X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=dc22704ffebd62006b2d55be030b5ac20ee2e6d3;hb=23169813062957122bc246f05c2479cb36a9c509;hp=054896b2eca8854988efd7ebb52e5f8aa5cf6582;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 054896b..dc22704 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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 +113,106 @@ public class SequenceGroup
         endRes = end;
     }
 
+    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
+    {
+      int iSize = sequences.size();
+      SequenceI [] seqs = new SequenceI[iSize];
+      SequenceI [] inorder = getSequencesInOrder(align);
+
+
+    for (int i = 0; i < iSize; i++)
+    {
+      SequenceI seq = inorder[i];
+
+      seqs[i] = new Sequence(seq.getName(),
+                             seq.getSequence(startRes, endRes + 1),
+                             seq.findPosition(startRes),
+                             findEndRes(seq));
+
+      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;
+
+    }
+
+    /**
+     * 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)
+        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;
+      }
+    }
+
+    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!
      *
@@ -219,7 +317,7 @@ public class SequenceGroup
      */
     public void addSequence(SequenceI s, boolean recalc)
     {
-        if (!sequences.contains(s))
+        if (s!=null && !sequences.contains(s))
         {
             sequences.addElement(s);
         }
@@ -235,32 +333,40 @@ 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 +448,24 @@ 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;
+      }
     }
 
     /**
@@ -474,25 +595,16 @@ public class SequenceGroup
      */
     public SequenceI[] getSequencesInOrder(AlignmentI al)
     {
-        int sz = sequences.size();
-        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-        SequenceI[] seqs = new SequenceI[sz];
+        int sSize = sequences.size();
+        int alHeight = al.getHeight();
 
-        for (int i = 0; i < sz; i++)
-        {
-            SequenceI seq = (SequenceI) sequences.elementAt(i);
-            int index = al.findIndex(seq);
-            orderedSeqs.put(index + "", seq);
-        }
+        SequenceI[] seqs = new SequenceI[sSize];
 
         int index = 0;
-
-        for (int i = 0; i < al.getHeight(); i++)
+        for (int i = 0; i < alHeight && index<sSize; i++)
         {
-            if (orderedSeqs.containsKey(i + ""))
-            {
-                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
-            }
+          if(sequences.contains( al.getSequenceAt(i) ) )
+            seqs[index++] = al.getSequenceAt(i);
         }
 
         return seqs;