X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=602ce9fb29aa7d53618ac749d65149742653a4c6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=7112c77b63514ee9391ee5090755870dfacf2f26;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 7112c77..602ce9f 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -24,27 +24,21 @@ import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; -import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; -import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; -import jalview.datamodel.AlignedCodonFrame; +import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Mapping; 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; import java.io.IOException; -import java.util.Iterator; import java.util.Map; -import java.util.Set; import org.testng.annotations.Test; @@ -59,7 +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); @@ -73,61 +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.sanger.ac.uk/family/PF00111", - sf.links.get(0).toString()); + assertEquals("Pfam 8_8|http://pfam.xfam.org/family/PF00111", + 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); @@ -146,10 +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, @@ -160,14 +165,14 @@ 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() .getSequenceFeatures(); assertEquals(1, sfs.length); SequenceFeature sf = sfs[0]; - assertEquals("Iron-sulfur; 2Fe-2S", sf.description); + assertEquals("Iron-sulfur,2Fe-2S", sf.description); assertEquals(44, sf.begin); assertEquals(45, sf.end); assertEquals("uniprot", sf.featureGroup); @@ -201,45 +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 @@ -250,7 +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" @@ -268,7 +234,7 @@ public class FeaturesFileTest assertEquals(1, sfs.length); SequenceFeature sf = sfs[0]; // description parsed from Note attribute - assertEquals("Iron-sulfur (2Fe-2S); another note", sf.description); + assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description); assertEquals(39, sf.begin); assertEquals(39, sf.end); assertEquals("uniprot", sf.featureGroup); @@ -281,7 +247,8 @@ public class FeaturesFileTest sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); assertEquals(1, sfs.length); sf = sfs[0]; - assertEquals("uniprot", sf.description); + // ID used for description if available + assertEquals("$23", sf.description); assertEquals(55, sf.begin); assertEquals(130, sf.end); assertEquals("uniprot", sf.featureGroup); @@ -301,7 +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(); /* @@ -338,7 +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); @@ -369,7 +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" }) @@ -386,9 +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); @@ -409,12 +375,79 @@ 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); checkDatasetfromSimpleGff3(dataset); } + + @Test(groups = { "Functional" }) + public void testPrintJalviewFormat() throws Exception + { + File f = new File("examples/uniref50.fa"); + AlignmentI al = readAlignmentFile(f); + AlignFrame af = new AlignFrame(al, 500, 500); + Map colours = af.getFeatureRenderer() + .getFeatureColours(); + String features = "METAL\tcc9900\n" + + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n" + + "Pfam\tred\n" + + "STARTGROUP\tuniprot\n" + + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + + "ENDGROUP\tuniprot\n"; + FeaturesFile featuresFile = new FeaturesFile(features, + FormatAdapter.PASTE); + featuresFile.parse(al.getDataset(), colours, false); + + /* + * first with no features displayed + */ + FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); + Map visible = fr.getDisplayedFeatureCols(); + String exported = featuresFile.printJalviewFormat( + al.getSequencesArray(), visible); + String expected = "No Features Visible"; + assertEquals(expected, exported); + + /* + * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam + */ + fr.setVisible("METAL"); + fr.setVisible("GAMMA-TURN"); + visible = fr.getDisplayedFeatureCols(); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), + visible); + expected = "METAL\tcc9900\n" + + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n" + + "\nSTARTGROUP\tuniprot\n" + + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + + "ENDGROUP\tuniprot\n"; + assertEquals(expected, exported); + + /* + * now set Pfam visible + */ + fr.setVisible("Pfam"); + visible = fr.getDisplayedFeatureCols(); + exported = featuresFile.printJalviewFormat(al.getSequencesArray(), + visible); + /* + * note the order of feature types is uncontrolled - derives from + * FeaturesDisplayed.featuresDisplayed which is a HashSet + */ + expected = "METAL\tcc9900\n" + + "Pfam\tff0000\n" + + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n" + + "\nSTARTGROUP\tuniprot\n" + + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + + "ENDGROUP\tuniprot\n"; + assertEquals(expected, exported); + } }