</script>
diff --git a/src/config.js b/src/config.js
new file mode 100644
index 0000000..ee6cbd0
--- /dev/null
+++ b/src/config.js
@@ -0,0 +1,23 @@
+import axios from './axios'
+
+const config = {
+ maxUploadSize: 1024 * 1024 * 1024, //size in bytes: 10 * 1024 * 1024
+
+ batchWatcher: {
+ interval: 10000, //interval between batch checks
+ maxTries: 20, //max amount of batch watcher retries
+ },
+}
+
+/**
+ * loads config from backend and combines with local values
+ */
+export default new Promise((resolve, reject) => {
+ axios.get('management/info').then(response => {
+ config.app = response.data.app
+ config.analysis = response.data.analysis
+ config.maxUploadSize = parseInt(response.data.limits.multipart.maxFileSize) * 1024 * 1024
+
+ resolve(config)
+ }, reject)
+})
diff --git a/src/formatters.js b/src/formatters.js
new file mode 100644
index 0000000..0efa06e
--- /dev/null
+++ b/src/formatters.js
@@ -0,0 +1,46 @@
+export default {
+ /**
+ * convert timestamp to local date and time string
+ *
+ * @param ts
+ * @returns {string}
+ */
+ dateTime(ts, locale) {
+ var d = new Date(ts)
+ return d.toLocaleDateString(locale) + ' ' + d.toLocaleTimeString(locale)
+ },
+
+ /**
+ * convert timestamp to local date string
+ *
+ * @param ts
+ */
+ date(ts, locale) {
+ var d = new Date(ts)
+ return d.toLocaleDateString(locale)
+ },
+
+ /**
+ * format number with given amount of decimals
+ *
+ * @param number
+ * @param decimals
+ * @returns {string}
+ */
+ number(number, decimals, locale) {
+ return new Number(number).toLocaleString(locale, {
+ maximumFractionDigits: decimals,
+ useGrouping: true,
+ })
+ },
+
+ /**
+ * format position in sequence
+ *
+ * @param pos
+ * @returns {*}
+ */
+ genePos(pos) {
+ return pos + 1
+ },
+}
diff --git a/src/helpers.js b/src/helpers.js
new file mode 100644
index 0000000..63776ff
--- /dev/null
+++ b/src/helpers.js
@@ -0,0 +1,20 @@
+import Vue from 'vue'
+
+export default {
+ /**
+ * add ui state variable to object
+ *
+ * @param arr
+ * @param propTitle
+ * @param value
+ */
+ setUIState(arr, propTitle, value, uiProperty) {
+ if (!uiProperty) {
+ uiProperty = 'ui'
+ }
+ return arr.forEach(item => {
+ Vue.set(item, uiProperty, {})
+ Vue.set(item[uiProperty], propTitle, value)
+ })
+ },
+}
diff --git a/src/less/custom.less b/src/less/custom.less
new file mode 100644
index 0000000..95cc9fe
--- /dev/null
+++ b/src/less/custom.less
@@ -0,0 +1,65 @@
+html {
+ font-size: 11pt;
+ background-color: #FFFFFF;
+}
+
+body {
+ padding-bottom: 50px;
+}
+
+.cursor-pointer {
+ cursor: pointer;
+}
+
+a {
+ cursor: pointer;
+ &:hover {
+ text-decoration: none;
+ }
+}
+
+.processing {
+ background-image: url('../assets/loader.gif');
+ background-repeat: no-repeat;
+ background-position: right;
+ display: inline-block;
+ width: 1rem;
+ height: 1rem;
+}
+
+input, select, textarea {
+
+ &.valid {
+ border-left: 5px solid #42A948; /* green */
+ }
+
+ &.invalid {
+ border-left: 5px solid #a94442; /* red */
+ }
+
+}
+
+.text-monospace {
+ font-family:monospace;
+}
+
+.text-bold {
+ font-weight: bold;
+}
+
+label.mandatory:after {
+ content: '*';
+ color: #FF0000;
+}
+
+span.fa-spinner.animate {
+ animation: spin 4s linear infinite;
+ @keyframes spin {
+ from {
+ transform: rotate(0deg);
+ }
+ to {
+ transform: rotate(360deg);
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/main.js b/src/main.js
new file mode 100644
index 0000000..dc5db92
