X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FFinder.java;h=f641f4b71d3968626a5b13baa30c4d650f6c6ea5;hb=4468c1e39c57fbb67192207b4c8750dab1b1dedd;hp=0bf4600dbf992628ba29f6cf2c62d43b0af2e324;hpb=c1f5dd54ab8caa7e76ca50f9c3a85f2731b66862;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 0bf4600..f641f4b 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -75,7 +75,7 @@ public class Finder extends GFinder
 
   private AlignmentPanel ap;
 
-  private JInternalFrame frame;
+  private JalviewInternalFrame frame;
 
   /*
    * Finder agent per viewport searched
@@ -107,7 +107,7 @@ public class Finder extends GFinder
     ap = alignPanel;
     focusFixed = fixedFocus;
     finders = new HashMap<>();
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -254,6 +254,17 @@ public class Finder extends GFinder
     new FeatureEditor(ap, seqs, features, true).showDialog();
   }
 
+  @Override
+  protected void copyToClipboard_actionPerformed()
+  {
+    if (searchResults.isEmpty())
+    {
+      return; // shouldn't happen
+    }
+    // assume viewport controller has same searchResults as we do...
+    ap.alignFrame.avc.copyHighlightedRegionsToClipboard();
+  }
+
   /**
    * Search the alignment for the next or all matches. If 'all matches', a
    * dialog is shown with the number of sequence ids and subsequences matched.
@@ -263,6 +274,7 @@ public class Finder extends GFinder
   void doSearch(boolean doFindAll)
   {
     createFeatures.setEnabled(false);
+    copyToClipboard.setEnabled(false);
 
     String searchString = searchBox.getUserInput();
 
@@ -283,19 +295,21 @@ public class Finder extends GFinder
       finder = new jalview.analysis.Finder(av);
       finders.put(av, finder);
     }
+    finder.setFeatureRenderer(ap.getFeatureRenderer());
 
     boolean isCaseSensitive = caseSensitive.isSelected();
     boolean doSearchDescription = searchDescription.isSelected();
+    boolean doSearchfeatures = searchFeatures.isSelected();
     boolean skipHidden = ignoreHidden.isSelected();
     if (doFindAll)
     {
       finder.findAll(searchString, isCaseSensitive, doSearchDescription,
-              skipHidden);
+              doSearchfeatures, skipHidden);
     }
     else
     {
       finder.findNext(searchString, isCaseSensitive, doSearchDescription,
-              skipHidden);
+              doSearchfeatures, skipHidden);
     }
 
     searchResults = finder.getSearchResults();
@@ -309,6 +323,7 @@ public class Finder extends GFinder
     else
     {
       createFeatures.setEnabled(true);
+      copyToClipboard.setEnabled(true);
     }
 
     searchBox.updateCache();