JAL-2388 Hidden cols separated from column selection (almost complete)

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index b7c766a..23b23be 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,14 +20,29 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class TreePanel extends EmbmenuFrame implements ActionListener,
         ItemListener
 {
@@ -54,6 +69,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     return tree;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     ap = null;
@@ -157,7 +173,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       }
       ;
       Object[] alAndColsel = tree.seqData
-              .getAlignmentAndColumnSelection(gc);
+              .getAlignmentAndHiddenColumns(gc);
 
       if (alAndColsel != null && alAndColsel[0] != null)
       {
@@ -165,7 +181,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
         AlignFrame af = new AlignFrame(al, av.applet,
                 "Original Data for Tree", false);
 
-        af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+        af.viewport.getAlignment().setHiddenColumns(
+                (HiddenColumns) alAndColsel[1]);
       }
     }
     else
@@ -185,6 +202,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       this.newtree = newtree;
     }
 
+    @Override
     public void run()
     {
       if (newtree != null)
@@ -204,8 +222,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         int start, end;
         SequenceI[] seqs;
-        boolean selview = (av.getSelectionGroup() != null)
-                && (av.getSelectionGroup().getSize() > 1);
+        boolean selview = av.getSelectionGroup() != null
+                && av.getSelectionGroup().getSize() > 1;
         AlignmentView seqStrings = av.getAlignmentView(selview);
         if (!selview)
         {
@@ -220,8 +238,27 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            System.err.println("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+            q.printStackTrace();
+          }
+          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        }
+        else
+        {
+          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+                  end);
+        }
       }
 
       tree.reCount(tree.getTopNode());
@@ -252,6 +289,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == newickOutput)
@@ -268,6 +306,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == fitToWindow)