X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=22d23bc299735b1c469e7f4559ed4ae021099c0d;hb=08b87509ada06ac8614424247346daef4054b41a;hp=b214934a34263fb33fbf9aaa36a2b81102619e81;hpb=5721b73c6d5de84b21a989a8734e4c161f5dc630;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index b214934..22d23bc 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -59,6 +59,15 @@ public class Alignment implements AlignmentI
 
   private boolean nucleotide = true;
 
+  private List<AlignedCodonFrame> codonFrameList;
+
+  private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+  /*
+   * persistent object to hold result of findAllGroups(SequenceI)
+   */
+  private List<SequenceGroup> groupsForSequence = new ArrayList<>();
+
   public boolean hasRNAStructure = false;
 
   public AlignmentAnnotation[] annotations;
@@ -69,8 +78,6 @@ public class Alignment implements AlignmentI
 
   public Hashtable alignmentProperties;
 
-  private List<AlignedCodonFrame> codonFrameList;
-
   private void initAlignment(SequenceI[] seqs)
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
@@ -407,11 +414,14 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<>();
-
     synchronized (groups)
     {
       int gSize = groups.size();
+      if (gSize == 0)
+      {
+        return noGroups;
+      }
+      groupsForSequence.clear();
       for (int i = 0; i < gSize; i++)
       {
         SequenceGroup sg = groups.get(i);
@@ -424,12 +434,12 @@ public class Alignment implements AlignmentI
 
         if (sg.getSequences().contains(s))
         {
-          temp.add(sg);
+          groupsForSequence.add(sg);
         }
       }
     }
-    SequenceGroup[] ret = new SequenceGroup[temp.size()];
-    return temp.toArray(ret);
+    SequenceGroup[] ret = new SequenceGroup[groupsForSequence.size()];
+    return groupsForSequence.toArray(ret);
   }
 
   /**    */
@@ -2026,4 +2036,17 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void resetColors()
+  {
+    for (int i = getHeight(); --i >= 0;)
+    {
+      sequences.get(i).resetColors();
+    }
+    // if (dataset != null)
+    // {
+    // dataset.resetColors();
+    // }
+  }
+
 }