Merge branch 'releases/Release_2_10_4_Branch' into develop

[jalview.git] / test / jalview / renderer / OverviewRendererTest.java

diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
new file mode 100644 (file)
index 0000000..bc9c2e4
--- /dev/null
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -0,0 +1,73 @@
+package jalview.renderer;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+public class OverviewRendererTest
+{
+
+  @Test
+  public void testGetColumnColourFromSequence()
+  {
+    OverviewResColourFinder cf = new OverviewResColourFinder(false,
+            Color.PINK, Color.green); // gapColour, hiddenColour
+    Sequence seq1 = new Sequence("seq1", "PQ-RL-");
+    Sequence seq2 = new Sequence("seq2", "FVE");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignmentViewport av = new AlignViewport(al);
+    OverviewDimensions od = new OverviewDimensionsShowHidden(new ViewportRanges(al), false);
+    ResidueShaderI rs = new ResidueShader(new ZappoColourScheme());
+    FeatureRenderer fr = new FeatureRenderer(av);
+    OverviewRenderer or = new OverviewRenderer(fr, od, al, rs, cf);
+
+    // P is magenta (see ResidueProperties.zappo)
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0), Color.magenta.getRGB());
+    // Q is green
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 1),
+            Color.green.getRGB());
+    // gap is pink (specified in OverviewResColourFinder constructor above)
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 2),
+            Color.pink.getRGB());
+    // F is orange
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 0),
+            Color.orange.getRGB());
+    // E is red
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 2),
+            Color.red.getRGB());
+    // past end of sequence colour as gap (JAL-2929)
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 3),
+            Color.pink.getRGB());
+
+    /*
+     * now add a feature on seq1
+     */
+    seq1.addSequenceFeature(
+            new SequenceFeature("Pfam", "desc", 1, 4, null));
+    fr.findAllFeatures(true);
+    av.setShowSequenceFeatures(true);
+    fr.setColour("Pfam", new FeatureColour(Color.yellow));
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
+            Color.yellow.getRGB());
+
+    // don't show sequence features
+    av.setShowSequenceFeatures(false);
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
+            Color.magenta.getRGB());
+  }
+}