X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=a055106a6877102e8a2e9d239ff4b0e645fff43f;hb=9d4dbc8a3e7616145210154e8dfe8feb0afc49cf;hp=1179435eca37405fa0e42a910907be725465bc9d;hpb=9ba5c46b6fb472ffa1a9299e98d1825f61557c53;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 1179435..a055106 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -84,7 +85,6 @@ public class Finder
     boolean found = false;
     int end = alignment.getHeight();
 
-
     // /////////////////////////////////////////////
 
     if (selection != null)
@@ -99,7 +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))
       {
@@ -121,9 +121,10 @@ public class Finder
           {
             searchResults.addResult(seq, res, res);
             hasResults = true;
-            //resIndex=seq.getLength();
+            // resIndex=seq.getLength();
             // seqIndex++;
-            if (!findAll) {
+            if (!findAll)
+            {
               found = true;
               break;
             }
@@ -185,7 +186,7 @@ public class Finder
           {
             continue;
           }
-
+// if invalid string used, then regex has no matched to/from
           int sres = seq
                   .findPosition(resIndex
                           + Integer.parseInt(spaces.elementAt(resIndex)