JAL-1632 JAL-2416 load score matrices from file, as float[][]

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 9522144..7a205b6 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
@@ -41,7 +42,7 @@ import jalview.io.JalviewFileChooser;
 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;
 
@@ -161,6 +162,7 @@ public class TreePanel extends GTreePanel
 
     av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -196,6 +198,7 @@ public class TreePanel extends GTreePanel
 
   }
 
+  @Override
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();
@@ -231,6 +234,7 @@ public class TreePanel extends GTreePanel
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent evt)
         {
           treeCanvas.applyToAllViews = false;
@@ -249,6 +253,7 @@ public class TreePanel extends GTreePanel
     itemf.setSelected(treeCanvas.applyToAllViews);
     itemf.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         treeCanvas.applyToAllViews = itemf.isSelected();
@@ -276,6 +281,7 @@ public class TreePanel extends GTreePanel
       }
     }
 
+    @Override
     public void run()
     {
 
@@ -315,7 +321,7 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
         if (sm instanceof ViewBasedAnalysisI)
         {
           try
@@ -389,6 +395,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void textbox_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -434,6 +441,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -474,12 +482,14 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void printMenu_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
     treeCanvas.startPrinting();
   }
 
+  @Override
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
     if (!tree.hasOriginalSequenceData())
@@ -511,8 +521,8 @@ public class TreePanel extends GTreePanel
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+      AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
               .getAlignment().getDataset() : null;
       if (dataset != null)
       {
@@ -547,6 +557,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void fitToWindow_actionPerformed(ActionEvent e)
   {
     treeCanvas.fitToWindow = fitToWindow.isSelected();
@@ -637,6 +648,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void font_actionPerformed(ActionEvent e)
   {
     if (treeCanvas == null)
@@ -666,6 +678,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void distanceMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setShowDistances(distanceMenu.isSelected());
@@ -677,6 +690,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void bootstrapMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
@@ -688,6 +702,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void placeholdersMenu_actionPerformed(ActionEvent e)
   {
     treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
@@ -699,6 +714,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void epsTree_actionPerformed(ActionEvent e)
   {
     boolean accurateText = true;
@@ -732,24 +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);
@@ -772,6 +786,7 @@ public class TreePanel extends GTreePanel
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pngTree_actionPerformed(ActionEvent e)
   {
     int width = treeCanvas.getWidth();
@@ -779,10 +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
@@ -828,6 +841,7 @@ public class TreePanel extends GTreePanel
     tree.applyToNodes(new NodeTransformI()
     {
 
+      @Override
       public void transform(BinaryNode node)
       {
         if (node instanceof SequenceNode