From ce2cab659a1572b52e636f4e51952d0b6eef44b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Petrovi=C4=8D?= <mifo.petrovic@gmail.com>
Date: Sat, 8 Feb 2025 19:59:48 +0100
Subject: [PATCH] remove not working palindrome analyser (unfinished)
---
.../analyse/palindrome/PalindromeAnalyse.java | 72 -------
.../PalindromeAnalyseController.java | 144 -------------
.../PalindromeAnalyseRepository.java | 27 ---
.../palindrome/PalindromeAnalyseService.java | 139 -------------
.../detector/AtatPalindromeDetector.java | 91 ---------
.../detector/CompositePalindromeDetector.java | 189 ------------------
.../detector/PalindromeDetector.java | 13 --
.../detector/PalindromeDetectorBuilder.java | 13 --
.../detector/PalindromeMatcher.java | 16 --
.../detector/Simple2PalindromeDetector.java | 86 --------
.../detector/SimplePalindromeDetector.java | 83 --------
.../analyse/palindrome/model/NumberRange.java | 62 ------
.../palindrome/model/PalindromeModel.java | 129 ------------
.../palindrome/model/StabilityModel.java | 23 ---
.../stability/NNModelStabilityCalculator.java | 78 --------
.../stability/StabilityCalculator.java | 13 --
.../dnaAnalyser/overlay/OverlayService.java | 3 -
17 files changed, 1181 deletions(-)
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyse.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseController.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseRepository.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseService.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/AtatPalindromeDetector.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/CompositePalindromeDetector.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetector.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetectorBuilder.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeMatcher.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/Simple2PalindromeDetector.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/SimplePalindromeDetector.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/NumberRange.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/PalindromeModel.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/StabilityModel.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/NNModelStabilityCalculator.java
delete mode 100644 src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/StabilityCalculator.java
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyse.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyse.java
deleted file mode 100644
index 80a9f61..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyse.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.StabilityModel;
-import cz.mendelu.dnaAnalyser.sequence.Sequence;
-import cz.mendelu.dnaAnalyser.user.User;
-import cz.mendelu.dnaAnalyser.utils.analyse.model.Analyse;
-import cz.mendelu.dnaAnalyser.utils.model.Identifiable;
-import lombok.Builder;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.ToString;
-
-import javax.persistence.Entity;
-import javax.persistence.Transient;
-import java.util.Date;
-import java.util.Set;
-import java.util.UUID;
-
-@Data
-@Entity
-@ToString(callSuper = true)
-@EqualsAndHashCode(callSuper = true)
-public class PalindromeAnalyse extends Analyse implements Identifiable {
-
- /*
- public PalindromeModel() {
- super(PalindromeModel.class.getPackage().getName());
- }
- */
-
- private String mismatches;
- @Transient
- private int size;
- @Transient
- private int mismatche;
- @Transient
- private int spacer;
- @Transient
- private String spacers;
- @Transient
- private int position;
- @Transient
- private StabilityModel stabilityModel;
-
- public PalindromeAnalyse() {
- }
-
- @Builder
- private PalindromeAnalyse(UUID id, Date created, Sequence sequence, User owner, Set<String> tags, Date finished, String title, Long resultCount, Integer size, String spacers, Integer spacer, String mismatches, Integer mismatche, int position) {
- super((id != null) ? id : UUID.randomUUID(), created, sequence, owner, tags, finished, title, resultCount);
- this.size = size;
- this.spacers = spacers;
- this.spacer = spacer;
- this.mismatches = mismatches;
- this.mismatche = mismatche;
- this.position = position;
- }
-
- /*
- public NumberRange sizeAsNumberRange() {
- return (size == null) ? null : new NumberRange(size);
- }
-
- public NumberRange spacerAsNumberRange() {
- return (spacer == null) ? null : new NumberRange(spacer);
- }
-
- public NumberRange mismatchesAsNumberRange() {
- return (mismatches == null) ? null : new NumberRange(mismatches);
- }
- */
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseController.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseController.java
deleted file mode 100644
index d5daa3c..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseController.java
+++ /dev/null
@@ -1,144 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.StabilityModel;
-import cz.mendelu.dnaAnalyser.sequence.SequenceService;
-import cz.mendelu.dnaAnalyser.utils.controller.DeleteMapping;
-import cz.mendelu.dnaAnalyser.utils.controller.GetMapping;
-import cz.mendelu.dnaAnalyser.utils.controller.*;
-import cz.mendelu.dnaAnalyser.utils.controller.PostMapping;
-import cz.mendelu.dnaAnalyser.utils.controller.PutMapping;
-import cz.mendelu.dnaAnalyser.utils.swagger.ApiPaginationParams;
-import io.swagger.annotations.Api;
-import io.swagger.annotations.ApiOperation;
-import lombok.Data;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.security.core.Authentication;
-import org.springframework.web.bind.annotation.*;
-import springfox.documentation.annotations.ApiIgnore;
-
-import javax.validation.Valid;
-import java.util.List;
-import java.util.Set;
-import java.util.UUID;
-import java.util.stream.Collectors;
-
-@RestController
-@Api(tags = "api/analyse/palindrome")
-@RequestMapping("api/analyse/palindrome")
-public class PalindromeAnalyseController {
-
- @Data
- static class PalindromeAnalyseRequest {
-
- private List<UUID> sequences;
-
- private Boolean dinucleotide;
-
- private String size = "6-30";
-
- private String spacer = "0-10";
-
- private String mismatches = "0,1";
-
- private Set<String> tags;
-
- private StabilityModel stabilityModel;
-
- }
-
-
- @Autowired
- private PalindromeAnalyseService palindromeAnalyseService;
-
- @Autowired
- private SequenceService sequenceService;
-
- @GetMapping
- @ResponseStatus(HttpStatus.OK)
- @PreAuthorize("isAutheticated()")
- @ApiPaginationParams
- @ApiOperation("Get page with PalindromeModel analysis")
- public ResponsePage<PalindromeModel> getPageWithPalindromeAnalysis(
- PaginationParam paginationParam,
- SortParam sortParam,
- TagFilterParam tagFilterParam
- ){
-
- throw new UnsupportedOperationException("Not implemented yet.");
- }
-
- @GetMapping("/tag")
- @ResponseStatus(HttpStatus.OK)
- @PreAuthorize("isAuthenticated()")
- @ApiPaginationParams
- @ApiOperation("Get all tags defined for sequences")
- public ResponsePage<String> getPageWithTags(
- PaginationParam paginationParam,
- SortParam sortParam
- ) {
- throw new UnsupportedOperationException("Not implemented yet.");
- }
-
- @GetMapping("/{id}")
- @ResponseStatus(HttpStatus.OK)
- @PreAuthorize("isAuthenticated()")
- @ApiOperation("Get one PalindromeModel analyse by ID.")
