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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 3d1a70c..c584903 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.analysis;
 
@@ -53,7 +52,9 @@ public class Finder
   }
 
   /**
-   * restart search at given sequence and residue on alignment and (optionally) contained in selection
+   * restart search at given sequence and residue on alignment and (optionally)
+   * contained in selection
+   * 
    * @param alignment
    * @param selectionGroup
    * @param seqIndex
@@ -119,7 +120,7 @@ public class Finder
     {
       seq = (Sequence) alignment.getSequenceAt(seqIndex);
 
-      if ((selection != null && selection.getSize()>0)
+      if ((selection != null && selection.getSize() > 0)
               && !selection.getSequences(null).contains(seq))
       {
         seqIndex++;
@@ -127,8 +128,9 @@ public class Finder
 
         continue;
       }
-      if (resIndex<0) {
-        resIndex=0;
+      if (resIndex < 0)
+      {
+        resIndex = 0;
         if (regex.search(seq.getName()))
         {
           idMatch.addElement(seq);
@@ -136,7 +138,7 @@ public class Finder
           if (!findAll)
           {
             // stop and return the match
-            found=true;
+            found = true;
             break;
           }
         }
@@ -176,7 +178,7 @@ public class Finder
         {
           resIndex = regex.matchedFrom();
 
-          if ((selection != null && selection.getSize()>0)
+          if ((selection != null && selection.getSize() > 0)
                   && ((resIndex + Integer.parseInt(spaces.elementAt(
                           resIndex).toString())) < selection.getStartRes()))
           {
@@ -219,15 +221,11 @@ public class Finder
     }
 
     /**
-     * We now search the Id string in the main search loop.
-     * for (int id = 0; id < alignment.getHeight(); id++)
-    {
-      if (regex.search(alignment.getSequenceAt(id).getName()))
-      {
-        idMatch.addElement(alignment.getSequenceAt(id));
-        hasResults = true;
-      }
-    } */
+     * We now search the Id string in the main search loop. for (int id = 0; id
+     * < alignment.getHeight(); id++) { if
+     * (regex.search(alignment.getSequenceAt(id).getName())) {
+     * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
+     */
     return hasResults;
   }
 
@@ -241,7 +239,7 @@ public class Finder
 
   /**
    * @param alignment
-   *                the alignment to set
+   *          the alignment to set
    */
   public void setAlignment(AlignmentI alignment)
   {
@@ -258,7 +256,7 @@ public class Finder
 
   /**
    * @param caseSensitive
-   *                the caseSensitive to set
+   *          the caseSensitive to set
    */
   public void setCaseSensitive(boolean caseSensitive)
   {
@@ -275,7 +273,7 @@ public class Finder
 
   /**
    * @param findAll
-   *                the findAll to set
+   *          the findAll to set
    */
   public void setFindAll(boolean findAll)
   {
@@ -292,7 +290,7 @@ public class Finder
 
   /**
    * @param selection
-   *                the selection to set
+   *          the selection to set
    */
   public void setSelection(jalview.datamodel.SequenceGroup selection)
   {
@@ -333,7 +331,7 @@ public class Finder
 
   /**
    * @param resIndex
-   *                the resIndex to set
+   *          the resIndex to set
    */
   public void setResIndex(int resIndex)
   {
@@ -350,7 +348,7 @@ public class Finder
 
   /**
    * @param seqIndex
-   *                the seqIndex to set
+   *          the seqIndex to set
    */
   public void setSeqIndex(int seqIndex)
   {