Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 756fe5a..bccacfa 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -33,10 +33,12 @@ import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.schemes.ColourSchemeI;
@@ -472,6 +474,34 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
+  public boolean copyHighlightedRegionsToClipboard()
+  {
+    if (!viewport.hasSearchResults())
+    {
+      // do nothing if no selection exists
+      return false;
+    }
+
+    SearchResultsI searchResults = viewport.getSearchResults();
+    if (searchResults.isEmpty())
+    {
+      return false; // shouldn't happen
+    }
+    List<SequenceI> seqs = searchResults.getMatchingSubSequences();
+
+    // TODO: pass in hiddenColumns according to intersection of searchResults
+    // and visible columns. Currently this isn't done, since each contig becomes
+    // a single subsequence
+    Desktop.jalviewClipboard = new Object[] {
+        seqs.toArray(new SequenceI[0]),
+        alignPanel.getAlignment().getDataset(), null };
+    avcg.setStatus(MessageManager.formatMessage(
+            "label.copied_sequences_to_clipboard", seqs.size()));
+    // Technically we should return false, since view has not changed
+    return false;
+  }
+  
+  @Override
   public boolean justify_Region(boolean left)
   {
     AlignmentI al = viewport.getAlignment();