- public Response<PalindromeModel> getOnePalindromeAnalyse(
- @PathVariable UUID id)
- {
- throw new UnsupportedOperationException("Not implemented yet.");
- }
-
- @PostMapping()
- @ResponseStatus(HttpStatus.CREATED)
- @PreAuthorize("isAuthenticated()")
- @ApiOperation("Create palindrome analyze.")
- public ResponseList<PalindromeAnalyse> postPalindromeAnalyse(
- @ApiIgnore Authentication authentication,
- @RequestBody @Valid PalindromeAnalyseRequest request
- ) {
-
- List<PalindromeAnalyse> analysis = request.getSequences()
- .stream()
- .map(uuid ->
- palindromeAnalyseService.executePalindromeAnalyse(null /*
- PalindromeModel.builder()
- .sequence(sequenceService.findOne(uuid))
- .owner(AuthenticationUtils.toUser(authentication))
- .tags(request.getTags())
- .mismatches(request.getMismatches())
- .size(request.getSize())
- .spacer(request.getSpacer())
- .stabilityModel(request.getStabilityModel())
- .build() */
- )
- ).collect(Collectors.toList());
-
- return ResponseList.responseList(analysis);
- }
-
- @PutMapping("/{id}/tags")
- @ResponseStatus(HttpStatus.ACCEPTED)
- @PreAuthorize("isAuthenticated()")
- @ApiOperation("Modify tags")
- public Response<PalindromeModel> modifyTags(
- @PathVariable UUID id,
- @RequestBody TagModifyRequest request)
- {
- throw new UnsupportedOperationException("Not implemented yet.");
- }
-
- @DeleteMapping("/{id}")
- @ResponseStatus(HttpStatus.NO_CONTENT)
- @PreAuthorize("isAuthenticated()")
- @ApiOperation("Delete one PalindromeModel analyse by ID")
- public void deletePalindrome(
- @PathVariable UUID id)
- {
- throw new UnsupportedOperationException("Not implemented yet.");
- }
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseRepository.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseRepository.java
deleted file mode 100644
index 079d0ec..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseRepository.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome;
-
-import cz.mendelu.dnaAnalyser.utils.repository.BaseRepository;
-import org.springframework.data.domain.Page;
-import org.springframework.data.domain.Pageable;
-import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.query.Param;
-import org.springframework.stereotype.Repository;
-
-import java.util.Optional;
-import java.util.UUID;
-
-@Repository
-public interface PalindromeAnalyseRepository extends BaseRepository<PalindromeAnalyse, UUID> {
-
- @Query("select a from PalindromeAnalyse as a join a.owner o where o.id = ?#{principal.id}")
- Page<PalindromeAnalyse> findAll(Pageable pageable);
-
- @Query("select a from PalindromeAnalyse as a join a.owner o join a.tags t where t = :tag and o.id = ?#{principal.id}")
- Page<PalindromeAnalyse> findAll(Pageable pageable, @Param("tag") String tag);
-
- @Query("select a from PalindromeAnalyse as a join a.owner o where a.id = :id and o.id = ?#{principal.id}")
- Optional<PalindromeAnalyse> findById(@Param("id") UUID id);
-
- @Query("select t from PalindromeAnalyse as s join s.owner o join s.tags t where o.id = ?#{principal.id}")
- Page<String> findAllTags(Pageable pageable);
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseService.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseService.java
deleted file mode 100644
index 0706fda..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/PalindromeAnalyseService.java
+++ /dev/null
@@ -1,139 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.detector.AtatPalindromeDetector;
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-import cz.mendelu.dnaAnalyser.batch.BatchService;
-import cz.mendelu.dnaAnalyser.sequence.NucleicBuffer;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceDataRepository;
-import lombok.Data;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-
-import java.util.*;
-
-@Service
-public class PalindromeAnalyseService {
-
- private static final Logger LOG = LoggerFactory.getLogger(PalindromeAnalyseService.class);
-
- private List<PalindromeModel> palindromes = new LinkedList<>();
-
- private boolean cycleMode = false;
-
- //@Autowired
- //private PalindromeDataSessionService palindromDataSessionService;
-
- @Autowired
- private PalindromeAnalyseRepository palindromeRepository;
-
- @Autowired
- private SequenceDataRepository sequenceDataRepository;
-
- @Autowired
- private BatchService batchService;
-
