X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModelTest.java;h=2dc2ac3c359cb87c38da3c5e7433a32e2b527449;hb=547575f4b08f2cc25adcd438e8bce24e4e7af04e;hp=221b230b6878f11cfb12e1a0e9baabc2665d2d64;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 221b230..2dc2ac3 100644
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
@@ -14,20 +34,17 @@ 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(groups ={ "Functional" })
+  @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();
     AssertJUnit.assertEquals(4, al.getHeight());
     AssertJUnit.assertEquals(5, al.getWidth());
@@ -56,19 +73,20 @@ public class FeatureScoreModelTest
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
     AssertJUnit.assertEquals("Number of feature types", 3, alf
-            .getFeatureRenderer().getDisplayedFeatureTypes().length);
+            .getFeatureRenderer().getDisplayedFeatureTypes().size());
     AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
     FeatureScoreModel fsm = new FeatureScoreModel();
-    AssertJUnit.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));
     AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
             dm[0][2] == 0f);
-    AssertJUnit.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]);
 
   }
 }