JAL-1738 JAL-345 fix for JAL-2302 only report Matches that are not contained by the...

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 0494896..ff03788 100644 (file)
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,33 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * 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.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 
-import jalview.datamodel.*;
+import java.util.Vector;
 
 public class Finder
 {
   /**
    * Implements the search algorithms for the Find dialog box.
    */
-  SearchResults searchResults;
+  SearchResultsI searchResults;
 
   AlignmentI alignment;
 
@@ -37,6 +44,8 @@ public class Finder
 
   boolean caseSensitive = false;
 
+  private boolean includeDescription = false;
+
   boolean findAll = false;
 
   com.stevesoft.pat.Regex regex = null;
@@ -95,6 +104,7 @@ public class Finder
         selection = null;
       }
     }
+    SearchResultMatchI lastm = null;
 
     while (!found && (seqIndex < end))
     {
@@ -144,6 +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();
 
@@ -172,7 +195,6 @@ public class Finder
       }
 
       String noGaps = noGapsSB.toString();
-
       for (int r = resIndex; r < noGaps.length(); r++)
       {
 
@@ -186,7 +208,7 @@ 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)
@@ -195,8 +217,13 @@ public class Finder
                   - 1
                   + Integer.parseInt(spaces
                           .elementAt(regex.matchedTo() - 1).toString()));
-
-          searchResults.addResult(seq, sres, eres);
+          // only add result if not contained in previous result
+          if (lastm == null
+                  || (lastm.getSequence() != seq || (!(lastm.getStart() <= sres && lastm
+                          .getEnd() >= eres))))
+          {
+            lastm = searchResults.addResult(seq, sres, eres);
+          }
           hasResults = true;
           if (!findAll)
           {
@@ -318,7 +345,7 @@ public class Finder
   /**
    * @return the searchResults
    */
-  public SearchResults getSearchResults()
+  public SearchResultsI getSearchResults()
   {
     return searchResults;
   }
@@ -356,4 +383,14 @@ public class Finder
   {
     this.seqIndex = seqIndex;
   }
+
+  public boolean isIncludeDescription()
+  {
+    return includeDescription;
+  }
+
+  public void setIncludeDescription(boolean includeDescription)
+  {
+    this.includeDescription = includeDescription;
+  }
 }