From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 27 Sep 2018 15:23:16 +0000 (+0100)
Subject: JAL-2791 method that tests all conditions for feature visibility
X-Git-Tag: Release_2_11_0~17^2~81^2~3
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=356260e6aa37640091849355ed97cd4103cc4c6c

JAL-2791 method that tests all conditions for feature visibility
---

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index cf3c8da..28fe550 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -265,4 +265,19 @@ public interface FeatureRenderer
    * @return
    */
   Color getColour(SequenceFeature feature);
+
+  /**
+   * Answers true if feature would be shown, else false. A feature is shown if
+   * <ul>
+   * <li>its feature type is set to visible</li>
+   * <li>its feature group is either null, or set to visible</li>
+   * <li>it is not excluded by a colour threshold on score or other numeric
+   * attribute</li>
+   * <li>it is not excluded by a filter condition</li>
+   * </ul>
+   * 
+   * @param feature
+   * @return
+   */
+  boolean isVisible(SequenceFeature feature);
 }
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 553f813..2aadee4 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1150,4 +1150,32 @@ public abstract class FeatureRendererModel
     return filter == null ? true : filter.matches(sf);
   }
 
+  @Override
+  public boolean isVisible(SequenceFeature feature)
+  {
+    if (feature == null)
+    {
+      return false;
+    }
+    if (getFeaturesDisplayed() == null
+            || !getFeaturesDisplayed().isVisible(feature.getType()))
+    {
+      return false;
+    }
+    if (featureGroupNotShown(feature))
+    {
+      return false;
+    }
+    FeatureColourI fc = featureColours.get(feature.getType());
+    if (fc != null && fc.isOutwithThreshold(feature))
+    {
+      return false;
+    }
+    if (!featureMatchesFilters(feature))
+    {
+      return false;
+    }
+    return true;
+  }
+
 }
diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 11b129e..7c9927f 100644
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -535,4 +535,71 @@ public class FeatureRendererTest
     csqData.put("Feature", "ENST01234");
     assertEquals(fr.getColour(sf2), expected);
   }
+
+  @Test(groups = "Functional")
+  public void testIsVisible()
+  {
+    String seqData = ">s1\nMLQGIFPRS\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+    SequenceFeature sf = new SequenceFeature("METAL", "Desc", 10, 10, 1f,
+            "Group");
+    sf.setValue("AC", "11");
+    sf.setValue("CLIN_SIG", "Likely Pathogenic");
+    seq.addSequenceFeature(sf);
+
+    assertFalse(fr.isVisible(null));
+
+    /*
+     * initial state FeatureRenderer hasn't 'found' feature
+     * and so its feature type has not yet been set visible
+     */
+    assertFalse(fr.getDisplayedFeatureCols().containsKey("METAL"));
+    assertFalse(fr.isVisible(sf));
+
+    fr.findAllFeatures(true);
+    assertTrue(fr.isVisible(sf));
+
+    /*
+     * feature group not visible
+     */
+    fr.setGroupVisibility("Group", false);
+    assertFalse(fr.isVisible(sf));
+    fr.setGroupVisibility("Group", true);
+    assertTrue(fr.isVisible(sf));
+
+    /*
+     * feature score outwith colour threshold (score > 2)
+     */
+    FeatureColourI fc = new FeatureColour(Color.white, Color.black,
+            Color.white, 0, 10);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(2f);
+    fr.setColour("METAL", fc);
+    assertFalse(fr.isVisible(sf)); // score 1 is not above threshold 2
+    fc.setBelowThreshold(true);
+    assertTrue(fr.isVisible(sf)); // score 1 is below threshold 2
+
+    /*
+     * colour with threshold on attribute AC (value is 11)
+     */
+    fc.setAttributeName("AC");
+    assertFalse(fr.isVisible(sf)); // value 11 is not below threshold 2
+    fc.setAboveThreshold(true);
+    assertTrue(fr.isVisible(sf)); // value 11 is above threshold 2
+
+    fc.setAttributeName("AF"); // attribute AF is absent in sf
+    assertTrue(fr.isVisible(sf)); // feature is not excluded by threshold
+
+    FeatureMatcherSetI filter = new FeatureMatcherSet();
+    filter.and(FeatureMatcher.byAttribute(Condition.Contains, "pathogenic",
+            "CLIN_SIG"));
+    fr.setFeatureFilter("METAL", filter);
+    assertTrue(fr.isVisible(sf)); // feature matches filter
+    filter.and(FeatureMatcher.byScore(Condition.LE, "0.4"));
+    assertFalse(fr.isVisible(sf)); // feature doesn't match filter
+  }
 }