JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 13e2360..0a33ea8 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -23,7 +23,7 @@ package jalview.gui;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.NJTree;
 import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -300,26 +300,9 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-        DistanceModelI sm = ScoreModels.getInstance().forName(pwtype);
-        if (sm instanceof ViewBasedAnalysisI)
-        {
-          try
-          {
-            sm = sm.getClass().newInstance();
-            ((ViewBasedAnalysisI) sm)
-                    .configureFromAlignmentView(treeCanvas.ap);
-          } catch (Exception q)
-          {
-            Cache.log.error("Couldn't create a scoremodel instance for "
-                    + sm.getName());
-          }
-          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
-        }
-        else
-        {
-          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
-                  end);
-        }
+        ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
+        sm = configureScoreModel(sm);
+        tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
         showDistances(true);
       }
 
@@ -898,4 +881,28 @@ 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, allow it to do so
+   * 
+   * @param sm
+   * @return
+   */
+  protected ScoreModelI configureScoreModel(ScoreModelI sm)
+  {
+    if (sm instanceof ViewBasedAnalysisI)
+    {
+      try
+      {
+        sm = sm.getClass().newInstance();
+        ((ViewBasedAnalysisI) sm).configureFromAlignmentView(treeCanvas.ap);
+      } catch (Exception q)
+      {
+        Cache.log.error("Couldn't create a scoremodel instance for "
+                + sm.getName());
+      }
+    }
+    return sm;
+  }
 }