From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 9 May 2017 08:59:13 +0000 (+0100)
Subject: JAL-2403 use preferred factory method to create score model
X-Git-Tag: Release_2_10_3b1~289
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=917622345899487d12d4e12bc1e0272d6ca86a87;p=jalview.git

JAL-2403 use preferred factory method to create score model
---

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 0577fae..4bcf5ab 100644
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,6 +23,7 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -113,12 +114,12 @@ public class FeatureDistanceModelTest
   public void testFeatureScoreModel() throws Exception
   {
     AlignFrame alf = getTestAlignmentFrame();
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI dm = fsm.findDistances(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
@@ -133,11 +134,11 @@ public class FeatureDistanceModelTest
     AlignFrame alf = getTestAlignmentFrame();
     // hiding first two columns shouldn't affect the tree
     alf.getViewport().hideColumns(0, 1);
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm.findDistances(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
@@ -153,11 +154,12 @@ public class FeatureDistanceModelTest
     // hide columns and check tree changes
     alf.getViewport().hideColumns(3, 4);
     alf.getViewport().hideColumns(0, 1);
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    // getName() can become static in Java 8
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm.findDistances(
+    MatrixI dm = sm.findDistances(
             alf.getViewport().getAlignmentView(true),
             SimilarityParams.Jalview);
     assertEquals(
@@ -252,13 +254,15 @@ public class FeatureDistanceModelTest
     alf.setShowSeqFeatures(true);
     alf.getFeatureRenderer().findAllFeatures(true);
 
-    FeatureDistanceModel fsm = new FeatureDistanceModel();
-    assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            alf.getCurrentView().getAlignPanel());
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI distances = fsm.findDistances(alf.getViewport()
-            .getAlignmentView(true), SimilarityParams.Jalview);
+    AlignmentView alignmentView = alf.getViewport()
+            .getAlignmentView(true);
+    MatrixI distances = sm.findDistances(alignmentView,
+            SimilarityParams.Jalview);
     assertEquals(distances.width(), 2);
     assertEquals(distances.height(), 2);
     assertEquals(distances.getValue(0, 0), 0d);
@@ -279,9 +283,10 @@ public class FeatureDistanceModelTest
     AlignViewport viewport = af.getViewport();
     AlignmentView view = viewport.getAlignmentView(false);
 
-    FeatureDistanceModel sm = new FeatureDistanceModel();
-    sm.configureFromAlignmentView(af.alignPanel);
-  
+    ScoreModelI sm = new FeatureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            af.alignPanel);
+
     /*
      * feature distance model always normalises by region width
      * gap-gap is always included (but scores zero)