Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d4c6009..32c5702 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -25,9 +25,9 @@ import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.TreeModel;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
@@ -35,8 +35,8 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.NodeTransformI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -76,7 +76,7 @@ public class TreePanel extends GTreePanel
 {
   String treeType;
 
-  ScoreModelI scoreModel; // if tree computed
+  String scoreModelName; // if tree computed
 
   String treeTitle; // if tree loaded
 
@@ -93,15 +93,15 @@ public class TreePanel extends GTreePanel
    * 
    * @param ap
    * @param type
-   * @param sm
+   * @param modelName
    * @param options
    */
-  public TreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
+  public TreePanel(AlignmentPanel ap, String type, String modelName,
           SimilarityParamsI options)
   {
     super();
     this.similarityParams = options;
-    initTreePanel(ap, type, sm, null, null);
+    initTreePanel(ap, type, modelName, null, null);
 
     // We know this tree has distances. JBPNote TODO: prolly should add this as
     // a userdefined default
@@ -126,13 +126,13 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av;
   }
 
-  void initTreePanel(AlignmentPanel ap, String type, ScoreModelI sm,
+  void initTreePanel(AlignmentPanel ap, String type, String modelName,
           NewickFile newTree, AlignmentView inputData)
   {
 
     av = ap.av;
     this.treeType = type;
-    this.scoreModel = sm;
+    this.scoreModelName = modelName;
 
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
     scrollPane.setViewportView(treeCanvas);
@@ -275,7 +275,8 @@ public class TreePanel extends GTreePanel
       }
       else
       {
-        ScoreModelI sm = configureScoreModel();
+        ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+                scoreModelName, treeCanvas.ap);
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
                 av, sm, similarityParams) : new AverageDistanceTree(av, sm,
                 similarityParams);
@@ -431,8 +432,7 @@ public class TreePanel extends GTreePanel
     {
     }
 
-    Object[] alAndColsel = originalData
-            .getAlignmentAndColumnSelection(gc);
+    Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
@@ -449,8 +449,8 @@ public class TreePanel extends GTreePanel
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al,
-                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+        AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+                AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
@@ -789,19 +789,17 @@ public class TreePanel extends GTreePanel
             }
             if (newname == null)
             {
-              SequenceFeature sf[] = sq.getSequenceFeatures();
-              for (int i = 0; sf != null && i < sf.length; i++)
+              List<SequenceFeature> features = sq.getFeatures()
+                      .getPositionalFeatures(labelClass);
+              for (SequenceFeature feature : features)
               {
-                if (sf[i].getType().equals(labelClass))
+                if (newname == null)
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = feature.getDescription();
+                }
+                else
+                {
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }
@@ -839,10 +837,9 @@ public class TreePanel extends GTreePanel
             + treeType.toLowerCase());
 
     /*
-     * i18n description (if available) of score model used
+     * short score model name (long description can be too long)
      */
-    String smn = MessageManager.getStringOrReturn("label.score_model_",
-            scoreModel.getName());
+    String smn = scoreModelName;
 
     /*
      * put them together as <method> Using <model>
@@ -851,28 +848,4 @@ public class TreePanel extends GTreePanel
             treecalcnm, smn);
     return ttl;
   }
-
-  /**
-   * If the score model is one that requires to get state data from the current
-   * view, create and configure a new instance of it
-   * 
-   * @return
-   */
-  protected ScoreModelI configureScoreModel()
-  {
-    if (scoreModel instanceof ViewBasedAnalysisI)
-    {
-      try
-      {
-        scoreModel = scoreModel.getClass().newInstance();
-        ((ViewBasedAnalysisI) scoreModel)
-                .configureFromAlignmentView(treeCanvas.ap);
-      } catch (Exception q)
-      {
-        Cache.log.error("Couldn't create a scoremodel instance for "
-                + scoreModel.getName());
-      }
-    }
-    return scoreModel;
-  }
 }