If sequence is null, dont add it

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 161c010..dc22704 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -119,39 +119,16 @@ public class SequenceGroup
       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
+                             seq.findPosition(startRes),\r
+                             findEndRes(seq));\r
+\r
       seqs[i].setDescription(seq.getDescription());\r
       seqs[i].setDBRef(seq.getDBRef());\r
       seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
@@ -169,6 +146,34 @@ public class SequenceGroup
 \r
     }\r
 \r
+    /**\r
+     * If sequence ends in gaps, the end residue can\r
+     * be correctly calculated here\r
+     * @param seq SequenceI\r
+     * @return int\r
+     */\r
+    public int findEndRes(SequenceI seq)\r
+    {\r
+      int eres = 0;\r
+      char ch;\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
+      return eres;\r
+    }\r
+\r
     public Vector getSequences(boolean includeHidden)\r
     {\r
       if(!includeHidden)\r
@@ -196,6 +201,18 @@ public class SequenceGroup
       }\r
     }\r
 \r
+    public SequenceI[] getSequencesAsArray(boolean includeHidden)\r
+    {\r
+      Vector tmp = getSequences(includeHidden);\r
+      if(tmp==null)\r
+        return null;\r
+      SequenceI [] result = new SequenceI[tmp.size()];\r
+      for(int i=0; i<result.length; i++)\r
+        result[i] = (SequenceI)tmp.elementAt(i);\r
+\r
+      return result;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -300,7 +317,7 @@ public class SequenceGroup
      */\r
     public void addSequence(SequenceI s, boolean recalc)\r
     {\r
-        if (!sequences.contains(s))\r
+        if (s!=null && !sequences.contains(s))\r
         {\r
             sequences.addElement(s);\r
         }\r
@@ -319,31 +336,37 @@ 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
@@ -572,25 +595,16 @@ public class SequenceGroup
      */\r
     public SequenceI[] getSequencesInOrder(AlignmentI al)\r
     {\r
-        int sz = sequences.size();\r
-        java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
-        SequenceI[] seqs = new SequenceI[sz];\r
+        int sSize = sequences.size();\r
+        int alHeight = al.getHeight();\r
 \r
-        for (int i = 0; i < sz; i++)\r
-        {\r
-            SequenceI seq = (SequenceI) sequences.elementAt(i);\r
-            int index = al.findIndex(seq);\r
-            orderedSeqs.put(index + "", seq);\r
-        }\r
+        SequenceI[] seqs = new SequenceI[sSize];\r
 \r
         int index = 0;\r
-\r
-        for (int i = 0; i < al.getHeight(); i++)\r
+        for (int i = 0; i < alHeight && index<sSize; i++)\r
         {\r
-            if (orderedSeqs.containsKey(i + ""))\r
-            {\r
-                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");\r
-            }\r
+          if(sequences.contains( al.getSequenceAt(i) ) )\r
+            seqs[index++] = al.getSequenceAt(i);\r
         }\r
 \r
         return seqs;\r