X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModelTest.java;h=66eb5a51241dfa1c1143a94fabce71820d869d5b;hb=f831ddf7f52d6c4a1918e87d94877b22bd322648;hp=029483f34ea4b28ba0fe09071ed0b0f126ff4558;hpb=f2110aa168a187f3207ad4dee2ab54f92f39b984;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 029483f..66eb5a5 100644
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -24,14 +24,26 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
+
+import java.util.Arrays;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FeatureScoreModelTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   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 };
@@ -43,7 +55,7 @@ public class FeatureScoreModelTest
   public AlignFrame getTestAlignmentFrame()
   {
     AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
-            alntestFile, FormatAdapter.PASTE);
+            alntestFile, DataSourceType.PASTE);
     AlignmentI al = alf.getViewport().getAlignment();
     Assert.assertEquals(al.getHeight(), 4);
     Assert.assertEquals(al.getWidth(), 5);
@@ -82,8 +94,8 @@ public class FeatureScoreModelTest
   {
     AlignFrame alf = getTestAlignmentFrame();
     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));
@@ -124,15 +136,58 @@ public class FeatureScoreModelTest
     alf.selectAllSequenceMenuItem_actionPerformed(null);
     float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
             true));
-    Assert.assertTrue(dm[0][2] == 0f,
+    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,
+    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++)
+    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)");
     }
   }
+
+  /**
+   * Check findFeatureAt doesn't return contact features except at contact
+   * points TODO:move to under the FeatureRendererModel test suite
+   */
+  @Test(groups = { "Functional" })
+  public void testFindFeatureAt_PointFeature() throws Exception
+  {
+    String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
+            + "c CCCCCCGGGGGGCCCCCC\n";
+    AlignFrame af = new jalview.io.FileLoader(false)
+            .LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
+    SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
+    SequenceFeature sf = null;
+    sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
+    aseq.addSequenceFeature(sf);
+    Assert.assertTrue(sf.isContactFeature());
+    af.refreshFeatureUI(true);
+    af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
+    Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
+            .size(), 1, "Should be just one feature type displayed");
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
+            .size(), 0);
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
+            .size(), 1);
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
+            .size(), 0);
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
+            .size(), 0);
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
+            .size(), 1);
+    // step through and check for pointwise feature presence/absence
+    Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
+            .size(), 0);
+  }
+
 }