apply version 2.7 copyright

[jalview.git] / src / jalview / analysis / Finder.java

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index c584903..2dd6a74 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -82,31 +82,11 @@ public class Finder
     Sequence seq;
     String item = null;
     boolean found = false;
+    int end = alignment.getHeight();
 
-    // //// is the searchString a residue number?
-    try
-    {
-      int res = Integer.parseInt(searchString);
-      found = true;
-      if (selection == null || selection.getSize() < 1)
-      {
-        seq = (Sequence) alignment.getSequenceAt(0);
-      }
-      else
-      {
-        seq = (Sequence) (selection.getSequenceAt(0));
-      }
-
-      searchResults.addResult(seq, res, res);
-      hasResults = true;
-    } catch (NumberFormatException ex)
-    {
-    }
 
     // /////////////////////////////////////////////
 
-    int end = alignment.getHeight();
-
     if (selection != null)
     {
       if ((selection.getSize() < 1)
@@ -119,7 +99,7 @@ public class Finder
     while (!found && (seqIndex < end))
     {
       seq = (Sequence) alignment.getSequenceAt(seqIndex);
-
+      
       if ((selection != null && selection.getSize() > 0)
               && !selection.getSequences(null).contains(seq))
       {
@@ -131,6 +111,27 @@ public class Finder
       if (resIndex < 0)
       {
         resIndex = 0;
+        // test for one off matches - sequence position and sequence ID
+        // //// is the searchString a residue number?
+        try
+        {
+          int res = Integer.parseInt(searchString);
+          // possibly a residue number - check if valid for seq
+          if (seq.getEnd() >= res)
+          {
+            searchResults.addResult(seq, res, res);
+            hasResults = true;
+            //resIndex=seq.getLength();
+            // seqIndex++;
+            if (!findAll) {
+              found = true;
+              break;
+            }
+          }
+        } catch (NumberFormatException ex)
+        {
+        }
+
         if (regex.search(seq.getName()))
         {
           idMatch.addElement(seq);