Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index af84dbc..96d0746 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -31,8 +31,8 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -515,7 +515,7 @@ public class TreePanel extends GTreePanel
     {
     }
     ;
-    Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+    Object[] alAndColsel = tree.seqData.getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -532,8 +532,8 @@ public class TreePanel extends GTreePanel
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al,
-                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+        AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+                AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
@@ -749,9 +749,7 @@ public class TreePanel extends GTreePanel
     try
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
-              Cache.getProperty("LAST_DIRECTORY"),
-              ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION,
-              ImageMaker.EPS_EXTENSION);
+              ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
               .getString("label.create_eps_from_tree"));
@@ -797,9 +795,7 @@ public class TreePanel extends GTreePanel
     try
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
-              Cache.getProperty("LAST_DIRECTORY"),
-              ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION,
-              ImageMaker.PNG_DESCRIPTION);
+              ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
 
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle(MessageManager