From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 21 Nov 2016 16:22:19 +0000 (+0000)
Subject: JAL-2335 failing test for FeatureRendererModel.findFeaturesAt and contact features
X-Git-Tag: Release_2_10_1~10^2~1^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2fb8ded1937a137d5bb33abfd8f103ff4edd9747;p=jalview.git

JAL-2335 failing test for FeatureRendererModel.findFeaturesAt and contact features
---

diff --git a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
index 309790f..292b576 100644
--- a/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureScoreModelTest.java
@@ -27,6 +27,8 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
+import java.util.Arrays;
+
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -137,4 +139,45 @@ public class FeatureScoreModelTest
               + "(" + 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, FormatAdapter.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);
+  }
+
 }