X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModelTest.java;h=309790fe71f117428bdf1dee12358a51e4f54e42;hb=1d123a551af539931e27fb96f4c8e767608bf3ab;hp=7776ccbd590e6468c88852916c29f2c4fc1472d6;hpb=a8ab01a310aa5c5cbbceef54f6ea6705fe427853;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 7776ccb..309790f 100644
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -40,8 +40,7 @@ public class FeatureScoreModelTest
 
   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);
@@ -75,9 +74,34 @@ public class FeatureScoreModelTest
     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();
+    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()));
+    Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+            .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
             true));
@@ -85,6 +109,32 @@ public class FeatureScoreModelTest
             "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)");
+    }
   }
 }