X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=ff4fe603a736233f03ed9eb2714879e56455f64c;hb=848bef9fdc243cfab564acb0b82fc7ee3bcffe9f;hp=5f683cb07bb4d82884537274c217ccea8934120f;hpb=f5c630601eccc201dd73f34227acf97f59a9168f;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 5f683cb..ff4fe60 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -181,6 +181,8 @@ public class Finder extends GFinder
         createNewGroup.setEnabled(false);
 
         String searchString = textfield.getText().toUpperCase().trim();
+        if(searchString.length()<1)
+          return;
 
         com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
@@ -197,19 +199,18 @@ public class Finder extends GFinder
         {
             int res = Integer.parseInt(searchString);
             found = true;
-
-            if (av.getSelectionGroup().getSize() > 0)
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
             {
-                seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+              seq = (Sequence) av.getAlignment().getSequenceAt(0);
             }
             else
             {
-                seq = (Sequence) av.getAlignment().getSequenceAt(0);
+              seq = (Sequence) (av.getSelectionGroup().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));
+            searchResults.add(res+"");
+            searchResults.add(res+"");
         }
         catch (NumberFormatException ex)
         {
@@ -261,7 +262,7 @@ public class Finder extends GFinder
             }
 
             ///Shall we ignore gaps????
-            StringBuffer noGaps = new StringBuffer();
+            StringBuffer noGapsSB = new StringBuffer();
             int insertCount = 0;
             Vector spaces = new Vector();
 
@@ -269,7 +270,7 @@ 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
@@ -278,9 +279,12 @@ 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();
 
@@ -314,6 +318,10 @@ public class Finder extends GFinder
 
                     r = resIndex;
                 }
+                else
+                {
+                  break;
+                }
             }
 
             if (!found)