JAL-3453 Some tests require different Desktop constructor

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 98510e3..7b97d49 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -42,13 +42,13 @@ import java.util.Vector;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
- */
-/**
- * @author JimP
  * 
+ * @author JimP
  */
 public class Alignment implements AlignmentI
 {
+  private static final SequenceGroup[] NO_GROUPS = new SequenceGroup[0];
+
   private Alignment dataset;
 
   private List<SequenceI> sequences;
@@ -59,6 +59,13 @@ public class Alignment implements AlignmentI
 
   private boolean nucleotide = true;
 
+  private List<AlignedCodonFrame> codonFrameList;
+
+  /*
+   * persistent object to hold result of findAllGroups(SequenceI)
+   */
+  private List<SequenceGroup> groupsForSequence = new ArrayList<>();
+
   public boolean hasRNAStructure = false;
 
   public AlignmentAnnotation[] annotations;
@@ -69,8 +76,6 @@ public class Alignment implements AlignmentI
 
   public Hashtable alignmentProperties;
 
-  private List<AlignedCodonFrame> codonFrameList;
-
   private void initAlignment(SequenceI[] seqs)
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
@@ -398,10 +403,6 @@ public class Alignment implements AlignmentI
     return null;
   }
 
-  private static final SequenceGroup[] noGroups = new SequenceGroup[0];
-
-  private ArrayList<SequenceGroup> temp = new ArrayList<>();
-
   /*
    * (non-Javadoc)
    * 
@@ -411,15 +412,14 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-
     synchronized (groups)
     {
       int gSize = groups.size();
       if (gSize == 0)
       {
-        return noGroups;
+        return NO_GROUPS;
       }
-      temp.clear();
+      groupsForSequence.clear();
       for (int i = 0; i < gSize; i++)
       {
         SequenceGroup sg = groups.get(i);
@@ -432,12 +432,12 @@ 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);
   }
 
   /**    */
@@ -2034,17 +2034,4 @@ public class Alignment implements AlignmentI
     }
   }
 
-  @Override
-  public void resetColors()
-  {
-    for (int i = getHeight(); --i >= 0;)
-    {
-      sequences.get(i).resetColors();
-    }
-    // if (dataset != null)
-    // {
-    // dataset.resetColors();
-    // }
-  }
-
 }