JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b5fc817..5f0e5d3 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
+import jalview.analysis.NJTree;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignExportSettingI;
@@ -34,7 +35,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
@@ -69,6 +70,7 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FileLoader;
+import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -77,12 +79,12 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
+import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -360,7 +362,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
-    buildTreeMenu();
+    calculateTree.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        new TreeChooser(AlignFrame.this);
+      }
+    });
     buildColourMenu();
 
     if (Desktop.desktop != null)
@@ -3580,54 +3590,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("AV", "PID", "Average distance tree using PID");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-    newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param type
    *          DOCUMENT ME!
    * @param pwType
@@ -3834,48 +3796,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * call. Listeners are added to remove the menu item when the treePanel is
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
-   * 
-   * @param treePanel
-   *          Displayed tree window.
-   * @param title
-   *          SortBy menu item title.
    */
   @Override
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
-    calculateTree.removeAll();
-    // build the calculate menu
-
-    for (final String type : new String[] { "NJ", "AV" })
-    {
-      String treecalcnm = MessageManager.getString("label.tree_calc_"
-              + type.toLowerCase());
-      for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
-      {
-        JMenuItem tm = new JMenuItem();
-        ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
-                || sm.isProtein() == !viewport.getAlignment()
-                        .isNucleotide())
-        {
-          String smn = MessageManager.getStringOrReturn(
-                  "label.score_model_", sm.getName());
-          final String title = MessageManager.formatMessage(
-                  "label.treecalc_title", treecalcnm, smn);
-          tm.setText(title);//
-          tm.addActionListener(new java.awt.event.ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              newTreePanel(type, pwtype, title);
-            }
-          });
-          calculateTree.add(tm);
-        }
-
-      }
-    }
     sortByTreeMenu.removeAll();
 
     List<Component> comps = PaintRefresher.components.get(viewport
@@ -4102,7 +4026,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (nf.getTree() != null)
       {
-        tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
+        tp = new TreePanel(alignPanel, NJTree.FROM_FILE, title, nf, input);
 
         tp.setSize(w, h);
 
@@ -4684,10 +4608,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Attempt to load a "dropped" file or URL string: First by testing whether
-   * it's an Annotation file, then a JNet file, and finally a features file. If
-   * all are false then the user may have dropped an alignment file onto this
-   * AlignFrame.
+   * Attempt to load a "dropped" file or URL string, by testing in turn for
+   * <ul>
+   * <li>an Annotation file</li>
+   * <li>a JNet file</li>
+   * <li>a features file</li>
+   * <li>else try to interpret as an alignment file</li>
+   * </ul>
    * 
    * @param file
    *          either a filename or a URL string.
@@ -4761,7 +4688,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             format = new IdentifyFile().identify(file, sourceType);
           }
-          if (FileFormat.Jnet.equals(format))
+          if (FileFormat.ScoreMatrix == format)
+          {
+            ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
+                    sourceType));
+            sm.parse();
+            // todo: i18n this message
+            statusBar
+                    .setText(MessageManager.formatMessage(
+                            "label.successfully_loaded_matrix",
+                            sm.getMatrixName()));
+          }
+          else if (FileFormat.Jnet.equals(format))
           {
             JPredFile predictions = new JPredFile(file, sourceType);
             new JnetAnnotationMaker();
@@ -5699,6 +5637,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
+
+  public void newTreePanel(String treeType, DistanceModelI sm)
+  {
+    String scoreModelName = sm.getName();
+    final String ttl = TreePanel.getPanelTitle(treeType, scoreModelName);
+    newTreePanel(treeType, scoreModelName, ttl);
+  }
 }
 
 class PrintThread extends Thread