From 73e6ed31b0328def2a94c643fc71380acf16d17c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:48:39 +0000
Subject: [PATCH] Break if regex not found

---
 src/jalview/appletgui/Finder.java |    2 ++
 src/jalview/gui/Finder.java       |   13 ++++++++++---
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 06fc9e1..7cb3763 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -246,6 +246,8 @@ public class Finder
 
           r = resIndex;
         }
+        else
+          break;
       }
       if (!found)
       {
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e5c94bd..ec45b0c 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -260,7 +260,7 @@ public class Finder extends GFinder
             }
 
             ///Shall we ignore gaps????
-            StringBuffer noGaps = new StringBuffer();
+            StringBuffer noGapsSB = new StringBuffer();
             int insertCount = 0;
             Vector spaces = new Vector();
 
@@ -268,7 +268,7 @@ public class Finder extends GFinder
             {
                 if (!jalview.util.Comparison.isGap(item.charAt(j)))
                 {
-                    noGaps.append(item.charAt(j));
+                    noGapsSB.append(item.charAt(j));
                     spaces.add(new Integer(insertCount));
                 }
                 else
@@ -277,9 +277,12 @@ public class Finder extends GFinder
                 }
             }
 
+            String noGaps = noGapsSB.toString();
+
             for (int r = resIndex; r < noGaps.length(); r++)
             {
-                if (regex.searchFrom(noGaps.toString(), r))
+
+                if (regex.searchFrom(noGaps, r))
                 {
                     resIndex = regex.matchedFrom();
 
@@ -313,6 +316,10 @@ public class Finder extends GFinder
 
                     r = resIndex;
                 }
+                else
+                {
+                  break;
+                }
             }
 
             if (!found)
-- 
1.7.10.2