--- /dev/null
+++ b/src/main.js
@@ -0,0 +1,69 @@
+import Vue from 'vue'
+import axios from './axios'
+import App from './components/core/app'
+import UserAuth from './services/user-auth'
+import BootstrapVue from 'bootstrap-vue'
+import ModalConfirm from './components/core/modal-confirm'
+import ModalAlert from './components/core/modal-alert'
+import router from './router.js'
+import store from './store/index.js'
+import Vuelidate from 'vuelidate'
+import AppForm from './components/core/app-form'
+import VueAnalytics from 'vue-analytics'
+import configLoader from './config'
+import 'font-awesome/css/font-awesome.css'
+import 'bootstrap/dist/css/bootstrap.css'
+import 'bootstrap-vue/dist/bootstrap-vue.css'
+
+if (process.env.NODE_ENV == 'production') {
+ Vue.use(VueAnalytics, {
+ id: 'UA-74932754-3',
+ router,
+ })
+}
+
+Vue.config.productionTip = false
+
+const userAuth = new UserAuth(axios, store)
+
+Vue.use(BootstrapVue)
+Vue.use(Vuelidate)
+
+Vue.component('modal-confirm', ModalConfirm)
+Vue.component('modal-alert', ModalAlert)
+Vue.component('app-form', AppForm)
+
+configLoader.then(
+ config => {
+ userAuth.renew().then(
+ () => {
+ //global event bus
+ var bus = new Vue()
+
+ //register axios
+ Vue.prototype.$http = axios
+
+ new Vue({
+ el: '#app',
+ router,
+ store,
+ render: h => h(App),
+ template: '<app></app>',
+ provide() {
+ return {
+ EventBus: bus,
+ UserAuth: userAuth,
+ config,
+ }
+ },
+ })
+ },
+ () => {
+ //TODO
+ }
+ )
+ },
+ () => {
+ //TODO
+ }
+)
diff --git a/src/router.js b/src/router.js
new file mode 100644
index 0000000..30dd00e
--- /dev/null
+++ b/src/router.js
@@ -0,0 +1,258 @@
+import Vue from 'vue'
+import Router from 'vue-router'
+import Index from './components/core/index'
+import Login from './components/user/login'
+import Register from './components/user/register'
+import ResetPassword from './components/user/reset-password'
+import ChangePassword from './components/user/change-password'
+import NotFound from './components/core/not-found'
+import HelpCruciform from './components/help/help-cruciform'
+import HelpG4Killer from './components/help/help-g4killer'
+import HelpImport from './components/help/help-import'
+import HelpP53 from './components/help/help-p53'
+import HelpFAQ from './components/help/faq'
+import HelpAbout from './components/help/about'
+import HelpStatus from './components/help/status'
+import HelpQuadruplex from './components/help/help-quadruplex'
+import HelpRloopr from './components/help/help-rloopr'
+import AnalyseCruciform from './components/cruciform/cruciform'
+import SequenceTools from './components/sequence/sequence'
+import AnalyseQuadruplex from './components/quadruplex/quadruplex'
+import QuadruplexResults from './components/quadruplex/stored-results'
+import QuadruplexResultsDetail from './components/quadruplex/stored-results-details'
+import P53Predictor from './components/p53predictor/p53-predictor'
+import P53PredictorResults from './components/p53predictor/stored-results'
+import P53PredictorResultsDetail from './components/p53predictor/stored-results-detail'
+import Test from './components/test/test'
+//import G4Killer from './components/g4killer/g4killer';
+import G4KillerTool from './components/g4killer/g4killer-tool'
+import store from './store/index.js'
+import P53PredictorTool from './components/p53predictor/p53-predictor-tool'
+import Rloopr from './components/rloopr/rloopr'