- public PalindromeAnalyse executePalindromeAnalyse(PalindromeAnalyse palindromeAnalyse) {
- palindromeAnalyse = palindromeRepository.save(palindromeAnalyse);
- batchService.createBatch(palindromeAnalyse.getOwner(), palindromeAnalyse);
- /* .execute(analyse->{
-
- Sequence sequence = analyse.getSequence();
- SequenceData sequenceData = sequenceDataRepository.load(sequence);
-
- //inicializace proměnných potřebných pro algoritmus
- int size = analyse.getSize();
- boolean atatFilter = analyse.isAtatFilter();
- boolean cycle = analyse.isCycle();
- String mismatcheString = analyse.getMismatches();
- String spacerString = analyse.getSpacers();
-
- NumberRange mm = new NumberRange(mismatcheString); //prevedu mismatche a spacer
- NumberRange sp = new NumberRange(spacerString);
-
- final SortedSet<Integer> spacers = sp.getValues();
- final SortedSet<Integer> mismatches = mm.getValues();
-
- SqlSession sqlSession = palindromDataSessionService.openDataSession(analyse);
-
- analyse.finishNow();
- sqlSession.commit();
- analyse = palindromeRepository.save(analyse); //na konci uloĹľĂm
- return analyse;
- }).start();
-
-*/
- return palindromeAnalyse;
- }
-
- private boolean isSubSequenceToCompare(SequenceData sequence, int nextSequencePosition, int size, boolean cycleMode) {
- return (cycleMode)
- ? true
- : sequence.getLength() > nextSequencePosition + size;
- }
-
- private NucleicBuffer getSubSequence(SequenceData sequence, int nextSequencePosition, int size) {
- return sequence.getBuffer(nextSequencePosition, size);
- }
-
- public List<PalindromeModel> findPalindromes(final int size, SortedSet<Integer> spacers, SortedSet<Integer> mismatches, SequenceData sequence, boolean cycleMode, boolean atatFilter) {
- Integer nextSequencePosition, mismatche;
- NucleicBuffer testedSequence, oppositSequence, nextSequence;
-
- int searchToPosition = sequence.getLength();
- for (int i = 0; i < searchToPosition; i++) { // v cyklu prochazim cely genom
-
- testedSequence = getSubSequence(sequence, i, size); //vezme se část sekvence z celé sekvence a ta se testuje
-
- LOG.debug("tested = {} ", testedSequence);
- if (atatFilter && AtatPalindromeDetector.isAtat(testedSequence)) continue;
-
- oppositSequence = testedSequence.revert(); //otočà se testovaná podsekvence
- // LOG.debug("OppositSeq = {} ", oppositSequence.getLength());
-
- for (int spacer : spacers) { // Postupne natahuji mezeru a porovnavam shodu
- nextSequencePosition = i + size + spacer;
-
- if (isSubSequenceToCompare(sequence, nextSequencePosition, size, cycleMode)) { //zde je problĂ©m, neprocházĂ
- nextSequence = getSubSequence(sequence, nextSequencePosition, size);
-
- if (atatFilter && AtatPalindromeDetector.isAtat(testedSequence)) continue;
- LOG.debug("opposite = {} ", oppositSequence);
- LOG.debug("next = {} ", nextSequence);
-
- mismatche = oppositSequence.mismatches(nextSequence); // mismatche null.. proč??? ZDE JE HLAVNÍ problém
- LOG.debug("mismatche = {} ", mismatche);
- if (mismatche != null && mismatches.contains(mismatche)) { // Pokud jsem nalezl odpovidaji sekvenci pridam ji do vysledku
-
- PalindromeModel p = (new PalindromeModel(sequence, i, size, spacer, mismatche));
- palindromes.add(p);
- break;
- }
- }
- }
- }
- return palindromes;
- }
-
-
-
- @Data
- private static class Palindrome {
- private SequenceData sequenceData;
- private int position;
- private int mismatche;
- private int spacer;
- private int size;
-
- public Palindrome(SequenceData sequenceData, int position, int mismatche, int spacer, int size) {
- this.sequenceData = sequenceData;
- this.position = position;
- this.mismatche = mismatche;
- this.spacer = spacer;
- this.size = size;
- }
- }
-
- }
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/AtatPalindromeDetector.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/AtatPalindromeDetector.java
deleted file mode 100644
index 6b03d03..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/AtatPalindromeDetector.java
+++ /dev/null
@@ -1,91 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-import cz.mendelu.dnaAnalyser.sequence.NucleicBuffer;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-import cz.mendelu.dnaAnalyser.sequence.nucleotide.Nucleotide;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.Iterator;
-import java.util.SortedSet;
-
-/**
- * Created by xkoloma1 on 03.03.2016.
