currentSeq and set description in dataset

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 679997e..df8c6ea 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -119,6 +119,7 @@ public class SequenceGroup
       SequenceI [] seqs = new SequenceI[iSize];\r
       SequenceI [] inorder = getSequencesInOrder(align);\r
 \r
+\r
     for (int i = 0; i < iSize; i++)\r
     {\r
       SequenceI seq = inorder[i];\r
@@ -200,6 +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
@@ -304,7 +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
@@ -325,7 +338,7 @@ public class SequenceGroup
 \r
         try\r
         {\r
-          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+          cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));\r
 \r
           if (cs instanceof ClustalxColourScheme)\r
           {\r
@@ -336,7 +349,7 @@ public class SequenceGroup
           {\r
             Conservation c = new Conservation(groupName,\r
                                               ResidueProperties.propHash, 3, sequences,\r
-                                              0, getWidth());\r
+                                              startRes, endRes+1);\r
             c.calculate();\r
             c.verdict(false, 25);\r
 \r