+import RlooprResults from './components/rloopr/stored-results'
+import RlooprResultsDetail from './components/rloopr/stored-results-details'
+import Zdna from "./components/zdna/zdna";
+import ZdnaResults from "./components/zdna/zdna-results";
+import ZdnaResultsDetail from './components/zdna/stored-results-details';
+
+Vue.use(Router)
+
+var router = new Router({
+ routes: [
+ {
+ name: 'not-found',
+ path: '*',
+ component: NotFound,
+ },
+ {
+ name: 'index',
+ path: '/',
+ component: Index,
+ },
+
+ //user-related routes
+ {
+ name: 'login',
+ path: '/login',
+ component: Login,
+ meta: {
+ anonymousOnly: true,
+ },
+ },
+ {
+ name: 'register',
+ path: '/register',
+ component: Register,
+ meta: {
+ anonymousOnly: true,
+ },
+ },
+ {
+ name: 'reset-password',
+ path: '/reset-password',
+ component: ResetPassword,
+ meta: {
+ anonymousOnly: true,
+ },
+ },
+ {
+ name: 'change-password',
+ path: '/change-password',
+ component: ChangePassword,
+ meta: {
+ authOnly: true,
+ },
+ },
+
+ //sequence related routes
+ {
+ name: 'sequence.tools',
+ path: '/sequence/tools',
+ component: SequenceTools,
+ },
+
+ //analysis related routes
+ {
+ name: 'analyse.cruciform',
+ path: '/analyse/cruciform',
+ component: AnalyseCruciform,
+ },
+
+ //quadruplex
+ {
+ name: 'analyse.quadruplex',
+ path: '/analyse/quadruplex',
+ component: AnalyseQuadruplex,
+ },
+ {
+ name: 'results.quadruplex',
+ path: '/results/quadruplex',
+ component: QuadruplexResults,
+ },
+ {
+ name: 'results.quadruplex.detail',
+ path: '/results/quadruplex/:id',
+ component: QuadruplexResultsDetail,
+ },
+
+ //p53 predictor
+ {
+ name: 'analyse.p53predictor',
+ path: '/analyse/p53-predictor',
+ component: P53Predictor,
+ },
+ {
+ name: 'results.p53predictor',
+ path: '/results/p53-predictor',
+ component: P53PredictorResults,
+ },
+ {
+ name: 'results.p53predictor.detail',
+ path: '/results/p53-predictor/:id',
+ component: P53PredictorResultsDetail,
+ },
+ {
+ name: 'tools.p53predictor',
+ path: '/tools/p53-predictor',
+ component: P53PredictorTool,
+ },
+
+ //G4 killer
+ {
+ name: 'analyse.g4killer',
+ path: '/analyse/g4-killer',
+ component: G4KillerTool,
+ },
+
+ //R-loop-R
+ {
+ name: 'analyse.rloopr',
+ path: '/analyse/rloopr',
+ component: Rloopr,
+ },
+ {
+ name: 'results.rloopr',
+ path: '/results/rloopr',
+ component: RlooprResults,
+ },
+ {
+ name: 'results.rloopr.detail',
+ path: '/results/rloopr/:id',
+ component: RlooprResultsDetail,
+ },
+
+ //Z-DNA
+ {
+ name: 'analyse.zdna',
+ path: '/analyse/zdna',
+ component: Zdna,
+ },
+ {
+ name: 'results.zdna',
+ path: '/results/zdna',
+ component: ZdnaResults,
+ },
+ {
+ name: 'results.zdna.detail',
+ path: '/results/zdna/:id',
+ component: ZdnaResultsDetail,
+ },
+
+ //help routes
+ {
+ name: 'help.cruciform',
+ path: '/help/cruciform',
+ component: HelpCruciform,
+ meta: {},
+ },
+ {
+ name: 'help.quadruplex',
+ path: '/help/quadruplex',
+ component: HelpQuadruplex,
+ meta: {},
+ },
+ {
+ name: 'help.import',
+ path: '/help/import',
+ component: HelpImport,
+ meta: {},
+ },
+ {
+ name: 'help.p53',
+ path: '/help/p53',
+ component: HelpP53,
+ meta: {},
+ },
+ {
+ name: 'help.faq',
+ path: '/help/faq',
+ component: HelpFAQ,
+ meta: {},
+ },
+ {
+ name: 'help.g4killer',
+ path: '/help/g4killer',
+ component: HelpG4Killer,
+ meta: {},
+ },
+ {
+ name: 'help.rloopr',
+ path: '/help/rloopr',
+ component: HelpRloopr,
+ meta: {},