- */
-public class AtatPalindromeDetector implements PalindromeDetector {
-
- private static final Logger LOG = LoggerFactory.getLogger(AtatPalindromeDetector.class);
-
- public static boolean isAtat(NucleicBuffer nucleicBuffer) {
- if (nucleicBuffer.getLength() == 0) {
- return false;
- }
-
- Nucleotide current, expects = nucleicBuffer.next().supplement(nucleicBuffer.getType());
- while (nucleicBuffer.hasNext()) {
- current = nucleicBuffer.next();
- if (expects != current) {
- return false;
- }
- expects = current.supplement(nucleicBuffer.getType());
- }
- return true;
- }
-
-
- private final int minSize, maxSize, maxSpacer;
-
- public AtatPalindromeDetector(SortedSet<Integer> size, SortedSet<Integer> spacers) {
- this.minSize = size.first();
- this.maxSize = size.last();
- this.maxSpacer = spacers.last() - (spacers.last() % 2);
- }
-
- @Override
- public PalindromeMatcher findPalindrome(SequenceData sequence) {
- SimplePalindromeDetector.SimplePalindromeMatcher result = new SimplePalindromeDetector.SimplePalindromeMatcher();
- if(sequence.getLength() < minSize * 2) {
- return result; //TODO nebo radeji vyvolat vyjimku?
- }
-
- Iterator<Nucleotide> i = sequence.iterator();
- Nucleotide current, expects = i.next().supplement(sequence.getType());
- int start = 0, length = 0;
-
- while (i.hasNext()) {
- current = i.next();
- length++;
- if (expects != current) {
- // Testuji zda sekvence atat je dostatecna na vytvoreni palindromu
- if (length >= (minSize * 2)) {
- result.add(newPalindrome(sequence, start, length));
- }
- start += length;
- length = 0;
- }
- expects = current.supplement(sequence.getType());
- }
-
- // Pridani palindromu na konci genomu.
- if (length >= minSize * 2) {
- result.add(newPalindrome(sequence, start, length));
- }
- return result;
- }
-
- @Override
- public void setAtatFilter(boolean atatFilter) {
- // Ignore
- }
-
- private PalindromeModel newPalindrome(SequenceData sequence, int start, int length) {
- length -= (length % 2); // DĂ©lka musĂ bĂ˝t sudĂ© ÄŤĂslo!
- int size = Math.min(length / 2, maxSize);
- int remainder = Math.max(0, length - (size * 2));
- int spacer = Math.min(remainder, maxSpacer);
- spacer -= (spacer % 2); // DĂ©lka spaceru musĂ bĂ˝t takĂ© sudĂ© ÄŤĂslo.
- return new PalindromeModel(sequence, start, size, spacer, 0);
- }
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/CompositePalindromeDetector.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/CompositePalindromeDetector.java
deleted file mode 100644
index 52e47ba..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/CompositePalindromeDetector.java
+++ /dev/null
@@ -1,189 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-
-
-import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-/**
- * Created by xkoloma1 on 06.10.2015.
- */
-public class CompositePalindromeDetector implements PalindromeDetector {
-
- public static PalindromeDetectorBuilder palindromeDetectorBuilder() {
- return (size, spacers, mismatches) -> {
- List<PalindromeDetector> palindromeDetectors = size.stream()
- .map(s -> new Simple2PalindromeDetector(s, spacers, mismatches))
- .collect(Collectors.toList());
-
- AtatPalindromeDetector atatPalindromeDetector = new AtatPalindromeDetector(size, spacers);
-
- return new CompositePalindromeDetector(palindromeDetectors, atatPalindromeDetector);
- };
- }
-
- private List<PalindromeDetector> palindromeDetectors;
- private AtatPalindromeDetector atatPalindromeDetector;
- private boolean usadAtatPalindromeDetector = true;
-
- private PalindromeMergeEvalutor evalutor = (f, s) -> f.getSize() - f.getMismatches() <= s.getSize() - s.getMismatches();
-
- public CompositePalindromeDetector(List<PalindromeDetector> palindromeDetectors, AtatPalindromeDetector atatPalindromeDetector) {
- this.palindromeDetectors = palindromeDetectors;
- this.atatPalindromeDetector = atatPalindromeDetector;
- }
-
- @Override
- public PalindromeMatcher findPalindrome(SequenceData sequence) {
- PalindromeMatcher result = palindromeDetectors.parallelStream()
- .map(pd -> pd.findPalindrome(sequence)) /* VYBER JEDEN Z NASLEDUJICH DVOU RADKU */
- .reduce(null, (a, b) -> merge(a, b)); // Redukce podle stredu palindromu
- //.reduce(null, (a, b) -> sum(a, b)); // Jednoduche spojeni vsech vysledku do jednoho za ucelem demonstrace na clanek
- if (usadAtatPalindromeDetector)
- result = merge(result, atatPalindromeDetector.findPalindrome(sequence));
-
- Map<Object, PalindromeModel> filter = spaceRiseFilter(result);
- return new MergePalindromeMatcher(filter);
- }
-
- /**
- * Tento filter odstranĂ palindromy, kterĂ© jsou na stejnĂ©m mĂstÄ› a vnikly nárustem spaceru. Tedy ebÄ› jejich části
- * (sekvence i oposite) zaÄŤĂnajĂ na stejnmĂ©m mĂstÄ›.
