JAL-961 allow calcId to be specified independently of alignment annotation row label

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6c11936..271374f 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1381,12 +1381,14 @@ public class Alignment implements AlignmentI
 
   @Override
   public AlignmentAnnotation findOrCreateAnnotation(String name,
-          boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
+          String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
   {
+    assert(name!=null);
     for (AlignmentAnnotation annot : getAlignmentAnnotation())
     {
       if (annot.autoCalculated == autoCalc
-              && annot.getCalcId().equals(name)
+              && (name.equals(annot.label))
+              && (calcId==null || annot.getCalcId().equals(calcId))
               && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
       {
         return annot;
@@ -1395,7 +1397,7 @@ public class Alignment implements AlignmentI
     AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
             new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
     annot.hasText = false;
-    annot.setCalcId(new String(name));
+    annot.setCalcId(new String(calcId));
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
     {

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index d09c41d..7e55e36 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -438,15 +438,17 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * search for or create a specific annotation row on the alignment
-   *
-   * @param method - CalcId for the annotation (must match)
+   * @param name name for annotation (must match)
+   * @param calcId calcId for the annotation (null or must match)
    * @param autoCalc - value of autocalc flag for the annotation
    * @param seqRef - null or specific sequence reference
    * @param groupRef - null or specific group reference
+   * @param method - CalcId for the annotation (must match)
+   *
    * @return existing annotation matching the given attributes
    */
-  public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
-          SequenceI seqRef, SequenceGroup groupRef);
+  public AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
+          boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
 
   /**
    * move the given group up or down in the alignment by the given number of rows.

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index cf33671..9c75878 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -482,7 +482,7 @@ public class TCoffeeScoreFile extends AlignFile {
              }
            }
            // this will overwrite any existing t-coffee scores for the alignment
-           AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,false,s,null);
+           AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,TCOFFEE_SCORE,false,s, null);
            if (s!=null)
            {
              aa.label="T-COFFEE";

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index 2c2c7cb..b2c9d4d 100644 (file)
--- a/src/jalview/ws/jws2/AAConsClient.java
+++ b/src/jalview/ws/jws2/AAConsClient.java
@@ -73,8 +73,9 @@ public class AAConsClient extends JabawsAlignCalcWorker
           {
             // simple annotation row
             annotation = alignViewport.getAlignment()
-                    .findOrCreateAnnotation(scr.getMethod(), true, null,
-                            null);
+                    .findOrCreateAnnotation(scr.getMethod(), getCalcId(), true,
+                            null, null);
+
             Annotation[] elm = new Annotation[alWidth];
             if (alWidth == gapMap.length) // scr.getScores().size())
             {