+ },
+ {
+ name: 'help.about',
+ path: '/help/about',
+ component: HelpAbout,
+ meta: {},
+ },
+ {
+ name: 'help.status',
+ path: '/help/status',
+ component: HelpStatus,
+ meta: {},
+ },
+ //test route
+ {
+ name: 'test',
+ path: '/test',
+ component: Test,
+ },
+ ],
+})
+
+router.beforeEach((to, from, next) => {
+ //TODO when already on authOnly route and user logs off, the route stays
+ if (store.getters.isGuest && to.meta.authOnly) {
+ //guest is trying to access auth-only route
+ next({ name: 'login' })
+ } else if (!store.getters.isGuest && to.meta.anonymousOnly) {
+ //logged in user cannot navigate to guest-only routes
+ next(false)
+ } else {
+ next()
+ }
+})
+
+export default router
diff --git a/src/services/auth-store.js b/src/services/auth-store.js
new file mode 100644
index 0000000..97f77a8
--- /dev/null
+++ b/src/services/auth-store.js
@@ -0,0 +1,32 @@
+/**
+ * store token to localStorage and optionally retrieve token when asked for it
+ */
+
+import AuthToken from './auth-token'
+
+class AuthStore {
+ constructor(key) {
+ this.key = key ? key : 'jwt_token'
+ }
+
+ store(token) {
+ localStorage.setItem(this.key, token.getRaw())
+ }
+
+ clear() {
+ localStorage.removeItem(this.key)
+ }
+
+ recall() {
+ var rawToken = localStorage.getItem(this.key)
+ if (rawToken) {
+ var token = new AuthToken(rawToken)
+ if (token.parse()) {
+ return token
+ }
+ }
+ return false
+ }
+}
+
+export default AuthStore
diff --git a/src/services/auth-token.js b/src/services/auth-token.js
new file mode 100644
index 0000000..e679bbf
--- /dev/null
+++ b/src/services/auth-token.js
@@ -0,0 +1,43 @@
+/**
+ * handles JWT auth token
+ */
+class AuthToken {
+ constructor(token) {
+ this.token = token
+ this.header = null
+ this.payload = null
+ this.verify = ''
+ }
+
+ parse() {
+ var parts = this.token.split('.')
+ if (parts.length == 3) {
+ var tmp = JSON.parse(atob(parts[1]))
+ if (tmp.exp * 1000 > Date.now()) {
+ this.header = JSON.parse(atob(parts[0]))
+ this.payload = tmp
+ this.verify = parts[2]
+ return true
+ }
+ }
+ return false
+ }
+
+ getRaw() {
+ return this.token
+ }
+
+ getHeader() {
+ return this.header
+ }
+
+ getPayload() {
+ return this.payload
+ }
+
+ getVerify() {
+ return this.verify
+ }
+}
+
+export default AuthToken
diff --git a/src/services/batch-watcher.js b/src/services/batch-watcher.js
new file mode 100644
index 0000000..78c1e5d
--- /dev/null
+++ b/src/services/batch-watcher.js
@@ -0,0 +1,64 @@
+export const BatchStates = {
+ CREATED: 'CREATED',
+ WAITING: 'WAITING',
+ RUNNING: 'RUNNING',
+ FINISHED: 'FINISH',
+ FAILED: 'FAILED',
+}
+
+/**
+ * watches for batches to complete
+ */
+export default class BatchWatcher {
+ constructor($http, interval = 10000, maxTries = 20) {
+ this.watches = new Map()
+ this.$http = $http
+ this.batchFinalState = BatchStates.FINISHED
+ this.batchFailState = BatchStates.FAILED
+ this.interval = interval
+ this.maxTries = maxTries
+ }
+
+ /**
+ * start watching batch, returns a promise which is resolved once batch is completed
+ * or rejected on batch failure
+ *
+ * @param url
+ * @returns {Promise}
+ */
+ wait(url) {
+ this.watches.set(url, {
+ retries: 0,
+ })
+ return new Promise((resolve, reject) => {
+ var coef = 0.2
+ var checkBatch = () => {
+ var b = this.watches.get(url)
+ b.retries++
+ this.$http.get(url).then(
+ response => {
+ if (response.data.batch && response.data.batch.status == this.batchFinalState) {