- * @param result
- * @return
- */
- private Map<Object, PalindromeModel> spaceRiseFilter(PalindromeMatcher result) {
- Map<Object, PalindromeModel> filter = new HashMap<>();
- result.forEach(palindrome -> {
- int palindromeStart = palindrome.getPosition();
- int oppositeStart = palindromeStart + palindrome.getSequence().getLength() + palindrome.getSpacer().getLength();
- FilterSignature signature = new FilterSignature(palindromeStart, oppositeStart);
- // Otestuji, jestli mam jiz ulozeny podezdeli palindrom,
- if (filter.containsKey(signature)) { // Pokud mam, tak vyhodnotim ten lepsi
- PalindromeModel oldPalindromeModel = filter.get(signature);
- if (palindrome.getSequence().getLength() > oldPalindromeModel.getSequence().getLength()) {
- filter.put(signature, palindrome);
- }
- } else { // Jinak pouze pridam do mapy
- filter.put(signature, palindrome);
- }
- });
- return filter;
- }
-
- @Override
- public void setAtatFilter(boolean atatFilter) {
- palindromeDetectors.forEach(p -> p.setAtatFilter(atatFilter));
- usadAtatPalindromeDetector = atatFilter;
- }
-
- private MergePalindromeMatcher merge(PalindromeMatcher a, PalindromeMatcher b) {
- MergePalindromeMatcher result = new MergePalindromeMatcher();
- if (a != null) {
- result.merge(a);
- }
- if (b != null) {
- result.merge(b);
- }
- return result;
- }
-
- private PalindromeMatcher sum(PalindromeMatcher a, PalindromeMatcher b) {
- return new PalindromeMatcher() {
- private List<PalindromeModel> sum = new LinkedList<>();
- {
- if (a != null) a.forEach(p -> sum.add(p));
- if (b != null) b.forEach(p -> sum.add(p));
- }
-
- @Override
- public int getCount() {
- return sum.size();
- }
-
- @Override
- public Stream<PalindromeModel> stream() {
- return sum.stream();
- }
-
- @Override
- public Iterator<PalindromeModel> iterator() {
- return sum.iterator();
- }
- };
- }
-
- class MergePalindromeMatcher implements PalindromeMatcher {
-
- private Map<Object, PalindromeModel> map = new HashMap<>();
-
- public MergePalindromeMatcher() {}
-
- public MergePalindromeMatcher(Map<Object, PalindromeModel> map) {
- this.map = map;
- }
-
- private void merge(PalindromeMatcher matcher) {
- matcher.forEach(p -> {
- if (map.containsKey(p.getMidlePosition())) {
- PalindromeModel o = map.get(p.getMidlePosition());
- if (evalutor.evaluate(o, p)) {
- map.put(p.getMidlePosition(), p);
- }
- } else {
- map.put(p.getMidlePosition(), p);
- }
- });
- }
-
-
- @Override
- public int getCount() {
- return map.size();
- }
-
- @Override
- public Stream<PalindromeModel> stream() {
- return map.values().stream();
- }
-
- @Override
- public Iterator<PalindromeModel> iterator() {
- return map.values().iterator();
- }
- }
-
- public interface PalindromeMergeEvalutor {
-
- boolean evaluate(PalindromeModel first, PalindromeModel second);
-
- }
-
- private static final class FilterSignature {
-
- public final int palindromeStart;
- public final int oppositeStart;
-
- public FilterSignature(int palindromeStart, int oppositeStart) {
- this.palindromeStart = palindromeStart;
- this.oppositeStart = oppositeStart;
- }
-
- @Override
- public boolean equals(Object o) {
- if (this == o) return true;
- if (o == null || getClass() != o.getClass()) return false;
- FilterSignature that = (FilterSignature) o;
- return palindromeStart == that.palindromeStart &&
- oppositeStart == that.oppositeStart;
- }
-
- @Override
- public int hashCode() {
- return Objects.hash(palindromeStart, oppositeStart);
- }
- }
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetector.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetector.java
deleted file mode 100644
index 116218d..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetector.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-
-/**
- * Created by Honza on 24. 7. 2015.
- */
-public interface PalindromeDetector {
-
- PalindromeMatcher findPalindrome(SequenceData sequence);
-
- void setAtatFilter(boolean atatFilter);
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetectorBuilder.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetectorBuilder.java
deleted file mode 100644
index 68a691e..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeDetectorBuilder.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import java.util.SortedSet;
-
-/**
- * Created by xkoloma1 on 06.10.2015.
- */
-public interface PalindromeDetectorBuilder {
-
- PalindromeDetector getPalindromeDetector(SortedSet<Integer> size, SortedSet<Integer> spacers, SortedSet<Integer> mismatches);
-
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeMatcher.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeMatcher.java
deleted file mode 100644
index 4fe6bdb..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/PalindromeMatcher.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-
-import java.util.stream.Stream;
-
-/**
- * Created by Honza on 29. 7. 2015.
- */
-public interface PalindromeMatcher extends Iterable<PalindromeModel> {
-
- int getCount();
-
- Stream<PalindromeModel> stream();
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/Simple2PalindromeDetector.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/Simple2PalindromeDetector.java
deleted file mode 100644
index 34b0a61..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/Simple2PalindromeDetector.java
+++ /dev/null
@@ -1,86 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-import cz.mendelu.dnaAnalyser.sequence.NucleicBuffer;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.SortedSet;
-
-/**
- * Created by xkoloma1 on 27. 7. 2015.
