JAL-1807

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 06d75ac..3562dee 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,26 +1,36 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.jsdev.RegExp;
+import jalview.jsdev.api.RegExpInterface;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.util.Vector;
+
+//import com.stevesoft.pat.Regex;
 
 public class Finder
 {
@@ -31,15 +41,17 @@ public class Finder
 
   AlignmentI alignment;
 
-  jalview.datamodel.SequenceGroup selection = null;
+  SequenceGroup selection = null;
 
   Vector idMatch = null;
 
   boolean caseSensitive = false;
 
+  private boolean includeDescription = false;
+
   boolean findAll = false;
 
-  com.stevesoft.pat.Regex regex = null;
+  RegExpInterface regex = null;
 
   /**
    * hold's last-searched position between calles to find(false)
@@ -76,7 +88,7 @@ public class Finder
     {
       searchString = searchString.toUpperCase();
     }
-    regex = new com.stevesoft.pat.Regex(searchString);
+    regex = RegExp.newRegex(searchString);
     regex.setIgnoreCase(!caseSensitive);
     searchResults = new SearchResults();
     idMatch = new Vector();
@@ -144,6 +156,19 @@ 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();
 
@@ -160,7 +185,7 @@ public class Finder
 
       for (int j = 0; j < item.length(); j++)
       {
-        if (!jalview.util.Comparison.isGap(item.charAt(j)))
+        if (!Comparison.isGap(item.charAt(j)))
         {
           noGapsSB.append(item.charAt(j));
           spaces.addElement(new Integer(insertCount));
@@ -186,7 +211,7 @@ 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)
@@ -285,7 +310,7 @@ public class Finder
   /**
    * @return the selection
    */
-  public jalview.datamodel.SequenceGroup getSelection()
+  public SequenceGroup getSelection()
   {
     return selection;
   }
@@ -294,7 +319,7 @@ public class Finder
    * @param selection
    *          the selection to set
    */
-  public void setSelection(jalview.datamodel.SequenceGroup selection)
+  public void setSelection(SequenceGroup selection)
   {
     this.selection = selection;
   }
@@ -310,7 +335,7 @@ public class Finder
   /**
    * @return the regex
    */
-  public com.stevesoft.pat.Regex getRegex()
+  public RegExpInterface getRegex()
   {
     return regex;
   }
@@ -356,4 +381,14 @@ public class Finder
   {
     this.seqIndex = seqIndex;
   }
+
+  public boolean isIncludeDescription()
+  {
+    return includeDescription;
+  }
+
+  public void setIncludeDescription(boolean includeDescription)
+  {
+    this.includeDescription = includeDescription;
+  }
 }