+ resolve(response)
+ } else if (response.data.batch && response.data.batch.status == this.batchFailState) {
+ reject(response)
+ } else {
+ if (b.retries <= this.maxTries) {
+ setTimeout(() => {
+ checkBatch()
+ }, this.interval * coef)
+ //next request will be a bit more delayed
+ coef = Math.min(1, coef * 1.5)
+ } else {
+ reject('max tries')
+ }
+ }
+ },
+ err => {
+ reject(err)
+ }
+ )
+ }
+ checkBatch()
+ })
+ }
+}
diff --git a/src/services/filetype-detector.js b/src/services/filetype-detector.js
new file mode 100644
index 0000000..7b64292
--- /dev/null
+++ b/src/services/filetype-detector.js
@@ -0,0 +1,25 @@
+export default {
+ typeFasta: 'FASTA',
+ typePlain: 'PLAIN',
+ detectType(fileInfo) {
+ return new Promise((resolve, reject) => {
+ if (fileInfo.size == 0) {
+ reject()
+ } else {
+ var blob = fileInfo.slice(0, 1)
+ var reader = new FileReader()
+ reader.onloadend = () => {
+ if (reader.result == '>') {
+ resolve(this.typeFasta)
+ } else {
+ resolve(this.typePlain)
+ }
+ }
+ reader.onerror = () => {
+ reject()
+ }
+ reader.readAsText(blob)
+ }
+ })
+ },
+}
diff --git a/src/services/token-updater.js b/src/services/token-updater.js
new file mode 100644
index 0000000..990aeb3
--- /dev/null
+++ b/src/services/token-updater.js
@@ -0,0 +1,23 @@
+/**
+ * watches token expiration and fires evemt when renew is needed
+ */
+class TokenUpdater {
+ constructor(token) {
+ this.timer = null
+ this.token = token
+ }
+
+ start(renewCallback) {
+ this.stop()
+ var delay = Math.max(0, this.token.getPayload().exp * 1000 - Date.now() - 10000)
+ this.timer = setTimeout(function() {
+ renewCallback()
+ }, delay)
+ }
+
+ stop() {
+ clearTimeout(this.timer)
+ }
+}
+
+export default TokenUpdater
diff --git a/src/services/user-auth.js b/src/services/user-auth.js
new file mode 100644
index 0000000..9378d19
--- /dev/null
+++ b/src/services/user-auth.js
@@ -0,0 +1,119 @@
+import AuthStore from './auth-store'
+import AuthToken from './auth-token'
+import TokenUpdater from './token-updater'
+
+/**
+ * handle user authorisation or login as guest
+ */
+class UserAuth {
+ constructor($http, $store) {
+ this.$http = $http
+ this.$store = $store
+
+ this.authStore = new AuthStore()
+ this.updater = null
+ }
+
+ _initTokenUpdater(token) {
+ if (this.updater) {
+ this.updater.stop()
+ }
+ this.updater = new TokenUpdater(token)
+ this.updater.start(() => {
+ this.$http.get('jwt').then(
+ response => {
+ var token = new AuthToken(response.data)
+ if (token.parse()) {
+ this.authStore.store(token)
+ this._processLogin(token)
+ } else {
+ this.logout()
+ }
+ },
+ () => {
+ //unable to obtain fresh token
+ this.logout()
+ }
+ )
+ })
+ }
+
+ _processLogin(token) {
+ this.$http.defaults.headers.common['Authorization'] = token.getRaw()
+ this.$store.dispatch('login', token.getPayload())
+ this._initTokenUpdater(token)
+ }
+
+ /**
+ * handle login
+ *
+ * @param email
+ * @param password
+ * @returns {Promise}
+ */
+ login(email, password) {
+ var formData = {
+ login: email,
+ password: password,
+ }
+
+ return new Promise((resolve, reject) => {
+ //remove possible old token
+ delete this.$http.defaults.headers.common['Authorization']
+ this.$http.put('jwt', formData).then(
+ response => {
+ var token = new AuthToken(response.data)
+ if (token.parse()) {
+ this.authStore.store(token)
+ this._processLogin(token)
+
+ resolve()
+ } else {
+ reject('Login failure.')
