X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=76a350f9a757c4c9af615592420b5f7b0fd78c74;hb=1d6bdfa4ce1d88c055a257e542de6b8542144d91;hp=2bdd5f84f170d727e589511c12f0bf06c8542ca8;hpb=7abeaf76ba3913ccb95139df58b353bdde49429c;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2bdd5f8..76a350f 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];
@@ -173,25 +178,27 @@ public class SequenceGroup
       return eres;
     }
 
-    public Vector getSequences(boolean includeHidden)
+    public Vector getSequences(Hashtable hiddenReps)
     {
-      if(!includeHidden)
+      if(hiddenReps == null)
         return sequences;
       else
       {
         Vector allSequences = new Vector();
-        SequenceI seq;
+        SequenceI seq, seq2;
         for (int i = 0; i < sequences.size(); i++)
         {
           seq = (SequenceI) sequences.elementAt(i);
           allSequences.addElement(seq);
-          if (seq.getHiddenSequences() != null)
+          if (hiddenReps.containsKey(seq) )
           {
-            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
+            SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);
+            for (int h = 0; h < hsg.getSize(); h++)
             {
-              allSequences.addElement(
-                  seq.getHiddenSequences().getSequenceAt(h)
-                  );
+              seq2 = hsg.getSequenceAt(h);
+              if (seq2 != seq
+                  && !allSequences.contains(seq2))
+                allSequences.addElement(seq2);
             }
           }
         }
@@ -200,9 +207,9 @@ public class SequenceGroup
       }
     }
 
-    public SequenceI[] getSequencesAsArray(boolean includeHidden)
+    public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
     {
-      Vector tmp = getSequences(includeHidden);
+      Vector tmp = getSequences(hiddenReps);
       if(tmp==null)
         return null;
       SequenceI [] result = new SequenceI[tmp.size()];
@@ -316,7 +323,7 @@ public class SequenceGroup
      */
     public void addSequence(SequenceI s, boolean recalc)
     {
-        if (!sequences.contains(s))
+        if (s!=null && !sequences.contains(s))
         {
             sequences.addElement(s);
         }
@@ -337,7 +344,7 @@ public class SequenceGroup
 
         try
         {
-          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+          cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
 
           if (cs instanceof ClustalxColourScheme)
           {
@@ -348,7 +355,7 @@ public class SequenceGroup
           {
             Conservation c = new Conservation(groupName,
                                               ResidueProperties.propHash, 3, sequences,
-                                              0, getWidth());
+                                              startRes, endRes+1);
             c.calculate();
             c.verdict(false, 25);
 
@@ -447,24 +454,9 @@ public class SequenceGroup
      *
      * @return DOCUMENT ME!
      */
-    public int getSize(boolean includeHidden)
+    public int getSize()
     {
-      if(!includeHidden)
         return sequences.size();
-      else
-      {
-        int total = sequences.size();
-        SequenceI seq;
-        for (int i = 0; i < sequences.size(); i++)
-        {
-          seq = (SequenceI) sequences.elementAt(i);
-          if (seq.getHiddenSequences() != null)
-          {
-            total += seq.getHiddenSequences().getSize(false);
-          }
-        }
-        return total;
-      }
     }
 
     /**