JAL-3446 adds Jmol viewer embedding.

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 91b773e..5696c3a 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -63,6 +63,7 @@ import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.SwingUtilities;
@@ -1895,5 +1896,42 @@ public class AlignmentPanel extends GAlignmentPanel implements
     super.repaint();
   }
 
+  public void selectAllSequences()
+  {
+    selectSequences(av.getAlignment().getSequences());
+  }
+
+  public void deselectAllSequences()
+  {
+    if (av.cursorMode)
+    {
+      getSeqPanel().keyboardNo1 = null;
+      getSeqPanel().keyboardNo2 = null;
+    }
+    av.setSelectionGroup(null);
+    av.getColumnSelection().clear();
+    av.setSelectionGroup(null);
+    getIdPanel().getIdCanvas().searchResults = null;
+    av.sendSelection();
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    paintAlignment(false, false);
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
+
+  public void selectSequences(List<SequenceI> seqs) 
+  {
+    SequenceGroup sg = new SequenceGroup(seqs);
+    sg.setEndRes(av.getAlignment().getWidth() - 1);
+    av.setSelectionGroup(sg);
+    av.isSelectionGroupChanged(true);
+    av.sendSelection();
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    paintAlignment(false, false);
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
 
 }