+ }
+ },
+ () => {
+ reject('Login failure.')
+ }
+ )
+ })
+ }
+
+ /**
+ * load token from localStorage or obtain new anonymous token
+ */
+ renew() {
+ return new Promise((resolve, reject) => {
+ var token = this.authStore.recall()
+ if (token) {
+ this._processLogin(token)
+ resolve()
+ } else {
+ this._anonymous().then(resolve, reject)
+ }
+ })
+ }
+
+ _anonymous() {
+ return this.$http.post('jwt').then(response => {
+ var token = new AuthToken(response.data)
+ if (token.parse()) {
+ this.authStore.store(token)
+ this._processLogin(token)
+ } else {
+ throw new Error('Auth token not acquired.')
+ }
+ })
+ }
+
+ /**
+ * logout current user and obtain new anonymous token
+ */
+ logout() {
+ this.authStore.clear()
+ this.$store.dispatch('logout')
+ this._anonymous()
+ }
+}
+
+export default UserAuth
diff --git a/src/store/index.js b/src/store/index.js
new file mode 100644
index 0000000..9ca3b81
--- /dev/null
+++ b/src/store/index.js
@@ -0,0 +1,38 @@
+import Vue from 'vue'
+import Vuex from 'vuex'
+import workProgress from '@/components/core/work-progress/store'
+
+Vue.use(Vuex)
+
+export const mutations = {
+ setUser(state, user) {
+ state.user = user
+ },
+}
+
+export const getters = {
+ isGuest(state) {
+ return state.user && state.user.roles.indexOf('ROLE_USER') == -1
+ },
+}
+
+export const actions = {
+ login(context, user) {
+ context.commit('setUser', user)
+ },
+ logout(context) {
+ context.commit('setUser', null)
+ },
+}
+
+export default new Vuex.Store({
+ state: {
+ user: null,
+ },
+ mutations,
+ getters,
+ actions,
+ modules: {
+ workProgress,
+ },
+})
diff --git a/src/utils.js b/src/utils.js
new file mode 100644
index 0000000..5272fa4
--- /dev/null
+++ b/src/utils.js
@@ -0,0 +1,14 @@
+// utils.js
+
+/**
+ * Split long string into several chunks based on given size
+ * @param {string} str string to chunk
+ * @param {number} size newly created string max length
+ * @returns {Array<string>}
+ */
+export const chunkString = (str, size) => {
+ if (!str) {
+ return []
+ }
+ return str.match(new RegExp('.{1,' + size + '}', 'g'))
+}
diff --git a/tests/unit/example.spec.js b/tests/unit/example.spec.js
new file mode 100644
index 0000000..f2db74a
--- /dev/null
+++ b/tests/unit/example.spec.js
@@ -0,0 +1,12 @@
+import { shallowMount } from '@vue/test-utils'
+import HelloWorld from '@/components/HelloWorld.vue'
+
+describe('HelloWorld.vue', () => {
+ it('renders props.msg when passed', () => {
+ const msg = 'new message'
+ const wrapper = shallowMount(HelloWorld, {
+ propsData: { msg },
+ })
+ expect(wrapper.text()).toMatch(msg)
+ })
+})
diff --git a/vue.config.js b/vue.config.js
new file mode 100644
index 0000000..4d5400c
--- /dev/null
+++ b/vue.config.js
@@ -0,0 +1,13 @@
+const path = require('path');
+
+module.exports = {
+ devServer: {
+ proxy: {
+ '/api': {
+ target: 'https://localhost:443',
+ ws: true,
+ changeOrigin: true,
+ }
+ },
+ }
+}
\ No newline at end of file
--
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