X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModelTest.java;h=029483f34ea4b28ba0fe09071ed0b0f126ff4558;hb=b4ae8736c4d0d6bcba332dc875dd5eabd8d4c851;hp=221b230b6878f11cfb12e1a0e9baabc2665d2d64;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 221b230..029483f 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;
@@ -7,30 +27,26 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
-import org.testng.AssertJUnit;
+import org.testng.Assert;
 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(groups ={ "Functional" })
-  public void testFeatureScoreModel() throws Exception
+  public AlignFrame getTestAlignmentFrame()
   {
-    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());
+    Assert.assertEquals(al.getHeight(), 4);
+    Assert.assertEquals(al.getWidth(), 5);
     for (int i = 0; i < 4; i++)
     {
       SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
@@ -55,20 +71,68 @@ public class FeatureScoreModelTest
     alf.getFeatureRenderer().setVisible("sf2");
     alf.getFeatureRenderer().setVisible("sf3");
     alf.getFeatureRenderer().findAllFeatures(true);
-    AssertJUnit.assertEquals("Number of feature types", 3, alf
-            .getFeatureRenderer().getDisplayedFeatureTypes().length);
-    AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+    Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
+            .size(), 3, "Number of feature types");
+    Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+    return alf;
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFeatureScoreModel() throws Exception
+  {
+    AlignFrame alf = getTestAlignmentFrame();
     FeatureScoreModel fsm = new FeatureScoreModel();
-    AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+    Assert.assertTrue(fsm.configureFromAlignmentView(alf
+            .getCurrentView().getAlignPanel()));
+    alf.selectAllSequenceMenuItem_actionPerformed(null);
+    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+            true));
+    Assert.assertTrue(dm[0][2] == 0f,
+            "FER1_MESCR (0) should be identical with RAPSA (2)");
+    Assert.assertTrue(dm[0][1] > dm[0][2],
+            "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
+  {
+    AlignFrame alf = getTestAlignmentFrame();
+    // hiding first two columns shouldn't affect the tree
+    alf.getViewport().hideColumns(0, 1);
+    FeatureScoreModel fsm = new FeatureScoreModel();
+    Assert.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]);
+    Assert.assertTrue(dm[0][2] == 0f,
+            "FER1_MESCR (0) should be identical with RAPSA (2)");
+    Assert.assertTrue(dm[0][1] > dm[0][2],
+            "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
+  }
 
+  @Test(groups = { "Functional" })
+  public void testFeatureScoreModel_HiddenColumns() throws Exception
+  {
+    AlignFrame alf = getTestAlignmentFrame();
+    // hide columns and check tree changes
+    alf.getViewport().hideColumns(3, 4);
+    alf.getViewport().hideColumns(0, 1);
+    FeatureScoreModel fsm = new FeatureScoreModel();
+    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+            .getAlignPanel()));
+    alf.selectAllSequenceMenuItem_actionPerformed(null);
+    float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+            true));
+    Assert.assertTrue(dm[0][2] == 0f,
+            "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
+    Assert.assertTrue(dm[0][1] == 0f,
+            "After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
+    for (int s=0;s<3;s++)
+    {
+      Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns "
+              + alf.getViewport().getAlignment().getSequenceAt(s).getName()
+              + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
+    }
   }
 }