- */
-public class Simple2PalindromeDetector implements PalindromeDetector {
-
- private static final Logger LOG = LoggerFactory.getLogger(Simple2PalindromeDetector.class);
-
- private final int size;
-
- private final SortedSet<Integer> spacers;
-
- private final SortedSet<Integer> mismatches;
-
- private boolean cycleMode = false;
-
- private boolean atatFilter = true;
-
- public Simple2PalindromeDetector(int size, SortedSet<Integer> spacers, SortedSet<Integer> mismatches) {
- LOG.debug("Create: size = {}, spacer = {}, mismatches = {}", size, spacers, mismatches);
- this.size = size;
- this.spacers = spacers;
- this.mismatches = mismatches;
- }
-
- @Override
- public void setAtatFilter(boolean atatFilter) {
- this.atatFilter = atatFilter;
- }
-
- @Override
- public PalindromeMatcher findPalindrome(SequenceData sequence) {
- SimplePalindromeDetector.SimplePalindromeMatcher palindromeMatcher = new SimplePalindromeDetector.SimplePalindromeMatcher();
- Integer nextSequencePosition, mismatche;
- NucleicBuffer testedSequence, oppositSequence, nextSequence;
- int searchToPosition = sequence.getLength(); /* Pokud je povoleno cyklicke
- hledánĂ, je sekvence prohledana az nakonec, jinak se prohledani zastavi pred tak, aby nebyli nalezeny
- palindromy mimo delku sekvence. */
-
- for (int i = 0; i < searchToPosition; i++) { // Cyklu prochazim cely genom
- testedSequence = getSubSeqvence(sequence, i);
-
- // pokud se maji filtrovat atat sekvence, jsou atomaticky vyrazeny z vysledku.
- if (atatFilter && AtatPalindromeDetector.isAtat(testedSequence)) continue;
-
- oppositSequence = testedSequence.revert();
-
- for (int spacer : spacers) { // Postupne natahuji mezeru a porovnavam shodu
- nextSequencePosition = i + size + spacer;
- if (isSubSeqvenceToComapere(sequence, nextSequencePosition)) {
- nextSequence = getSubSeqvence(sequence, nextSequencePosition);
-
- // pokud je dalšà sekvence, jsou atomaticky vyrazeny z vysledku.
- if (atatFilter && AtatPalindromeDetector.isAtat(testedSequence)) continue;
- mismatche = oppositSequence.mismatches(nextSequence);
- if (mismatche != null && mismatches.contains(mismatche)) { // Pokud jsem nalezl odpovidaji sekvenci pridam ji do vysledku
- palindromeMatcher.add(new PalindromeModel(sequence, i, size, spacer, mismatche));
- break; // Ukonceni cyklu zvytsujiho mezeru
- }
- }
- }
- }
- LOG.debug("AnalysePalindrome for size {} done, found {}", size, palindromeMatcher.getCount());
- return palindromeMatcher;
- }
-
- private boolean isSubSeqvenceToComapere(SequenceData sequence, int nextSequencePosition) {
- return (cycleMode)
- ? true
- : sequence.getLength() < nextSequencePosition + size;
- }
-
- private NucleicBuffer getSubSeqvence(SequenceData sequence, int nextSequencePosition) {
- return sequence.getBuffer(nextSequencePosition, size);
- }
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/SimplePalindromeDetector.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/SimplePalindromeDetector.java
deleted file mode 100644
index e7b5693..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/detector/SimplePalindromeDetector.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.detector;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-
-import cz.mendelu.dnaAnalyser.sequence.NucleicBuffer;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.stream.Stream;
-
-/**
- * Created by xkoloma1 on 27. 7. 2015.
- */
-public class SimplePalindromeDetector implements PalindromeDetector {
-
- private static final Logger LOG = LoggerFactory.getLogger(SimplePalindromeDetector.class);
-
- private final int size;
-
- private final int spacer;
-
- private final int mismatches;
-
- public SimplePalindromeDetector(int size, int spacer, int mismatches) {
- LOG.debug("Create: size = {}, spacer = {}, mismatches = {}", size, spacer, mismatches);
- this.size = size;
- this.spacer = spacer;
- this.mismatches = mismatches;
- }
-
- @Override
- public PalindromeMatcher findPalindrome(SequenceData sequence) {
- SimplePalindromeMatcher palindromeMatcher = new SimplePalindromeMatcher();
- Integer mismatche;
- NucleicBuffer testedSequence, oppositeSequence, nextSequence;
- if(sequence.getLength() >= (size + spacer + size)) {
- for (int i = 0; i < sequence.getLength() - (size + spacer + size - 1); i++) {
- testedSequence = sequence.getBuffer(i, size);
- oppositeSequence = testedSequence.revert();
- nextSequence = sequence.getBuffer(i + size + spacer, size);
- mismatche = oppositeSequence.mismatches(nextSequence);
- if (mismatche != null && mismatche == mismatches) {
- palindromeMatcher.add(new PalindromeModel(sequence, i, size, spacer, mismatches));
- }
- }
- }
- LOG.info("AnalysePalindrome done, found: {}", palindromeMatcher.getCount());
- return palindromeMatcher;
- }
-
- @Override
- public void setAtatFilter(boolean atatFilter) {
- // Ignore
- }
-
- public static class SimplePalindromeMatcher implements PalindromeMatcher {
-
- private List<PalindromeModel> palindromeModels = new LinkedList<>();
-
- void add(PalindromeModel palindromeModel) {
- palindromeModels.add(palindromeModel);
- }
-
- @Override
- public int getCount() {
- return palindromeModels.size();
- }
-
- @Override
- public Stream<PalindromeModel> stream() {
- return palindromeModels.stream();
- }
-
- @Override
- public Iterator<PalindromeModel> iterator() {
- return palindromeModels.iterator();
- }
- }
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/NumberRange.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/NumberRange.java
deleted file mode 100644
index 42829f7..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/NumberRange.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.model;
-
-import java.util.Collections;
-import java.util.NavigableSet;
-import java.util.TreeSet;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-/**
- * Created by xkoloma1 on 28. 7. 2015.
