JAL-1632 similarity options on TreeChooser panel affect tree by PID

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0da8381..681a700 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,6 +35,7 @@ import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
@@ -3587,17 +3588,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Constructs a tree panel and adds it to the desktop
    * 
    * @param type
-   *          DOCUMENT ME!
-   * @param pwType
-   *          DOCUMENT ME!
-   * @param title
-   *          DOCUMENT ME!
+   *          tree type (NJ or AV)
+   * @param sm
+   *          distance or similarity score model used to compute the tree
+   * @param options
+   *          parameters for the distance or similarity calculation
    */
-  void newTreePanel(String type, String pwType, String title)
+  void newTreePanel(String type, ScoreModelI sm, SimilarityParamsI options)
   {
+    String frameTitle = "";
     TreePanel tp;
 
     if (viewport.getSelectionGroup() != null
@@ -3636,8 +3638,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
-      title = title + " on region";
-      tp = new TreePanel(alignPanel, type, pwType);
+      tp = new TreePanel(alignPanel, type, sm, options);
+      frameTitle = tp.getPanelTitle() + " on region";
     }
     else
     {
@@ -3661,19 +3663,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      tp = new TreePanel(alignPanel, type, pwType);
+      tp = new TreePanel(alignPanel, type, sm, options);
+      frameTitle = tp.getPanelTitle();
     }
 
-    title += " from ";
+    frameTitle += " from ";
 
     if (viewport.viewName != null)
     {
-      title += viewport.viewName + " of ";
+      frameTitle += viewport.viewName + " of ";
     }
 
-    title += this.title;
+    frameTitle += this.title;
 
-    Desktop.addInternalFrame(tp, title, 600, 500);
+    Desktop.addInternalFrame(tp, frameTitle, 600, 500);
   }
 
   /**
@@ -3949,13 +3952,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      jalview.io.NewickFile fin = null;
+      String filePath = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", filePath);
+      NewickFile fin = null;
       try
       {
-        fin = new NewickFile(choice, DataSourceType.FILE);
-        viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
+        fin = new NewickFile(filePath, DataSourceType.FILE);
+        viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
       } catch (Exception ex)
       {
         JvOptionPane
@@ -3977,25 +3980,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  public TreePanel ShowNewickTree(NewickFile nf, String title)
+  public TreePanel showNewickTree(NewickFile nf, String treeTitle)
   {
-    return ShowNewickTree(nf, title, 600, 500, 4, 5);
+    return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
   }
 
-  public TreePanel ShowNewickTree(NewickFile nf, String title,
-          AlignmentView input)
-  {
-    return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
-  }
-
-  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
+  public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
           int h, int x, int y)
   {
-    return ShowNewickTree(nf, title, null, w, h, x, y);
+    return showNewickTree(nf, treeTitle, null, w, h, x, y);
   }
 
   /**
-   * Add a treeviewer for the tree extracted from a newick file object to the
+   * Add a treeviewer for the tree extracted from a Newick file object to the
    * current alignment view
    * 
    * @param nf
@@ -4014,7 +4011,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          position
    * @return TreePanel handle
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title,
+  public TreePanel showNewickTree(NewickFile nf, String treeTitle,
           AlignmentView input, int w, int h, int x, int y)
   {
     TreePanel tp = null;
@@ -4025,7 +4022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (nf.getTree() != null)
       {
-        tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
+        tp = new TreePanel(alignPanel, nf, treeTitle, input);
 
         tp.setSize(w, h);
 
@@ -4034,7 +4031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           tp.setLocation(x, y);
         }
 
-        Desktop.addInternalFrame(tp, title, w, h);
+        Desktop.addInternalFrame(tp, treeTitle, w, h);
       }
     } catch (Exception ex)
     {
@@ -5636,17 +5633,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
-
-  public void newTreePanel(String treeType, ScoreModelI 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);
-  }
 }
 
 class PrintThread extends Thread