Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 70a3cc2..5232f8e 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -195,6 +195,7 @@ public class Alignment implements AlignmentI, AutoCloseable
   {
     synchronized (sequences)
     {
+
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -616,15 +617,17 @@ public class Alignment implements AlignmentI, AutoCloseable
   @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
-
+    if (token == null)
+      return null;
     int i = 0;
     SequenceI sq = null;
     String sqname = null;
+    int nseq = sequences.size();
     if (startAfter != null)
     {
       // try to find the sequence in the alignment
       boolean matched = false;
-      while (i < sequences.size())
+      while (i < nseq)
       {
         if (getSequenceAt(i++) == startAfter)
         {
@@ -637,7 +640,7 @@ public class Alignment implements AlignmentI, AutoCloseable
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
@@ -740,7 +743,7 @@ public class Alignment implements AlignmentI, AutoCloseable
   public int getWidth()
   {
     int maxLength = -1;
-  
+
     for (int i = 0; i < sequences.size(); i++)
     {
       maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
@@ -1219,7 +1222,8 @@ public class Alignment implements AlignmentI, AutoCloseable
     int maxLength = -1;
 
     SequenceI current;
-    for (int i = 0; i < sequences.size(); i++)
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
@@ -1236,7 +1240,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
@@ -1628,34 +1632,50 @@ public class Alignment implements AlignmentI, AutoCloseable
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    if (annotations != null)
+    AlignmentAnnotation annot = annotations == null ? null
+            : AlignmentAnnotation.findFirstAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), name, calcId,
+              autoCalc, seqRef, groupRef);
+
+    if (annot == null)
     {
-      for (AlignmentAnnotation annot : getAlignmentAnnotation())
+
+      annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f,
+              AlignmentAnnotation.BAR_GRAPH);
+      annot.hasText = false;
+      if (calcId != null)
       {
-        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
-                && (calcId == null || annot.getCalcId().equals(calcId))
-                && annot.sequenceRef == seqRef
-                && annot.groupRef == groupRef)
-        {
-          return annot;
-        }
+        annot.setCalcId(calcId);
+      }
+      annot.autoCalculated = autoCalc;
+      if (seqRef != null)
+      {
+        annot.setSequenceRef(seqRef);
       }
+      annot.groupRef = groupRef;
+      addAnnotation(annot);
     }
-    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
-            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
-    annot.hasText = false;
-    if (calcId != null)
+    return annot;
+  }
+
+
+  @Override
+  public AlignmentAnnotation updateFromOrCopyAnnotation(
+          AlignmentAnnotation ala)
+  {
+    AlignmentAnnotation annot = AlignmentAnnotation.findFirstAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), ala.label, ala.calcId,
+            ala.autoCalculated, ala.sequenceRef, ala.groupRef);
+    if (annot == null)
     {
-      annot.setCalcId(calcId);
+      annot = new AlignmentAnnotation(ala);
+      addAnnotation(annot);
     }
-    annot.autoCalculated = autoCalc;
-    if (seqRef != null)
+    else
     {
-      annot.setSequenceRef(seqRef);
+      annot.updateAlignmentAnnotationFrom(ala);
     }
-    annot.groupRef = groupRef;
-    addAnnotation(annot);
-
+    validateAnnotation(annot);
     return annot;
   }