X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=f640ebbb66a19906392b18c37217c3038dd4f595;hb=01a838156a865a61389825b3c5c968b6d8eee8f3;hp=679997e3c1a4847bc086eaeb2d26445bf6da757e;hpb=70d8cbb3e0f3e4986c09d9e5e42a7997d77cf9d5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 679997e..f640ebb 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -49,6 +49,10 @@ public class SequenceGroup
     int startRes = 0;
     int endRes = 0;
     Color outlineColour = Color.black;
+    public int thresholdTextColour = 0;
+    public Color textColour = Color.black;
+    public Color textColour2 = Color.white;
+
 
     /**
      * Creates a new SequenceGroup object.
@@ -119,6 +123,7 @@ public class SequenceGroup
       SequenceI [] seqs = new SequenceI[iSize];
       SequenceI [] inorder = getSequencesInOrder(align);
 
+
     for (int i = 0; i < iSize; i++)
     {
       SequenceI seq = inorder[i];
@@ -200,6 +205,18 @@ public class SequenceGroup
       }
     }
 
+    public SequenceI[] getSequencesAsArray(boolean includeHidden)
+    {
+      Vector tmp = getSequences(includeHidden);
+      if(tmp==null)
+        return null;
+      SequenceI [] result = new SequenceI[tmp.size()];
+      for(int i=0; i<result.length; i++)
+        result[i] = (SequenceI)tmp.elementAt(i);
+
+      return result;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -304,7 +321,7 @@ public class SequenceGroup
      */
     public void addSequence(SequenceI s, boolean recalc)
     {
-        if (!sequences.contains(s))
+        if (s!=null && !sequences.contains(s))
         {
             sequences.addElement(s);
         }
@@ -325,7 +342,7 @@ public class SequenceGroup
 
         try
         {
-          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+          cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
 
           if (cs instanceof ClustalxColourScheme)
           {
@@ -336,7 +353,7 @@ public class SequenceGroup
           {
             Conservation c = new Conservation(groupName,
                                               ResidueProperties.propHash, 3, sequences,
-                                              0, getWidth());
+                                              startRes, endRes+1);
             c.calculate();
             c.verdict(false, 25);