JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index cc91ebf..5a2271d 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -182,7 +182,7 @@ public class Finder extends GFinder
               searchResults.getResultEnd(i), "Search Results");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.showSeqFeatures.setSelected(true);
@@ -214,6 +214,8 @@ public class Finder extends GFinder
     jalview.analysis.Finder finder = new jalview.analysis.Finder(
             av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
     finder.setCaseSensitive(caseSensitive.isSelected());
+    finder.setIncludeDescription(searchDescription.isSelected());
+
     finder.setFindAll(findAll);
 
     finder.find(searchString); // returns true if anything was actually found
@@ -229,11 +231,11 @@ public class Finder extends GFinder
     if ((idMatch.size() > 0))
     {
       haveResults = true;
-      ap.idPanel.highlightSearchResults(idMatch);
+      ap.getIdPanel().highlightSearchResults(idMatch);
     }
     else
     {
-      ap.idPanel.highlightSearchResults(null);
+      ap.getIdPanel().highlightSearchResults(null);
     }
 
     if (searchResults.getSize() > 0)