import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.FeatureColourI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
import java.awt.Color;
import java.io.File;
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", FormatAdapter.FILE);
*/
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("26 feature group colours not found", 26, colours.size());
- assertEquals(colours.get("Cath"), new Color(0x93b1d1));
- assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
+ assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
/*
* verify (some) features on sequences
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF2 uses space as name/value separator in column 9
String gffData = "METAL\tcc9900\n" + "GFF\n"
// verify colours read or synthesized
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("1 feature group colours not found", 1, colours.size());
- assertEquals(colours.get("METAL"), new Color(0xcc9900));
+ assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
// verify feature on FER_CAPAA
SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
}
/**
- * Test various ways of describing a feature colour scheme
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testParseGraduatedColourScheme() throws Exception
- {
- FeaturesFile ff = new FeaturesFile();
-
- // colour by label:
- GraduatedColor gc = ff.parseGraduatedColourScheme(
- "BETA-TURN-IR\t9a6a94", "label");
- assertTrue(gc.isColourByLabel());
- assertEquals(Color.white, gc.getMinColor());
- assertEquals(Color.black, gc.getMaxColor());
- assertTrue(gc.isAutoScale());
-
- // using colour name, rgb, etc:
- String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertFalse(gc.isColourByLabel());
- assertEquals(Color.blue, gc.getMinColor());
- assertEquals(new Color(255, 0, 255), gc.getMaxColor());
- assertFalse(gc.isAutoScale());
- assertFalse(gc.getTolow());
- assertEquals(20.0f, gc.getMin(), 0.001f);
- assertEquals(95.0f, gc.getMax(), 0.001f);
- assertEquals(AnnotationColourGradient.BELOW_THRESHOLD,
- gc.getThreshType());
- assertEquals(66.0f, gc.getThresh(), 0.001f);
-
- // inverse gradient high to low:
- spec = "blue|255,0,255|95.0|20.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertTrue(gc.isAutoScale());
- assertTrue(gc.getTolow());
- }
-
- /**
* Test parsing a features file with GFF formatted content only
*
* @throws Exception
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF3 uses '=' separator for name/value pairs in colum 9
String gffData = "##gff-version 3\n"
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
/*
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
String features = "METAL\tcc9900\n"
+ "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
* first with no features displayed
*/
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
- Map<String, Object> visible = fr
+ Map<String, FeatureColourI> visible = fr
.getDisplayedFeatureCols();
String exported = featuresFile.printJalviewFormat(
al.getSequencesArray(), visible);