X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=0cfe46a2a480ae114385d9a823d6321baae7b2c8;hb=019a78415854a8c7fbfe0b566174ede7e69f24b8;hp=73d8826c35302e7ba852b744df890d8a4018f929;hpb=36f0df29daedd58814b8a6ccd67a16dc3b1614b8;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 73d8826..0cfe46a 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNotNull; 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; @@ -33,8 +34,6 @@ import jalview.datamodel.SequenceDummy; 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; @@ -54,10 +53,10 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( - "examples/exampleFeatures.txt", FormatAdapter.FILE); + "examples/exampleFeatures.txt", DataSourceType.FILE); assertTrue("Test " + "Features file test" + "\nFailed to parse features file.", featuresFile.parse(al.getDataset(), colours, true)); @@ -68,61 +67,71 @@ public class FeaturesFileTest */ 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 */ SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); // FER_CAPAA - assertEquals(7, sfs.length); + assertEquals(8, sfs.length); SequenceFeature sf = sfs[0]; + assertEquals("Pfam family%LINK%", sf.description); + assertEquals(0, sf.begin); + assertEquals(0, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("Pfam", sf.type); + assertEquals(1, sf.links.size()); + assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111", + sf.links.get(0)); + + sf = sfs[1]; assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(39, sf.begin); assertEquals(39, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("METAL", sf.type); - sf = sfs[1]; + sf = sfs[2]; assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(44, sf.begin); assertEquals(44, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("METAL", sf.type); - sf = sfs[2]; + sf = sfs[3]; assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(47, sf.begin); assertEquals(47, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("METAL", sf.type); - sf = sfs[3]; + sf = sfs[4]; assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(77, sf.begin); assertEquals(77, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("METAL", sf.type); - sf = sfs[4]; + sf = sfs[5]; assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%", sf.description); assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111", - sf.links.get(0).toString()); + sf.links.get(0)); assertEquals(8, sf.begin); assertEquals(83, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("Pfam", sf.type); - sf = sfs[5]; + sf = sfs[6]; assertEquals("Ferredoxin_fold Status: True Positive ", sf.description); assertEquals(3, sf.begin); assertEquals(93, sf.end); assertEquals("uniprot", sf.featureGroup); assertEquals("Cath", sf.type); - sf = sfs[6]; + sf = sfs[7]; assertEquals( "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%", sf.description); assertEquals( "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0", - sf.links.get(0).toString()); + sf.links.get(0)); assertEquals(89, sf.begin); assertEquals(89, sf.end); assertEquals("netphos", sf.featureGroup); @@ -141,21 +150,21 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); // GFF2 uses space as name/value separator in column 9 String gffData = "METAL\tcc9900\n" + "GFF\n" + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n" + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t."; FeaturesFile featuresFile = new FeaturesFile(gffData, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); // 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() @@ -187,8 +196,8 @@ public class FeaturesFileTest String ff = f.getPath(); FormatAdapter rf = new FormatAdapter(); - AlignmentI al = rf.readFile(ff, FormatAdapter.FILE, - new IdentifyFile().identify(ff, FormatAdapter.FILE)); + AlignmentI al = rf.readFile(ff, DataSourceType.FILE, + new IdentifyFile().identify(ff, DataSourceType.FILE)); al.setDataset(null); // creates dataset sequences assertNotNull("Couldn't read supplied alignment data.", al); @@ -196,45 +205,6 @@ public class FeaturesFileTest } /** - * 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 @@ -245,7 +215,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); // GFF3 uses '=' separator for name/value pairs in colum 9 String gffData = "##gff-version 3\n" @@ -253,7 +223,7 @@ public class FeaturesFileTest + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n" + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23"; FeaturesFile featuresFile = new FeaturesFile(gffData, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); @@ -297,7 +267,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); /* @@ -306,7 +276,7 @@ public class FeaturesFileTest String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n" + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n"; FeaturesFile featuresFile = new FeaturesFile(featureData, - FormatAdapter.PASTE); + DataSourceType.PASTE); assertTrue("Failed to parse features file", featuresFile.parse(al.getDataset(), colours, true)); @@ -372,7 +342,7 @@ public class FeaturesFileTest public void readGff3File() throws IOException { FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile, - FormatAdapter.FILE); + DataSourceType.FILE); Alignment dataset = new Alignment(gffreader.getSeqsAsArray()); gffreader.addProperties(dataset); checkDatasetfromSimpleGff3(dataset); @@ -383,7 +353,7 @@ public class FeaturesFileTest { AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); + DataSourceType.FILE); boolean parseResult = ffile.parse(dataset, null, false, false); assertTrue("return result should be true", parseResult); @@ -394,7 +364,7 @@ public class FeaturesFileTest public void simpleGff3FileLoader() throws IOException { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( - simpleGffFile, FormatAdapter.FILE); + simpleGffFile, DataSourceType.FILE); assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); @@ -406,7 +376,7 @@ public class FeaturesFileTest { AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); + DataSourceType.FILE); boolean parseResult = ffile.parse(dataset, null, false, true); assertTrue("return result (relaxedID matching) should be true", @@ -420,7 +390,7 @@ public class FeaturesFileTest File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); - Map colours = af.getFeatureRenderer() + Map colours = af.getFeatureRenderer() .getFeatureColours(); String features = "METAL\tcc9900\n" + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n" @@ -431,14 +401,14 @@ public class FeaturesFileTest + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + "ENDGROUP\tuniprot\n"; FeaturesFile featuresFile = new FeaturesFile(features, - FormatAdapter.PASTE); + DataSourceType.PASTE); featuresFile.parse(al.getDataset(), colours, false); /* * first with no features displayed */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = fr + Map visible = fr .getDisplayedFeatureCols(); String exported = featuresFile.printJalviewFormat( al.getSequencesArray(), visible);