X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=29bd56769b1124972011494993eef11e599c458b;hb=c9439f328825bc3061835f39c81a79920f50ef32;hp=ed388a5f1aecae14f188fe16961174411d5c7cca;hpb=ab9351a591e5295be9e41bfa86238ccc2a8024f8;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index ed388a5..29bd567 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.FeatureRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; @@ -45,9 +46,7 @@ import org.testng.annotations.Test; public class FeaturesFileTest { - private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa", - exonerateOutput = "examples/testdata/exonerateoutput.gff", - simpleGffFile = "examples/testdata/simpleGff3.gff"; + private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; @Test(groups = { "Functional" }) public void testParse() throws Exception @@ -77,53 +76,63 @@ public class FeaturesFileTest */ 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); @@ -144,8 +153,9 @@ public class FeaturesFileTest AlignFrame af = new AlignFrame(al, 500, 500); 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.\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); @@ -162,7 +172,7 @@ public class FeaturesFileTest .getSequenceFeatures(); assertEquals(1, sfs.length); SequenceFeature sf = sfs[0]; - assertEquals("uniprot", sf.description); + assertEquals("Iron-sulfur,2Fe-2S", sf.description); assertEquals(44, sf.begin); assertEquals(45, sf.end); assertEquals("uniprot", sf.featureGroup); @@ -240,17 +250,18 @@ public class FeaturesFileTest * @throws Exception */ @Test(groups = { "Functional" }) - public void testParse_pureGff() throws Exception + public void testParse_pureGff3() 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 gffData = "##gff-version 2\n" + // GFF3 uses '=' separator for name/value pairs in colum 9 + String gffData = "##gff-version 3\n" + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t" + "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."; + + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23"; FeaturesFile featuresFile = new FeaturesFile(gffData, FormatAdapter.PASTE); assertTrue("Failed to parse features file", @@ -262,7 +273,7 @@ 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); @@ -275,7 +286,8 @@ 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); @@ -333,8 +345,8 @@ public class FeaturesFileTest assertEquals("no sequences extracted from GFF3 file", 2, dataset.getHeight()); - SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset - .findName("seq2"); + SequenceI seq1 = dataset.findName("seq1"); + SequenceI seq2 = dataset.findName("seq2"); assertNotNull(seq1); assertNotNull(seq2); assertFalse( @@ -389,14 +401,6 @@ public class FeaturesFileTest } @Test(groups = { "Functional" }) - public void simpleGff3FileIdentify() - { - assertEquals("Didn't recognise file correctly.", - IdentifyFile.FeaturesFile, - new IdentifyFile().identify(simpleGffFile, FormatAdapter.FILE)); - } - - @Test(groups = { "Functional" }) public void simpleGff3FileLoader() throws IOException { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( @@ -404,8 +408,7 @@ public class FeaturesFileTest assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); - // FIXME codon mappings are on the alignment but not on the dataset - checkDatasetfromSimpleGff3(af.getViewport().getAlignment()/* .getDataset() */); + checkDatasetfromSimpleGff3(af.getViewport().getAlignment()); } @Test(groups = { "Functional" }) @@ -422,23 +425,71 @@ public class FeaturesFileTest } @Test(groups = { "Functional" }) - public void testExonerateImport() + public void testPrintJalviewFormat() throws Exception { - // exonerate does not tag sequences after features, so we have a more - // conventional annotation import test here - - FileLoader loader = new FileLoader(false); - - AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs, - FormatAdapter.FILE); - - assertEquals("Unexpected number of DNA protein associations", 0, af - .getViewport().getAlignment().getCodonFrames().size()); - - af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null); - - assertTrue("Expected at least one DNA protein association", 0 != af - .getViewport().getAlignment().getDataset().getCodonFrames() - .size()); + 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); } }