From 6a144c3b2b7f5f04d908c065a017088453bb7fc7 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 9 Oct 2017 23:22:24 +0100
Subject: [PATCH] fixed incorrect panel title

---
 src/jalview/gui/AlignFrame.java         |    5 ++---
 src/jalview/gui/CalculationChooser.java |    6 +++---
 src/jalview/gui/TreePanel.java          |   12 ++++--------
 3 files changed, 9 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d740303..8f10621 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,7 +35,6 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
@@ -3566,7 +3565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    */
   void newTreePanel(TreeModel tree, String treeAlgo,
-          SimilarityParamsI params)
+          String substitutionMatrix)
   {
     String frameTitle = "";
     TreePanel tp;
@@ -3602,7 +3601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
     }
 
-    tp = new TreePanel(alignPanel, tree, treeAlgo, params);
+    tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
 
     frameTitle += " from ";
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index de4fd37..d0315a6 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -479,7 +479,7 @@ public class CalculationChooser extends JPanel
       TreeBuilder calculatedTree = treeCalculator
               .makeTree(af.getViewport());
       TreeModel tree = new TreeModel(calculatedTree);
-      openTreePanel(tree, treeAlgo, params);
+      openTreePanel(tree, treeAlgo, substitutionMatrix);
 
       ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
 
@@ -522,7 +522,7 @@ public class CalculationChooser extends JPanel
    * @param treeAlgo
    */
   protected void openTreePanel(TreeModel tree, String treeAlgo,
-          SimilarityParamsI params)
+          String substitutionMatrix)
   {
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave
@@ -530,7 +530,7 @@ public class CalculationChooser extends JPanel
      */
     checkEnoughSequences(af.getViewport());
 
-    af.newTreePanel(tree, treeAlgo, params);
+    af.newTreePanel(tree, treeAlgo, substitutionMatrix);
   }
 
   /**
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index dbd5752..67ac836 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.TreeModel;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
@@ -70,13 +69,10 @@ import org.jibble.epsgraphics.EpsGraphics2D;
  */
 public class TreePanel extends GTreePanel
 {
-
-  SimilarityParamsI similarityParams;
+  String substitutionMatrix;
 
   String treeType;
 
-  String scoreModelName; // if tree computed
-
   String treeTitle; // if tree loaded
 
   TreeCanvas treeCanvas;
@@ -92,11 +88,11 @@ public class TreePanel extends GTreePanel
    * @param tree
    */
   public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
-          SimilarityParamsI params)
+          String substitutionMatrix)
   {
     super();
     this.treeType = treeType;
-    this.similarityParams = params;
+    this.substitutionMatrix = substitutionMatrix;
     this.tree = tree;
     initNewTreePanel(ap, tree);
 
@@ -868,7 +864,7 @@ public void buildTreeCanvas(AlignmentPanel ap) {
       /*
        * short score model name (long description can be too long)
        */
-      String smn = scoreModelName;
+      String smn = substitutionMatrix;
 
       /*
        * put them together as <method> Using <model>
-- 
1.7.10.2