{
// aligned column 8 is sequence position 6
String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
- af = new FileLoader().LoadFileWaitTillLoaded(s,
- DataSourceType.PASTE);
+ af = new FileLoader().LoadFileWaitTillLoaded(s, DataSourceType.PASTE);
av = af.getViewport();
seq = av.getAlignment().getSequenceAt(0);
fr = af.getFeatureRenderer();
@Test(groups = "Functional")
public void testFindFeatureColour_gapPosition()
{
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
- null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Metal", "Metal", 2, 12, 0f, null));
fr.setColour("Metal", new FeatureColour(Color.red));
fr.featuresAdded();
av.setShowSequenceFeatures(true);
/*
* currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
*/
- seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
- "Contact", 2, 12, Float.NaN, "Disulphide"));
+ seq.addSequenceFeature(new SequenceFeature("Disulphide Bond", "Contact",
+ 2, 12, Float.NaN, "Disulphide"));
fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
fr.featuresAdded();
av.setShowSequenceFeatures(true);
@Test(groups = "Functional")
public void testFindFeatureColour_graduatedFeatureColour()
{
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2, 2,
+ 0f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4, 4,
+ 5f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7, 7,
+ 10f, "KdGroup"));
/*
* graduated colour from 0 to 10
fr.setColour("Metal", red);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
-
+
/*
* the FeatureSettings transparency slider has range 0-70 which
* corresponds to a transparency value of 1 - 0.3
fr.setColour("Domain", green);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
-
+
/*
* Domain (green) rendered above Metal (red) above background (cyan)
* 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
fr.setTransparency(0.6f);
Color c = finder.findFeatureColour(Color.cyan, seq, 10);
assertEquals(c, new Color(61, 194, 41));
-
+
/*
* now promote Metal above Domain
* - currently no way other than mimicking reordering of
fr.setFeaturePriority(data);
c = finder.findFeatureColour(Color.cyan, seq, 10);
assertEquals(c, new Color(153, 102, 41));
-
+
/*
* ..and turn off display of Metal
* Domain (green) above background (pink)
{
String kdFeature = "kd";
String metalFeature = "Metal";
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4,
- 5f, "MetalGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
-
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 2, 2, 0f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 4, 4, 5f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4, 5f,
+ "MetalGroup"));
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 7, 7, 10f, "KdGroup"));
+
/*
* kd feature has graduated colour from 0 to 10
* above threshold value of 5
fr.setFeaturePriority(data);
av.setShowSequenceFeatures(true);
-
+
/*
* position 2, column 1, score 0 - below threshold - default colour
*/
*/
c = finder.findFeatureColour(Color.blue, seq, 3);
assertEquals(c, Color.green);
-
+
/*
* position 7, column 9, score 10 - maximum colour in range
*/