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 97ecfb3fd11c6bf7152742ca23fa9b5a6c377c38..e3f1c36860d47bad87b9cc8585bbfbc21861a26f 100644 --- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java +++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyseResult.java @@ -21,6 +21,7 @@ public class ZdnaAnalyseResult implements Localised { protected double zdnaGTRichness; protected float score; + protected float score10bp; @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 fc4183bdc468d17e805b2ca655571672c1cf2288..44bcb331586c468f25cfd620f1d0562627833b8c 100644 --- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java +++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaAnalyser.java @@ -65,9 +65,10 @@ 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); + null, start, len, seq, richnessGC, richnessGT, kvScore, score10bp); allResults.add(zdnaResult); } 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 3b0b523ebe88d6bfe8e40820026cea2ab08fc775..e705a6098dba055f0436078dee5162d37a0fb77b 100644 --- a/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java +++ b/src/main/java/cz/mendelu/dnaAnalyser/analyse/zdna/ZdnaMapper.java @@ -20,6 +20,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { "ZDNAGCRICHNESS varchar, " + "ZDNAGTRICHNESS varchar, " + "SCORE float, " + + "SCORE10BP float," + "PRIMARY KEY (ID))"; // language=SQL @@ -35,7 +36,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) ArrayList<ZdnaAnalyseResult> getAll(); @@ -48,7 +50,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) ArrayList<ZdnaAnalyseResult> getByWindow(Integer start, Integer end); @@ -61,7 +64,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) Cursor<ZdnaAnalyseResult> getCursor(); @@ -74,7 +78,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) ZdnaAnalyseResult getById(int id); @@ -86,6 +91,7 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { "ZDNAGCRICHNESS = #{zdnaGCRichness}, " + "ZDNAGTRICHNESS = #{zdnaGTRichness} " + "SCORE = #{score} " + + "SCORE10BP = #{score10bp} " + "WHERE ID = #{id}") void update(ZdnaAnalyseResult result); @@ -94,9 +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)" + + @Insert("INSERT INTO ZDNA (ID, POSITION, LENGTH, SEQUENCE, ZDNAGCRICHNESS, ZDNAGTRICHNESS, SCORE, SCORE10BP)" + " VALUES " + - "(#{id}, #{position}, #{length}, #{sequence}, #{zdnaGCRichness}, #{zdnaGTRichness}, #{score})" + "(#{id}, #{position}, #{length}, #{sequence}, #{zdnaGCRichness}, #{zdnaGTRichness}, #{score}, #{score10bp})" ) @Options(useGeneratedKeys = true, keyProperty = "id") void insert(ZdnaAnalyseResult result); @@ -116,7 +122,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) List<ZdnaAnalyseResult> getAllBetweenPositionOrderAsc( @Param("startPosition") int startPosition, @@ -133,7 +140,8 @@ public interface ZdnaMapper extends DataLocalisedMapper<ZdnaAnalyseResult> { @Result(property = "sequence", column = "SEQUENCE"), @Result(property = "zdnaGCRichness", column = "ZDNAGCRICHNESS"), @Result(property = "zdnaGTRichness", column = "ZDNAGTRICHNESS"), - @Result(property = "score", column = "SCORE") + @Result(property = "score", column = "SCORE"), + @Result(property = "score10bp", column = "SCORE10BP") }) List<ZdnaAnalyseResult> getAllBetweenPositionOrderDesc( @Param("startPosition") int startPosition,