X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=602ce9fb29aa7d53618ac749d65149742653a4c6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=73d8826c35302e7ba852b744df890d8a4018f929;hpb=36f0df29daedd58814b8a6ccd67a16dc3b1614b8;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 73d8826..602ce9f 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; @@ -54,7 +53,7 @@ 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(); FeaturesFile featuresFile = new FeaturesFile( "examples/exampleFeatures.txt", FormatAdapter.FILE); @@ -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); @@ -141,10 +150,11 @@ 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" + 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, @@ -155,7 +165,7 @@ public class FeaturesFileTest // 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() @@ -196,45 +206,6 @@ 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 +216,7 @@ 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" @@ -297,7 +268,7 @@ 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(); /* @@ -334,7 +305,7 @@ public class FeaturesFileTest { assertEquals("no sequences extracted from GFF3 file", 2, dataset.getHeight()); - + SequenceI seq1 = dataset.findName("seq1"); SequenceI seq2 = dataset.findName("seq2"); assertNotNull(seq1); @@ -365,7 +336,7 @@ public class FeaturesFileTest "Expected at least one CDNA/Protein mapping for seq1", dataset.getCodonFrame(seq1) != null && dataset.getCodonFrame(seq1).size() > 0); - + } @Test(groups = { "Functional" }) @@ -382,9 +353,8 @@ public class FeaturesFileTest public void simpleGff3FileClass() throws IOException { AlignmentI dataset = new Alignment(new SequenceI[] {}); - FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); - + FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE); + boolean parseResult = ffile.parse(dataset, null, false, false); assertTrue("return result should be true", parseResult); checkDatasetfromSimpleGff3(dataset); @@ -405,9 +375,8 @@ public class FeaturesFileTest public void simpleGff3RelaxedIdMatching() throws IOException { AlignmentI dataset = new Alignment(new SequenceI[] {}); - FeaturesFile ffile = new FeaturesFile(simpleGffFile, - FormatAdapter.FILE); - + FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE); + boolean parseResult = ffile.parse(dataset, null, false, true); assertTrue("return result (relaxedID matching) should be true", parseResult); @@ -420,7 +389,7 @@ 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" @@ -438,8 +407,7 @@ public class FeaturesFileTest * first with no features displayed */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); - Map visible = fr - .getDisplayedFeatureCols(); + Map visible = fr.getDisplayedFeatureCols(); String exported = featuresFile.printJalviewFormat( al.getSequencesArray(), visible); String expected = "No Features Visible";