JAL-966 JAL-1738 JAL-345 interfaces for SearchResults and SearchResults.Match

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

diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index b87c170..086765c 100644 (file)
--- 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.
  * 
@@ -20,16 +20,20 @@
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+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;
 
@@ -39,6 +43,8 @@ public class Finder
 
   boolean caseSensitive = false;
 
+  private boolean includeDescription = false;
+
   boolean findAll = false;
 
   com.stevesoft.pat.Regex regex = null;
@@ -146,6 +152,19 @@ 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();
 
@@ -188,7 +207,7 @@ public class Finder
           {
             continue;
           }
-// if invalid string used, then regex has no matched to/from
+          // if invalid string used, then regex has no matched to/from
           int sres = seq
                   .findPosition(resIndex
                           + Integer.parseInt(spaces.elementAt(resIndex)
@@ -320,7 +339,7 @@ public class Finder
   /**
    * @return the searchResults
    */
-  public SearchResults getSearchResults()
+  public SearchResultsI getSearchResults()
   {
     return searchResults;
   }
@@ -358,4 +377,14 @@ public class Finder
   {
     this.seqIndex = seqIndex;
   }
+
+  public boolean isIncludeDescription()
+  {
+    return includeDescription;
+  }
+
+  public void setIncludeDescription(boolean includeDescription)
+  {
+    this.includeDescription = includeDescription;
+  }
 }