X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2Fseqfeatures%2FFeatureRendererTest.java;h=dc86605ea6219b389045b6ade5a04793911a2472;hb=2066caec85bf0b332d924472fcfdbdaa07f56f1e;hp=ab5c137cbb8e772c1a70af2ddbbc9ffd17575af4;hpb=f5c1419b96dc540087bcf565140e6bbcdc2096aa;p=jalview.git

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index ab5c137..dc86605 100644
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -14,6 +14,7 @@ import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
@@ -138,9 +139,9 @@ public class FeatureRendererTest
   }
 
   @Test(groups = "Functional")
-  public void testFindFeaturesAtRes()
+  public void testFindFeaturesAtColumn()
   {
-    String seqData = ">s1\nabcdefghijklmnopqrstuvwxyz\n";
+    String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
     AlignViewportI av = af.getViewport();
@@ -150,7 +151,7 @@ public class FeatureRendererTest
     /*
      * with no features
      */
-    List<SequenceFeature> features = fr.findFeaturesAtRes(seq, 3);
+    List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
     assertTrue(features.isEmpty());
 
     /*
@@ -159,34 +160,43 @@ public class FeatureRendererTest
     SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
             "Group"); // non-positional
     seq.addSequenceFeature(sf1);
-    SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 5, 15, 1f,
+    SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
             "Group1");
     seq.addSequenceFeature(sf2);
-    SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+    SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
             "Group2");
     seq.addSequenceFeature(sf3);
-    SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 5, 15, 1f,
+    SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
             null); // null group is always treated as visible
     seq.addSequenceFeature(sf4);
 
     /*
      * add contact features
      */
-    SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 4,
-            12, 1f, "Group1");
+    SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+            15, 1f, "Group1");
     seq.addSequenceFeature(sf5);
-    SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 4,
-            12, 1f, "Group2");
+    SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+            15, 1f, "Group2");
     seq.addSequenceFeature(sf6);
-    SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 4,
-            12, 1f, null);
+    SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
+            15, 1f, null);
     seq.addSequenceFeature(sf7);
 
+    // feature spanning B--C
+    SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
+            "Group");
+    seq.addSequenceFeature(sf8);
+    // contact feature B/C
+    SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
+            6, 1f, "Group");
+    seq.addSequenceFeature(sf9);
+
     /*
      * let feature renderer discover features (and make visible)
      */
     fr.findAllFeatures(true);
-    features = fr.findFeaturesAtRes(seq, 12); // all positional
+    features = fr.findFeaturesAtColumn(seq, 15); // all positional
     assertEquals(features.size(), 6);
     assertTrue(features.contains(sf2));
     assertTrue(features.contains(sf3));
@@ -198,7 +208,7 @@ public class FeatureRendererTest
     /*
      * at a non-contact position
      */
-    features = fr.findFeaturesAtRes(seq, 11);
+    features = fr.findFeaturesAtColumn(seq, 14);
     assertEquals(features.size(), 3);
     assertTrue(features.contains(sf2));
     assertTrue(features.contains(sf3));
@@ -214,7 +224,8 @@ public class FeatureRendererTest
     data[2] = new Object[] { "Type3", colour, true };
     data[3] = new Object[] { "Disulphide Bond", colour, true };
     fr.setFeaturePriority(data);
-    features = fr.findFeaturesAtRes(seq, 12);
+
+    features = fr.findFeaturesAtColumn(seq, 15);
     assertEquals(features.size(), 5); // no sf2
     assertTrue(features.contains(sf3));
     assertTrue(features.contains(sf4));
@@ -226,10 +237,127 @@ public class FeatureRendererTest
      * make "Group2" not displayed
      */
     fr.setGroupVisibility("Group2", false);
-    features = fr.findFeaturesAtRes(seq, 12);
+
+    features = fr.findFeaturesAtColumn(seq, 15);
     assertEquals(features.size(), 3); // no sf2, sf3, sf6
     assertTrue(features.contains(sf4));
     assertTrue(features.contains(sf5));
     assertTrue(features.contains(sf7));
+
+    // features 'at' a gap between b and c
+    // - returns enclosing feature BC but not contact feature B/C
+    features = fr.findFeaturesAtColumn(seq, 4);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf8));
+    features = fr.findFeaturesAtColumn(seq, 5);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf8));
+  }
+
+  @Test(groups = "Functional")
+  public void testFilterFeaturesForDisplay()
+  {
+    String seqData = ">s1\nabcdef\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    List<SequenceFeature> features = new ArrayList<>();
+    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, Float.NaN,
+            "group1");
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, 2f,
+            "group2");
+    seq.addSequenceFeature(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, 3f,
+            "group3");
+    seq.addSequenceFeature(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, 4f,
+            "group4");
+    seq.addSequenceFeature(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, 5f,
+            "group4");
+    seq.addSequenceFeature(sf5);
+
+    fr.findAllFeatures(true);
+
+    features = seq.getSequenceFeatures();
+    assertEquals(features.size(), 5);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filter out duplicate (co-located) features
+     * note: which gets removed is not guaranteed
+     */
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2) || features.contains(sf3));
+    assertFalse(features.contains(sf2) && features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 3 - sf3 is removed, sf2 is retained
+     */
+    fr.setGroupVisibility("group3", false);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2));
+    assertFalse(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 2, show group 3 - sf2 is removed, sf3 is retained
+     */
+    fr.setGroupVisibility("group2", false);
+    fr.setGroupVisibility("group3", true);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, null);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * no filtering of co-located features with graduated colour scheme
+     * filterFeaturesForDisplay does _not_ check colour threshold
+     * sf2 is removed as its group is hidden
+     */
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
+            Color.white, 0f, 1f));
+    assertEquals(features.size(), 4);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filtering of co-located features with colour by label
+     */
+    features = seq.getSequenceFeatures();
+    FeatureColour fc = new FeatureColour(Color.black);
+    fc.setColourByLabel(true);
+    fr.filterFeaturesForDisplay(features, fc);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
   }
 }