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 f2f0bf7..32c5702 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -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;
@@ -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)
+                {
+                  newname = feature.getDescription();
+                }
+                else
                 {
-                  if (newname == null)
-                  {
-                    newname = new String(sf[i].getDescription());
-                  }
-                  else
-                  {
-                    newname = newname + "; " + sf[i].getDescription();
-                  }
+                  newname = newname + "; " + feature.getDescription();
                 }
               }
             }
@@ -850,16 +848,4 @@ public class TreePanel extends GTreePanel
             treecalcnm, smn);
     return ttl;
   }
-
-  /**
-   * Instantiate an instance of the score model, configured for the current view
-   * if applicable
-   * 
-   * @return
-   */
-  protected ScoreModelI configureScoreModel()
-  {
-    return ScoreModels.getInstance().getScoreModel(scoreModelName,
-            treeCanvas.ap);
-  }
 }