test/jalview/renderer/OverviewRendererTest.java

   1 package jalview.renderer;
   2
   3 import static org.testng.Assert.assertEquals;
   4
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.gui.AlignViewport;
  11 import jalview.renderer.seqfeatures.FeatureRenderer;
  12 import jalview.schemes.FeatureColour;
  13 import jalview.schemes.ZappoColourScheme;
  14 import jalview.viewmodel.AlignmentViewport;
  15 import jalview.viewmodel.OverviewDimensions;
  16 import jalview.viewmodel.OverviewDimensionsShowHidden;
  17 import jalview.viewmodel.ViewportRanges;
  18
  19 import java.awt.Color;
  20
  21 import org.testng.annotations.Test;
  22 public class OverviewRendererTest
  23 {
  24
  25   @Test
  26   public void testGetColumnColourFromSequence()
  27   {
  28     OverviewResColourFinder cf = new OverviewResColourFinder(false,
  29             Color.PINK, Color.green); // gapColour, hiddenColour
  30     Sequence seq1 = new Sequence("seq1", "PQ-RL-");
  31     Sequence seq2 = new Sequence("seq2", "FVE");
  32     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
  33     AlignmentViewport av = new AlignViewport(al);
  34     OverviewDimensions od = new OverviewDimensionsShowHidden(new ViewportRanges(al), false);
  35     ResidueShaderI rs = new ResidueShader(new ZappoColourScheme());
  36     FeatureRenderer fr = new FeatureRenderer(av);
  37     OverviewRenderer or = new OverviewRenderer(fr, od, al, rs, cf);
  38
  39     // P is magenta (see ResidueProperties.zappo)
  40     assertEquals(or.getColumnColourFromSequence(null, seq1, 0), Color.magenta.getRGB());
  41     // Q is green
  42     assertEquals(or.getColumnColourFromSequence(null, seq1, 1),
  43             Color.green.getRGB());
  44     // gap is pink (specified in OverviewResColourFinder constructor above)
  45     assertEquals(or.getColumnColourFromSequence(null, seq1, 2),
  46             Color.pink.getRGB());
  47     // F is orange
  48     assertEquals(or.getColumnColourFromSequence(null, seq2, 0),
  49             Color.orange.getRGB());
  50     // E is red
  51     assertEquals(or.getColumnColourFromSequence(null, seq2, 2),
  52             Color.red.getRGB());
  53     // past end of sequence colour as gap (JAL-2929)
  54     assertEquals(or.getColumnColourFromSequence(null, seq2, 3),
  55             Color.pink.getRGB());
  56
  57     /*
  58      * now add a feature on seq1
  59      */
  60     seq1.addSequenceFeature(
  61             new SequenceFeature("Pfam", "desc", 1, 4, null));
  62     fr.findAllFeatures(true);
  63     av.setShowSequenceFeatures(true);
  64     fr.setColour("Pfam", new FeatureColour(Color.yellow));
  65     assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
  66             Color.yellow.getRGB());
  67
  68     // don't show sequence features
  69     av.setShowSequenceFeatures(false);
  70     assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
  71             Color.magenta.getRGB());
  72   }
  73 }