From ed52d72ae281a74a5496a605e51159931caa925c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Jul 2008 15:03:36 +0000
Subject: [PATCH] allow findSeq to begin *after* a given sequence in the
 alignment

---
 src/jalview/datamodel/Alignment.java  |   27 ++++++++++++++++++++++++++-
 src/jalview/datamodel/AlignmentI.java |    8 ++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3689433..a88fa9e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -344,10 +344,35 @@ public class Alignment
    */
   public SequenceI findName(String token, boolean b)
   {
-
+    return findName(null, token, b);
+  }
+  
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, boolean)
+   */
+  public SequenceI findName(SequenceI startAfter, String token, boolean b)
+  {
+  
     int i = 0;
     SequenceI sq=null;
     String sqname=null;
+    if (startAfter!=null)
+    {
+      // try to find the sequence in the alignment
+      boolean matched=false;
+      while (i<sequences.size())
+      {
+        if (getSequenceAt(i++)==startAfter)
+        {
+          matched = true;
+          break;
+        }
+      }
+      if (!matched)
+      {
+        i=0;
+      }
+    }
     while (i < sequences.size())
     {
       sq = getSequenceAt(i);
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 558b38d..f89602f 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -301,5 +301,13 @@ public interface AlignmentI
    * @return matched sequence or null
    */
   public SequenceI findName(String token, boolean b);
+  /**
+   * find next sequence with given name in alignment starting after a given sequence
+   * @param startAfter the sequence after which the search will be started (usually the result of the last call to findName) 
+   * @param token name to find
+   * @param b true implies that case insensitive matching will <em>also</em> be tried 
+   * @return matched sequence or null
+   */
+  public SequenceI findName(SequenceI startAfter, String token, boolean b);
   
 }
-- 
1.7.10.2