X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=fae459faaf637f4b1f7ea13058a3c20f362b2f2b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=0494896dee092c9714b8a9f5257b7776eb730dd8;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 0494896..fae459f 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,26 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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;
 
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 
-import jalview.datamodel.*;
+import java.util.Vector;
 
 public class Finder
 {
@@ -37,6 +42,8 @@ public class Finder
 
   boolean caseSensitive = false;
 
+  private boolean includeDescription = false;
+
   boolean findAll = false;
 
   com.stevesoft.pat.Regex regex = null;
@@ -144,6 +151,19 @@ public class Finder
             break;
           }
         }
+
+        if (isIncludeDescription() && seq.getDescription() != null
+                && regex.search(seq.getDescription()))
+        {
+          idMatch.addElement(seq);
+          hasResults = true;
+          if (!findAll)
+          {
+            // stop and return the match
+            found = true;
+            break;
+          }
+        }
       }
       item = seq.getSequenceAsString();
 
@@ -186,7 +206,7 @@ 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)
@@ -356,4 +376,14 @@ public class Finder
   {
     this.seqIndex = seqIndex;
   }
+
+  public boolean isIncludeDescription()
+  {
+    return includeDescription;
+  }
+
+  public void setIncludeDescription(boolean includeDescription)
+  {
+    this.includeDescription = includeDescription;
+  }
 }