diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java
index e3f1c36860d47bad87b9cc8585bbfbc21861a26f..fe13e79bef831c29316ae1ee6b080d7fb8f9cc25 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java
@@ -21,7 +21,7 @@ public class ZdnaAnalyseResult implements Localised {
protected double zdnaGTRichness;
protected float score;
- protected float score10bp;
+ protected float scorePerc;
@Override
public int getMiddle() {
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java
index 816145570f255c623fabd66cb5d3f723f32d341c..e938b306848508c466da4b7ae279314fd5802272 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java
@@ -26,11 +26,11 @@ public class ZdnaAnalyser {
* @param threshold minimal KV score of searched sequences.
* @return arraylist of ZdnaAnalyseResults.
*/
- public ArrayList<ZdnaAnalyseResult> getResults(Window sequenceWindow, int minSequenceSize, float threshold, float gc, float gtac, float at, float oth) {
+ public ArrayList<ZdnaAnalyseResult> getResults(Window sequenceWindow, int minSequenceSize, float threshold, float gc, float gtac, float at) {
GCscore = gc; // 1f;
GT_ACscore = gtac;// 0.5f;
ATscore = at; // 0.25f;
- notPossibleZDNA = oth; // 0;
+ notPossibleZDNA = 0;
ArrayList<ZdnaAnalyseResult> allResults = new ArrayList<>();
Pattern patternGC = Pattern.compile("(?=(GC|CG))");
@@ -55,7 +55,9 @@ public class ZdnaAnalyser {
} else {
if (len >= minSequenceSize) {
float kvScore = score/2;
- if (kvScore >= threshold) {
+ float maxPossibleScore = ((len-1) * Math.max(gc, Math.max(gtac, at))) / 2;
+ float scorePerc = (kvScore / maxPossibleScore) * 100;
+ if (scorePerc >= threshold) {
int start = i - len + 2;
StringBuilder seqB = new StringBuilder();
@@ -73,10 +75,10 @@ public class ZdnaAnalyser {
// GT
double countGT = patternGT.matcher(seq).results().count();
double richnessGT = countGT / pcLen * 100;
- float score10bp = kvScore / len * 10;
+
ZdnaAnalyseResult zdnaResult = new ZdnaAnalyseResult(
- null, start, len, seq, richnessGC, richnessGT, kvScore, score10bp*10);
+ null, start, len, seq, richnessGC, richnessGT, kvScore, scorePerc);
allResults.add(zdnaResult);
}
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaController.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaController.java
index f026f422245e21c47c7d17d807433902e39c325d..fd699e20f23b219b5fda0aff5e24b9c9495b5532 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaController.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaController.java
@@ -64,9 +64,6 @@ public class ZdnaController {
@NotNull
private float score_at = 0.25f;
- @NotNull
- private float score_oth = 0;
-
}
@Data
@@ -105,7 +102,6 @@ public class ZdnaController {
.score_gc(request.getScore_gc())
.score_gtac(request.getScore_gtac())
.score_at(request.getScore_at())
- .score_oth(request.getScore_oth())
.build()
);
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java
index e705a6098dba055f0436078dee5162d37a0fb77b..2abd75115e481124f51527bb5040cd08f615e52c 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java
@@ -20,7 +20,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
"ZDNAGCRICHNESS varchar, " +
"ZDNAGTRICHNESS varchar, " +
"SCORE float, " +
- "SCORE10BP float," +
+ "SCOREPERC float," +
"PRIMARY KEY (ID))";
// language=SQL
@@ -37,7 +37,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
ArrayList<ZdnaAnalyseResult> getAll();
@@ -51,7 +51,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
ArrayList<ZdnaAnalyseResult> getByWindow(Integer start, Integer end);
@@ -65,7 +65,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
Cursor<ZdnaAnalyseResult> getCursor();
@@ -79,7 +79,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
ZdnaAnalyseResult getById(int id);
@@ -91,7 +91,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
"ZDNAGCRICHNESS = #{zdnaGCRichness}, " +
"ZDNAGTRICHNESS = #{zdnaGTRichness} " +
"SCORE = #{score} " +
- "SCORE10BP = #{score10bp} " +
+ "SCOREPERC = #{scorePerc} " +
"WHERE ID = #{id}")
void update(ZdnaAnalyseResult result);
@@ -100,9 +100,9 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
void delete(int id);
// language=SQL
- @Insert("INSERT INTO ZDNA (ID, POSITION, LENGTH, SEQUENCE, ZDNAGCRICHNESS, ZDNAGTRICHNESS, SCORE, SCORE10BP)" +
+ @Insert("INSERT INTO ZDNA (ID, POSITION, LENGTH, SEQUENCE, ZDNAGCRICHNESS, ZDNAGTRICHNESS, SCORE, SCOREPERC)" +
" VALUES " +
- "(#{id}, #{position}, #{length}, #{sequence}, #{zdnaGCRichness}, #{zdnaGTRichness}, #{score}, #{score10bp})"
+ "(#{id}, #{position}, #{length}, #{sequence}, #{zdnaGCRichness}, #{zdnaGTRichness}, #{score}, #{scorePerc})"
)
@Options(useGeneratedKeys = true, keyProperty = "id")
void insert(ZdnaAnalyseResult result);
@@ -123,7 +123,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
List<ZdnaAnalyseResult> getAllBetweenPositionOrderAsc(
@Param("startPosition") int startPosition,
@@ -141,7 +141,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> {
@Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"),
@Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"),
@Result(property = "score", column = "SCORE"),
- @Result(property = "score10bp", column = "SCORE10BP")
+ @Result(property = "scorePerc", column = "SCOREPERC")
})
List<ZdnaAnalyseResult> getAllBetweenPositionOrderDesc(
@Param("startPosition") int startPosition,
diff --git a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaService.java b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaService.java
index d4fa6516291331fe7543d200c8969ba0dd487a44..37fe7580a58869fde33057a34b0051b3425bf210 100644
--- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaService.java
+++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaService.java
@@ -62,7 +62,6 @@ public class ZdnaService extends ModelService<Zdna> {
float score_gc = analyse.getScore_gc();
float score_gtac = analyse.getScore_gtac();
float score_at = analyse.getScore_at();
- float score_oth = analyse.getScore_oth();
if (sequence.getLength() < minSequenceSize) {
@@ -75,7 +74,7 @@ public class ZdnaService extends ModelService<Zdna> {
String sequenceDataPlain = sequenceData.toPlain();
Window sequenceWindow = BufferedWindow.wrap(sequenceDataPlain);
- ArrayList<ZdnaAnalyseResult> results = zdnaAnalyser.getResults(sequenceWindow, minSequenceSize, threshold, score_gc, score_gtac, score_at, score_oth);
+ ArrayList<ZdnaAnalyseResult> results = zdnaAnalyser.getResults(sequenceWindow, minSequenceSize, threshold, score_gc, score_gtac, score_at);
results.forEach(zdnaMapper::insert);
diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml
index b7e8d473a247e5ac0be8a617c173a74776db518d..c8778c4a7068e2e5829a0311b7840fa7dcb61679 100644
--- a/src/main/resources/application.yaml
+++ b/src/main/resources/application.yaml
@@ -94,7 +94,7 @@ security:
jwt:
header: Authorization
secret: secret
- expiration: 604800
+ expiration: 21600
importDefaultUsers: true
management:
swagger: enabled