JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / test / jalview / analysis / scoremodels / FeatureScoreModelTest.java

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 1dbaa4a..61c4913 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis.scoremodels;
 
 import jalview.datamodel.AlignmentI;
@@ -7,30 +27,27 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 public class FeatureScoreModelTest
 {
   public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
 
-  int[] sf1 = new int[]
-  { 74, 74, 73, 73, 23, 23, -1, -1 };
+  int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
 
-  int[] sf2 = new int[]
-  { -1, -1, 74, 75, -1, -1, 76, 77 };
+  int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
 
-  int[] sf3 = new int[]
-  { -1, -1, -1, -1, -1, -1, 76, 77 };
+  int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testFeatureScoreModel() throws Exception
   {
-    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
-            FormatAdapter.PASTE);
+    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+            alntestFile, FormatAdapter.PASTE);
     AlignmentI al = alf.getViewport().getAlignment();
-    Assert.assertEquals(4, al.getHeight());
-    Assert.assertEquals(5, al.getWidth());
+    AssertJUnit.assertEquals(4, al.getHeight());
+    AssertJUnit.assertEquals(5, al.getWidth());
     for (int i = 0; i < 4; i++)
     {
       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
@@ -55,20 +72,21 @@ public class FeatureScoreModelTest
     alf.getFeatureRenderer().setVisible("sf2");
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
-    Assert.assertEquals("Number of feature types", 3, alf
+    AssertJUnit.assertEquals("Number of feature types", 3, alf
             .getFeatureRenderer().getDisplayedFeatureTypes().length);
-    Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+    AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     FeatureScoreModel fsm = new FeatureScoreModel();
-    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
-            .getAlignPanel()));
+    AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf
+            .getCurrentView().getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
+    AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
             dm[0][2] == 0f);
-    Assert.assertTrue(
-            "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
-            dm[0][1] > dm[0][2]);
+    AssertJUnit
+            .assertTrue(
+                    "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
+                    dm[0][1] > dm[0][2]);
 
   }
 }