Output to text window added

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index daae7c5..5f0bf68 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -279,19 +279,13 @@ public class Alignment implements AlignmentI
 \r
 \r
     /**    */\r
-    public SequenceGroup findGroup(int i)\r
-    {\r
-        return findGroup(getSequenceAt(i));\r
-    }\r
-\r
-    /**    */\r
     public SequenceGroup findGroup(SequenceI s)\r
     {\r
         for (int i = 0; i < this.groups.size(); i++)\r
         {\r
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 \r
-            if (sg.sequences.contains(s))\r
+            if (sg.getSequences(false).contains(s))\r
             {\r
                 return sg;\r
             }\r
@@ -315,14 +309,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)\r
         {\r
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-            if(sg==null || sg.sequences==null)\r
+            if(sg==null || sg.getSequences(false)==null)\r
             {\r
               this.deleteGroup(sg);\r
               gSize--;\r
               continue;\r
             }\r
 \r
-            if (sg.sequences.contains(s))\r
+            if (sg.getSequences(false).contains(s))\r
             {\r
                 temp.addElement(sg);\r
             }\r
@@ -481,9 +475,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)\r
         {\r
             Sequence seq = (Sequence) sequences.elementAt(i);\r
-            seq.sequence = seq.sequence.replace('.', gc);\r
-            seq.sequence = seq.sequence.replace('-', gc);\r
-            seq.sequence = seq.sequence.replace(' ', gc);\r
+            seq.setSequence( seq.getSequence().replace('.', gc) );\r
+            seq.setSequence( seq.getSequence().replace('-', gc) );\r
+            seq.setSequence( seq.getSequence().replace(' ', gc) );\r
         }\r
     }\r
 \r