- */
-public class NumberRange {
-
- private static final Pattern RE_NUMBER = Pattern.compile("^\\d+$");
- private static final Pattern RE_RANGE = Pattern.compile("^(\\d+)-(\\d+)$");
-
- private final String input;
-
- private final NavigableSet<Integer> values;
-
- public NumberRange(int min, int max) {
- this.input = min + "-" + max;
- this.values = new TreeSet<>();
-
- for (int i = min; i <= max; i++) {
- values.add(i);
- }
- }
-
- public NumberRange(String input) {
- this.input = input.trim();
- this.values = new TreeSet<>();
-
- String[] parts = input.trim().split("\\s*,\\s*");
- Matcher matcher;
- for (String part : parts) {
- matcher = RE_NUMBER.matcher(part);
- if (matcher.find()) {
- values.add(Integer.parseInt(part));
- continue;
- }
-
- matcher = RE_RANGE.matcher(part);
- if (matcher.find()) {
- int min = Integer.parseInt(matcher.group(1));
- int max = Integer.parseInt(matcher.group(2));
- for (int i = min; i <= max; i++) {
- values.add(i);
- }
- continue;
- }
- }
- }
-
- public NavigableSet<Integer> getValues() {
- return Collections.unmodifiableNavigableSet(values);
- }
-
- public String toString() {
- return input;
- }
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/PalindromeModel.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/PalindromeModel.java
deleted file mode 100644
index 7ff0755..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/PalindromeModel.java
+++ /dev/null
@@ -1,129 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.model;
-
-
-import cz.mendelu.dnaAnalyser.sequence.NucleicBuffer;
-import cz.mendelu.dnaAnalyser.sequence.data.SequenceData;
-import cz.mendelu.dnaAnalyser.sequence.nucleotide.Nucleotide;
-import lombok.Data;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * Created by Honza on 24. 7. 2015.
- */
-public class PalindromeModel implements Iterable<PalindromeModel.Entry>/*, SubSequence*/ {
-
- public static final int SIZE_MARGIN = 5;
-
- private final SequenceData sequenceData;
-
- private final int position;
- private final int size;
- private final int spacer;
- private final int mismatches;
-
- public PalindromeModel(SequenceData sequenceData, int positions, int size, int spacer, int mismatches) {
- this.sequenceData = sequenceData;
- this.position = positions;
- this.size = size;
- this.spacer = spacer;
- this.mismatches = mismatches;
- }
-
- /*
- public Sequence getBefore() {
- int beforePosition = (position < SIZE_MARGIN) ? 0 : position - SIZE_MARGIN;
- int beforeSize = (position < SIZE_MARGIN) ? position : SIZE_MARGIN;
- return genom.getSequence(beforePosition, beforeSize);
- }
-
- */
- public NucleicBuffer getSequence() {
- return sequenceData.getBuffer(position, size);
- }
-
-
- public NucleicBuffer getSpacer() {
- return sequenceData.getBuffer(position + size, spacer);
- }
-
-
- public NucleicBuffer getOpposite() {
- return sequenceData.getBuffer(position + size + spacer, size);
- }
- /*
- public Sequence getAfter() {
- int afterPosition = position + size + spacer + size;
- int afterSize = (afterPosition > genom.getLength()) // Otestuji, zda pozice konce nalezeneho palindromu nekonci na zacatku genomu, jinymy slovy zda se nejedna o cyklu
- ? SIZE_MARGIN // Jde o cyklicky genom -> plna delka
- : (genom.getLength() > afterPosition + SIZE_MARGIN) // Nejde, pak vyberu zbytek do konce
- ? SIZE_MARGIN // Tady nezasahu je do konce
- : genom.getLength() - afterPosition; // Tady zasahuje a beru jen cast
- return genom.getSequence(afterPosition, afterSize);
- }
- */
-
- public float getMidlePosition() {
- return position + size + (spacer / 2f);
- }
-
-
- @Override
- public Iterator<Entry> iterator() {
- List<Entry> entries = new ArrayList<>();
- Iterator<Nucleotide> seq = getSequence();
- Iterator<Nucleotide> ops = getOpposite().revert();
- // Nejprve vytvorim dvojice z sekvence a jejiho protejsku
- while (seq.hasNext() && ops.hasNext()) {
- entries.add(new Entry(seq.next(), ops.next()));
- }
- // Pote pridam spacer, ale bez protejsku
- getSpacer().forEachRemaining(nuclid -> entries.add(new Entry(nuclid, Nucleotide.NONE)));
-
- // Z vytvorene sekvence vradim iterator
- // + obalim zamcenym listem, abych zabranil odsranovani polozek
- return Collections.unmodifiableList(entries).iterator();
- }
-
- public Iterator<Entry> linearFormIterator() {
- List<Entry> entries = new ArrayList<>();
- getSequence().forEachRemaining(b -> entries.add(new Entry(b, b.supplement(sequenceData.getType()))));
- getSpacer().forEachRemaining(b -> entries.add(new Entry(b, b.supplement(sequenceData.getType()))));
- getOpposite().forEachRemaining(b -> entries.add(new Entry(b, b.supplement(sequenceData.getType()))));
- // Z vytvorene sekvence vradim iterator
- // + obalim zamcenym listem, abych zabranil odsranovani polozek
- return Collections.unmodifiableList(entries).iterator();
- }
-
-
- public long getMismatches() {
- return mismatches;
- }
-
- public int getPosition() {
- return position;
- }
-
- public int getDirection() {
- return 0;
- }
-
- public int getSize() {
- return size;
- }
-
- public int getLength() {
- return 2 * size + spacer;
- }
-
- @Data
- public static class Entry {
-
