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 d6dfd9d..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;
@@ -77,6 +79,7 @@ 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;
@@ -4023,7 +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);
 
@@ -4605,10 +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.
@@ -4682,7 +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();
@@ -5621,15 +5638,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
 
-  public void newTreePanel(String treeType, ScoreModelI sm)
+  public void newTreePanel(String treeType, DistanceModelI sm)
   {
-    String treecalcnm = MessageManager.getString("label.tree_calc_"
-            + treeType.toLowerCase());
-    String smn = MessageManager.getStringOrReturn("label.score_model_",
-            sm.getName());
-    final String ttl = MessageManager.formatMessage("label.treecalc_title",
-            treecalcnm, smn);
-    newTreePanel(treeType, sm.getName(), ttl);
+    String scoreModelName = sm.getName();
+    final String ttl = TreePanel.getPanelTitle(treeType, scoreModelName);
+    newTreePanel(treeType, scoreModelName, ttl);
   }
 }