X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9a38d4caa25ad9345d038430b99ced076c2555bb;hb=844c332f108aba635608f13dedf2b08777b3a477;hp=279d9ad7b3d1acb16586f64c882582b69cdcf374;hpb=9b9b058f82be7403a76d41fe17016b8b44b12db7;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 279d9ad..9a38d4c 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.util.Format;
@@ -550,7 +549,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
-    PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+    PageFormat defaultPage = printJob.defaultPage();
+    PageFormat pf = printJob.pageDialog(defaultPage);
+
+    if (defaultPage == pf)
+    {
+      /*
+       * user cancelled
+       */
+      return;
+    }
 
     printJob.setPrintable(this, pf);
 
@@ -755,6 +763,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   @Override
   public void mouseReleased(MouseEvent e)
   {
+    /*
+     * isPopupTrigger is set on mouseReleased on Windows
+     */
+    if (e.isPopupTrigger())
+    {
+      chooseSubtreeColour();
+      e.consume(); // prevent mouseClicked happening
+    }
   }
 
   /**
@@ -792,15 +808,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       return;
     }
 
-    /*
-     * isPopupTrigger is set on mouseReleased /
-     * mouseClicked on Windows
-     */
-    if (evt.isPopupTrigger())
-    {
-      chooseSubtreeColour();
-    }
-    else if (evt.getClickCount() > 1)
+    if (evt.getClickCount() > 1)
     {
       tree.swapNodes(highlightNode);
       tree.reCount(tree.getTopNode());
@@ -812,8 +820,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       for (int i = 0; i < leaves.size(); i++)
       {
-        SequenceI seq = (SequenceI) leaves.elementAt(i)
-                .element();
+        SequenceI seq = (SequenceI) leaves.elementAt(i).element();
         treeSelectionChanged(seq);
       }
       av.sendSelection();
@@ -887,7 +894,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     /*
      * isPopupTrigger is set for mousePressed (Mac)
-     * or mouseReleased / mouseClicked (Windows)
+     * or mouseReleased (Windows)
      */
     if (e.isPopupTrigger())
     {
@@ -967,17 +974,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      setColor(tree.getGroups().elementAt(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
-              .getGroups().elementAt(i));
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
       Vector<SequenceI> sequences = new Vector<SequenceI>();
 
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) l.elementAt(j)
-                .element();
+        SequenceI s1 = (SequenceI) l.elementAt(j).element();
 
         if (!sequences.contains(s1))
         {
@@ -1000,17 +1006,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
-                  .getColourName(av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(sg,
+                  ColourSchemeProperty.getColourName(av
+                          .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs != null)
-        {
-          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.isIgnoreGapsConsensus());
-        }
+        // if (cs != null)
+        // {
+        // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+        // av.isIgnoreGapsConsensus());
+        // }
       }
-      sg.cs = cs;
+      sg.setColourScheme(cs);
+      sg.getGroupColourScheme().setThreshold(
+              av.getResidueShading().getThreshold(),
+              av.isIgnoreGapsConsensus());
       // sg.recalcConservation();
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -1018,12 +1028,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
-                && aps[a].av.getGlobalColourScheme().conservationApplied())
+                && aps[a].av.getResidueShading()
+                        .conservationApplied())
         {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null),
+          Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());
-
           c.calculate();
           c.verdict(false, aps[a].av.getConsPercGaps());
           sg.cs.setConservation(c);