only set new layout if 2 buttons visible

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index ecdf2bc..272d81d 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -113,6 +113,62 @@ public class SequenceGroup
         endRes = end;\r
     }\r
 \r
+    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)\r
+    {\r
+      int iSize = sequences.size();\r
+      SequenceI [] seqs = new SequenceI[iSize];\r
+      SequenceI [] inorder = getSequencesInOrder(align);\r
+\r
+    char ch;\r
+    int sres, eres;\r
+\r
+    for (int i = 0; i < iSize; i++)\r
+    {\r
+      SequenceI seq = inorder[i];\r
+\r
+      //FIND START RES\r
+      //Returns residue following index if gap\r
+      sres = seq.findPosition(startRes);\r
+\r
+      //FIND END RES\r
+      //Need to find the residue preceeding index if gap\r
+      eres = 0;\r
+\r
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+      {\r
+        ch = seq.getCharAt(j);\r
+        if (!jalview.util.Comparison.isGap( (ch)))\r
+        {\r
+          eres++;\r
+        }\r
+      }\r
+\r
+      if (eres > 0)\r
+      {\r
+        eres += seq.getStart() - 1;\r
+      }\r
+\r
+      seqs[i] = new Sequence(seq.getName(),\r
+                             seq.getSequence(startRes, endRes + 1),\r
+                             sres,\r
+                             eres);\r
+      seqs[i].setDescription(seq.getDescription());\r
+      seqs[i].setDBRef(seq.getDBRef());\r
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+      if (seq.getDatasetSequence() != null)\r
+        seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+      if(seq.getAnnotation()!=null)\r
+      {\r
+        for(int a=0; a<seq.getAnnotation().length; a++)\r
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+      }\r
+    }\r
+\r
+    return seqs;\r
+\r
+    }\r
+\r
     public Vector getSequences(boolean includeHidden)\r
     {\r
       if(!includeHidden)\r
@@ -263,31 +319,37 @@ public class SequenceGroup
         if(cs == null)\r
           return;\r
 \r
-        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
-\r
-\r
-        if (cs instanceof ClustalxColourScheme)\r
+        try\r
         {\r
-            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
-        }\r
+          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
 \r
+          if (cs instanceof ClustalxColourScheme)\r
+          {\r
+            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
+          }\r
 \r
-        if (cs.conservationApplied())\r
-        {\r
+          if (cs.conservationApplied())\r
+          {\r
             Conservation c = new Conservation(groupName,\r
-                    ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+                                              ResidueProperties.propHash, 3, sequences,\r
+                                              0, getWidth());\r
             c.calculate();\r
             c.verdict(false, 25);\r
 \r
-\r
             cs.setConservation(c);\r
 \r
             if (cs instanceof ClustalxColourScheme)\r
             {\r
-                ((ClustalxColourScheme) cs).resetClustalX(sequences,\r
-                    getWidth());\r
+              ( (ClustalxColourScheme) cs).resetClustalX(sequences,\r
+                                                         getWidth());\r
             }\r
+          }\r
+        }\r
+        catch (java.lang.OutOfMemoryError err)\r
+        {\r
+          System.out.println("Out of memory loading groups: " + err);\r
         }\r
+\r
     }\r
 \r
     /**\r