X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=f640ebbb66a19906392b18c37217c3038dd4f595;hb=7b3241c464d774516c4295a5023f4aef7939298e;hp=2eed50cb6f359c2919f432bdb3cf7345cae0bf6d;hpb=3193f6774b111974d609ea5d5adc95ff50f92b68;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2eed50c..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.
@@ -119,39 +123,16 @@ public class SequenceGroup
       SequenceI [] seqs = new SequenceI[iSize];
       SequenceI [] inorder = getSequencesInOrder(align);
 
-    char ch;
-    int sres, eres;
 
     for (int i = 0; i < iSize; i++)
     {
       SequenceI seq = inorder[i];
 
-      //FIND START RES
-      //Returns residue following index if gap
-      sres = seq.findPosition(startRes);
-
-      //FIND END RES
-      //Need to find the residue preceeding index if gap
-      eres = 0;
-
-      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
-      {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
-        {
-          eres++;
-        }
-      }
-
-      if (eres > 0)
-      {
-        eres += seq.getStart() - 1;
-      }
-
       seqs[i] = new Sequence(seq.getName(),
                              seq.getSequence(startRes, endRes + 1),
-                             sres,
-                             eres);
+                             seq.findPosition(startRes),
+                             findEndRes(seq));
+
       seqs[i].setDescription(seq.getDescription());
       seqs[i].setDBRef(seq.getDBRef());
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
@@ -169,6 +150,34 @@ public class SequenceGroup
 
     }
 
+    /**
+     * If sequence ends in gaps, the end residue can
+     * be correctly calculated here
+     * @param seq SequenceI
+     * @return int
+     */
+    public int findEndRes(SequenceI seq)
+    {
+      int eres = 0;
+      char ch;
+
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
+        {
+          eres++;
+        }
+      }
+
+      if (eres > 0)
+      {
+        eres += seq.getStart() - 1;
+      }
+
+      return eres;
+    }
+
     public Vector getSequences(boolean includeHidden)
     {
       if(!includeHidden)
@@ -196,6 +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!
      *
@@ -300,7 +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);
         }
@@ -321,7 +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)
           {
@@ -332,7 +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);