X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=3c72598179d0541eb6d445295361b8349b9b8543;hb=7d6575e94bed92bc06043d432576e3a39e8a8e75;hp=b87c170d6dc78b226ddb50793ebb114118b812fc;hpb=e1cd94839128776e14e51ded3f3be2dcc7e72273;p=jalview.git

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index b87c170..3c72598 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,9 +20,15 @@
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
 
 public class Finder
 {
@@ -33,15 +39,17 @@ 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;
+  Regex regex = null;
 
   /**
    * hold's last-searched position between calles to find(false)
@@ -78,7 +86,7 @@ public class Finder
     {
       searchString = searchString.toUpperCase();
     }
-    regex = new com.stevesoft.pat.Regex(searchString);
+    regex = new Regex(searchString);
     regex.setIgnoreCase(!caseSensitive);
     searchResults = new SearchResults();
     idMatch = new Vector();
@@ -146,6 +154,19 @@ 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();
 
@@ -162,7 +183,7 @@ 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));
@@ -287,7 +308,7 @@ public class Finder
   /**
    * @return the selection
    */
-  public jalview.datamodel.SequenceGroup getSelection()
+  public SequenceGroup getSelection()
   {
     return selection;
   }
@@ -296,7 +317,7 @@ public class Finder
    * @param selection
    *          the selection to set
    */
-  public void setSelection(jalview.datamodel.SequenceGroup selection)
+  public void setSelection(SequenceGroup selection)
   {
     this.selection = selection;
   }
@@ -312,7 +333,7 @@ public class Finder
   /**
    * @return the regex
    */
-  public com.stevesoft.pat.Regex getRegex()
+  public Regex getRegex()
   {
     return regex;
   }
@@ -358,4 +379,14 @@ public class Finder
   {
     this.seqIndex = seqIndex;
   }
+
+  public boolean isIncludeDescription()
+  {
+    return includeDescription;
+  }
+
+  public void setIncludeDescription(boolean includeDescription)
+  {
+    this.includeDescription = includeDescription;
+  }
 }