X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=41d3185f1899a94ade34b309589e9729b67f14d2;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=9f813b51cb7e1b8c9fd5157f6d5ca6ab9da6162c;hpb=4f3aa2d5b87614be76e66ab42f525b439378b850;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 9f813b5..41d3185 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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;
 
@@ -44,7 +43,7 @@ public class Finder
   /**
    * hold's last-searched position between calles to find(false)
    */
-  int seqIndex = 0, resIndex = 0;
+  int seqIndex = 0, resIndex = -1;
 
   public Finder(AlignmentI alignment, SequenceGroup selection)
   {
@@ -52,6 +51,15 @@ public class Finder
     this.selection = selection;
   }
 
+  /**
+   * restart search at given sequence and residue on alignment and (optionally)
+   * contained in selection
+   * 
+   * @param alignment
+   * @param selectionGroup
+   * @param seqIndex
+   * @param resIndex
+   */
   public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
           int seqIndex, int resIndex)
   {
@@ -68,6 +76,7 @@ public class Finder
       searchString = searchString.toUpperCase();
     }
     regex = new com.stevesoft.pat.Regex(searchString);
+    regex.setIgnoreCase(!caseSensitive);
     searchResults = new SearchResults();
     idMatch = new Vector();
     Sequence seq;
@@ -111,18 +120,30 @@ 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++;
-        resIndex = 0;
+        resIndex = -1;
 
         continue;
       }
-
+      if (resIndex < 0)
+      {
+        resIndex = 0;
+        if (regex.search(seq.getName()))
+        {
+          idMatch.addElement(seq);
+          hasResults = true;
+          if (!findAll)
+          {
+            // stop and return the match
+            found = true;
+            break;
+          }
+        }
+      }
       item = seq.getSequenceAsString();
-      if (!caseSensitive)
-        item = item.toUpperCase();
 
       if ((selection != null)
               && (selection.getEndRes() < alignment.getWidth() - 1))
@@ -157,7 +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()))
           {
@@ -195,18 +216,16 @@ public class Finder
       if (!found)
       {
         seqIndex++;
-        resIndex = 0;
+        resIndex = -1;
       }
     }
 
-    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;
   }
 
@@ -220,7 +239,7 @@ public class Finder
 
   /**
    * @param alignment
-   *                the alignment to set
+   *          the alignment to set
    */
   public void setAlignment(AlignmentI alignment)
   {
@@ -237,7 +256,7 @@ public class Finder
 
   /**
    * @param caseSensitive
-   *                the caseSensitive to set
+   *          the caseSensitive to set
    */
   public void setCaseSensitive(boolean caseSensitive)
   {
@@ -254,7 +273,7 @@ public class Finder
 
   /**
    * @param findAll
-   *                the findAll to set
+   *          the findAll to set
    */
   public void setFindAll(boolean findAll)
   {
@@ -271,7 +290,7 @@ public class Finder
 
   /**
    * @param selection
-   *                the selection to set
+   *          the selection to set
    */
   public void setSelection(jalview.datamodel.SequenceGroup selection)
   {
@@ -312,7 +331,7 @@ public class Finder
 
   /**
    * @param resIndex
-   *                the resIndex to set
+   *          the resIndex to set
    */
   public void setResIndex(int resIndex)
   {
@@ -329,7 +348,7 @@ public class Finder
 
   /**
    * @param seqIndex
-   *                the seqIndex to set
+   *          the seqIndex to set
    */
   public void setSeqIndex(int seqIndex)
   {