X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=272d81de257978e7dc9a3f4d56208bb37dc2ad5a;hb=89a0b775abfaa90242a171ca8133784a424a3d7b;hp=054896b2eca8854988efd7ebb52e5f8aa5cf6582;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 054896b..272d81d 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -41,9 +41,7 @@ public class SequenceGroup
     boolean displayBoxes;
     boolean displayText;
     boolean colourText;
-
-    /** DOCUMENT ME!! */
-    public Vector sequences = new Vector();
+    private Vector sequences = new Vector();
     int width = -1;
 
     /** DOCUMENT ME!! */
@@ -115,6 +113,89 @@ public class SequenceGroup
         endRes = end;
     }
 
+    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
+    {
+      int iSize = sequences.size();
+      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);
+      seqs[i].setDescription(seq.getDescription());
+      seqs[i].setDBRef(seq.getDBRef());
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
+      if (seq.getDatasetSequence() != null)
+        seqs[i].setDatasetSequence(seq.getDatasetSequence());
+
+      if(seq.getAnnotation()!=null)
+      {
+        for(int a=0; a<seq.getAnnotation().length; a++)
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+      }
+    }
+
+    return seqs;
+
+    }
+
+    public Vector getSequences(boolean includeHidden)
+    {
+      if(!includeHidden)
+        return sequences;
+      else
+      {
+        Vector allSequences = new Vector();
+        SequenceI seq;
+        for (int i = 0; i < sequences.size(); i++)
+        {
+          seq = (SequenceI) sequences.elementAt(i);
+          allSequences.addElement(seq);
+          if (seq.getHiddenSequences() != null)
+          {
+            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
+            {
+              allSequences.addElement(
+                  seq.getHiddenSequences().getSequenceAt(h)
+                  );
+            }
+          }
+        }
+
+        return allSequences;
+      }
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -235,32 +316,40 @@ public class SequenceGroup
      */
     public void recalcConservation()
     {
-        if (cs != null)
-        {
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-        }
+        if(cs == null)
+          return;
 
-        if (cs instanceof ClustalxColourScheme)
+        try
         {
-            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
+          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
 
-        if (cs instanceof ConservationColourScheme)
-        {
+          if (cs instanceof ClustalxColourScheme)
+          {
+            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+          }
+
+          if (cs.conservationApplied())
+          {
             Conservation c = new Conservation(groupName,
-                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
+                                              ResidueProperties.propHash, 3, sequences,
+                                              0, getWidth());
             c.calculate();
             c.verdict(false, 25);
 
-            ConservationColourScheme ccs = (ConservationColourScheme) cs;
-            ccs.conserve = c;
+            cs.setConservation(c);
 
-            if (ccs.cs instanceof ClustalxColourScheme)
+            if (cs instanceof ClustalxColourScheme)
             {
-                ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,
-                    getWidth());
+              ( (ClustalxColourScheme) cs).resetClustalX(sequences,
+                                                         getWidth());
             }
+          }
+        }
+        catch (java.lang.OutOfMemoryError err)
+        {
+          System.out.println("Out of memory loading groups: " + err);
         }
+
     }
 
     /**
@@ -342,9 +431,24 @@ public class SequenceGroup
      *
      * @return DOCUMENT ME!
      */
-    public int getSize()
+    public int getSize(boolean includeHidden)
     {
+      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;
+      }
     }
 
     /**