From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 2 Dec 2004 11:28:35 +0000 (+0000)
Subject: Search on residue position and within selection
X-Git-Tag: Release_2_0~876
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3a94ac879afa5d50c6c43eba8a12139adead7720;p=jalview.git

Search on residue position and within selection
---

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index a819a18..d78669c 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -78,9 +78,38 @@ public class Finder extends GFinder
     Sequence seq;
     String item;
     boolean found = false;
+
+    /// is the searchString a residue number?
+    try{
+      int res = Integer.parseInt(searchString);
+      found = true;
+
+      if(av.getSelection().size()>0)
+        seq = (Sequence)(av.getSelection().sequenceAt(0));
+      else
+        seq = (Sequence)av.getAlignment().getSequenceAt(0);
+
+      searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );
+      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
+      searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );
+
+
+      //av.getAlignment().getSequenceAt(seq).findPosition(res)
+    }catch(NumberFormatException ex){}
+
+
     while( !found && seqIndex<av.getAlignment().getHeight())
     {
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);
+
+      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))
+      {
+        // if a selection has been made, only search within that selection
+        seqIndex++;
+        resIndex=0;
+        continue;
+      }
+
       item = seq.getSequence();
 
       for(int r = resIndex; r<item.length(); r++)