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 0df1585..96d0746 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -42,6 +42,7 @@ import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
 import jalview.jbgui.GTreePanel;
 import jalview.schemes.ResidueProperties;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -514,7 +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)
     {
@@ -531,8 +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
@@ -747,24 +748,22 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "eps" }, new String[] { "Encapsulated Postscript" },
-              "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
               .getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if (value != JalviewFileChooser.APPROVE_OPTION)
       {
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-              .getSelectedFile().getParent());
+      Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
+              .getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
@@ -795,10 +794,8 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "png" }, new String[] { "Portable network graphics" },
-              "Portable network graphics");
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
 
       chooser.setFileView(new jalview.io.JalviewFileView());
       chooser.setDialogTitle(MessageManager