Don't parse input id, leave it as it is

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 309fdae..3a1b44a 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -458,11 +458,9 @@ public class Alignment implements AlignmentI
 \r
         while (i < sequences.size())\r
         {\r
-            SequenceI s = getSequenceAt(i);\r
-\r
-            if (s.getName().equals(name))\r
+            if (getSequenceAt(i).getName().equals(name))\r
             {\r
-                return s;\r
+                return getSequenceAt(i);\r
             }\r
 \r
             i++;\r
@@ -471,25 +469,6 @@ public class Alignment implements AlignmentI
         return null;\r
     }\r
 \r
-    /**    */\r
-    public SequenceI findbyDisplayId(String name)\r
-    {\r
-        int i = 0;\r
-\r
-        while (i < sequences.size())\r
-        {\r
-            SequenceI s = getSequenceAt(i);\r
-\r
-            if (s.getDisplayId().equals(name))\r
-            {\r
-                return s;\r
-            }\r
-\r
-            i++;\r
-        }\r
-\r
-        return null;\r
-    }\r
 \r
     /**    */\r
     public int findIndex(SequenceI s)\r
@@ -724,13 +703,15 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < getHeight(); i++)\r
         {\r
 \r
-          seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+          seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true),\r
                                  AlignSeq.extractGaps(\r
                                      jalview.util.Comparison.GapChars,\r
                                      getSequenceAt(i).getSequence()\r
                                  ),\r
                                  getSequenceAt(i).getStart(),\r
                                  getSequenceAt(i).getEnd());\r
+\r
+          getSequenceAt(i).setDatasetSequence(seqs[i]);\r
         }\r
 \r
         dataset = new Alignment(seqs);\r