- private final Nucleotide nuclid;
-
- private final Nucleotide oposite;
- }
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/StabilityModel.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/StabilityModel.java
deleted file mode 100644
index 69a61b8..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/model/StabilityModel.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.model;
-
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.stability.NNModelStabilityCalculator;
-import cz.mendelu.dnaAnalyser.analyse.palindrome.stability.StabilityCalculator;
-
-import java.util.function.Supplier;
-
-public enum StabilityModel {
-
- NN_MODEL_STABILITY(NNModelStabilityCalculator::new);
-
- private Supplier<StabilityCalculator> supplier;
-
- StabilityModel(Supplier<StabilityCalculator> supplier) {
- this.supplier = supplier;
- }
-
- public StabilityCalculator stabilityCalculator() {
- return supplier.get();
- }
-
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/NNModelStabilityCalculator.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/NNModelStabilityCalculator.java
deleted file mode 100644
index 5506d78..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/NNModelStabilityCalculator.java
+++ /dev/null
@@ -1,78 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.stability;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-
-public class NNModelStabilityCalculator implements StabilityCalculator {
-
- private static final Map<String, Double> table = new HashMap<>();
- static {
- table.put("AA/TT", -1.00);
- table.put("AT/TA", -0.88);
- table.put("AC/TG", -1.45);
- table.put("AG/TC", -1.00);
-
- table.put("TA/AT", -0.58);
- table.put("TT/AA", -1.00);
- table.put("TC/AG", -1.00);
- table.put("TG/AC", -1.45);
-
- table.put("CA/GT", -1.45);
- table.put("CT/GA", -1.28);
- table.put("CC/GG", -1.84);
- table.put("CG/GC", -2.17);
-
- table.put("GA/CT", -1.30);
- table.put("GT/CA", -1.44);
- table.put("GC/CG", -2.24);
- table.put("GG/CC", -1.84);
-
- table.put("G-C", 0.98);
- table.put("C-G", 0.98);
- table.put("A-T", 1.03);
- table.put("T-A", 1.03);
- }
-
- @Override
- public double calculateCruciForm(PalindromeModel palindromeModel) {
- return calculate(palindromeModel.iterator());
- }
-
- @Override
- public double calculateLinearForm(PalindromeModel palindromeModel) {
- return calculate(palindromeModel.linearFormIterator());
- }
-
- private double calculate(Iterator<PalindromeModel.Entry> i) {
- PalindromeModel.Entry first = i.next();
- PalindromeModel.Entry second;
-
- double sum = table.getOrDefault(makeKey(first), 0.0);
- while (i.hasNext()) {
- second = i.next();
- String key = makeKey(first, second);
- double value = table.getOrDefault(key, 0.0);
- sum += value;
- first = second;
- }
- sum += table.getOrDefault(makeKey(first), 0.0);
- return sum;
- }
-
- private String makeKey(PalindromeModel.Entry first, PalindromeModel.Entry second) {
- return first.getNuclid().name()
- + second.getNuclid().name()
- + "/"
- + first.getOposite().name()
- + second.getOposite().name();
- }
-
- private String makeKey(PalindromeModel.Entry entry) {
- return entry.getNuclid().name()
- + "-"
- + entry.getOposite().name();
- }
-}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/StabilityCalculator.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/StabilityCalculator.java
deleted file mode 100644
index c39b02f..0000000
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/palindrome/stability/StabilityCalculator.java
+++ /dev/null
@@ -1,13 +0,0 @@
-package cz.mendelu.dnaAnalyser.analyse.palindrome.stability;
-
-import cz.mendelu.dnaAnalyser.analyse.palindrome.model.PalindromeModel;
-
-/**
- * Created by xkoloma1 on 19.11.2015.
- */
-public interface StabilityCalculator {
-
- double calculateCruciForm(PalindromeModel palindromeModel);
-
- double calculateLinearForm(PalindromeModel palindromeModel);
-}
\ No newline at end of file
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/overlay/OverlayService.java b/src/main/java/cz/mendelu/dnaAnalyser/overlay/OverlayService.java
index 4877410..521c8a0 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/overlay/OverlayService.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/overlay/OverlayService.java
@@ -3,7 +3,6 @@ package cz.mendelu.dnaAnalyser.overlay;
import cz.mendelu.dnaAnalyser.analyse.g4hunter.G4Hunter;
import cz.mendelu.dnaAnalyser.analyse.g4hunter.G4HunterService;
import cz.mendelu.dnaAnalyser.analyse.g4hunter.quadruplex.*;
-import cz.mendelu.dnaAnalyser.analyse.palindrome.PalindromeAnalyse;
import cz.mendelu.dnaAnalyser.analyse.rloopr.*;
import cz.mendelu.dnaAnalyser.sequence.annotation.Annotation;
import cz.mendelu.dnaAnalyser.sequence.annotation.AnnotationService;
@@ -163,8 +162,6 @@ public class OverlayService {
}
}else if (analyse instanceof Rloop){
result = rloopDataSessionService.annotationOverlay(RloopMapper.class, annotation, session, result, groupBy, labelGroupBy, intervals, groupIntervals, from, to);
- }else if (analyse instanceof PalindromeAnalyse){
- //TODO PalindromeDataSessionService?
}
return result;
--
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