From 748cffd412de4d6951d8f746428ff601861fe144 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 11:59:13 +0000
Subject: [PATCH] findByShortName

---
 src/jalview/datamodel/Alignment.java  |   23 +++++++++++++++++++----
 src/jalview/datamodel/AlignmentI.java |    4 ++++
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d945ec6..0b3adff 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -451,6 +451,23 @@ public class Alignment implements AlignmentI
         }
     }
 
+    public SequenceI findShortName(String name)
+    {
+      int i = 0;
+
+      while (i < sequences.size())
+      {
+          if (getSequenceAt(i).getShortName().equals(name))
+          {
+              return getSequenceAt(i);
+          }
+
+          i++;
+      }
+
+        return null;
+    }
+
     /**    */
     public SequenceI findName(String name)
     {
@@ -458,11 +475,9 @@ public class Alignment implements AlignmentI
 
         while (i < sequences.size())
         {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getName().equals(name))
+            if (getSequenceAt(i).getName().equals(name))
             {
-                return s;
+                return getSequenceAt(i);
             }
 
             i++;
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index be3093c..ed1ec4e 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -125,6 +125,8 @@ public interface AlignmentI
      */
     public SequenceI findName(String name);
 
+    public SequenceI findShortName(String name);
+
 
     /**
      * Finds index of a given sequence in the alignment.
@@ -305,4 +307,6 @@ public interface AlignmentI
 
     public void setProvenance(Provenance prov);
 
+
+
 }
-- 
1.7.10.2