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 67864e8..3a1b44a 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -451,23 +451,6 @@ public class Alignment implements AlignmentI
         }\r
     }\r
 \r
-    public SequenceI findShortName(String name)\r
-    {\r
-      int i = 0;\r
-\r
-      while (i < sequences.size())\r
-      {\r
-          if (getSequenceAt(i).getShortName().equals(name))\r
-          {\r
-              return getSequenceAt(i);\r
-          }\r
-\r
-          i++;\r
-      }\r
-\r
-        return null;\r
-    }\r
-\r
     /**    */\r
     public SequenceI findName(String name)\r
     {\r
@@ -720,7 +703,7 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < getHeight(); i++)\r
         {\r
 \r
-          seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true,true),\r
+          seqs[i] = new Sequence(getSequenceAt(i).getDisplayId(true),\r
                                  AlignSeq.extractGaps(\r
                                      jalview.util.Comparison.GapChars,\r
                                      getSequenceAt(i).getSequence()\r