X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=602ce9fb29aa7d53618ac749d65149742653a4c6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=d65f9dfac3914d91349c78a049d1c284abface45;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index d65f9df..602ce9f 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -21,12 +21,18 @@ package jalview.io; 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.assertTrue; import jalview.api.FeatureColourI; +import jalview.api.FeatureRenderer; +import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import java.awt.Color; @@ -39,41 +45,11 @@ import org.testng.annotations.Test; public class FeaturesFileTest { - static String TestFiles[][] = { { "Test example features import/export", - "examples/uniref50.fa", "examples/exampleFeatures.txt" } }; + private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; @Test(groups = { "Functional" }) public void testParse() throws Exception { - testFeaturesFileIO("Features file test"); - } - - public static AlignmentI readAlignmentFile(File f) throws IOException - { - System.out.println("Reading file: " + f); - String ff = f.getPath(); - FormatAdapter rf = new FormatAdapter(); - - AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); - - al.setDataset(null); // creates dataset sequences - assertNotNull("Couldn't read supplied alignment data.", al); - return al; - } - - /** - * Helper method for testing - * - * @param testname - * @param f - * alignment file - * @param featFile - * features file to load on to the alignment - * @throws IOException - */ - public static void testFeaturesFileIO(String testname) throws IOException - { File f = new File("examples/uniref50.fa"); AlignmentI al = readAlignmentFile(f); AlignFrame af = new AlignFrame(al, 500, 500); @@ -81,7 +57,8 @@ public class FeaturesFileTest .getFeatureColours(); FeaturesFile featuresFile = new FeaturesFile( "examples/exampleFeatures.txt", FormatAdapter.FILE); - assertTrue("Test " + testname + "\nFailed to parse features file.", + assertTrue("Test " + "Features file test" + + "\nFailed to parse features file.", featuresFile.parse(al.getDataset(), colours, true)); /* @@ -98,56 +75,379 @@ 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); assertEquals("PHOSPHORYLATION (T)", sf.type); } + + /** + * Test parsing a features file with a mix of Jalview and GFF formatted + * content + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testParse_mixedJalviewGff() 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(); + // 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); + 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").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(44, sf.begin); + assertEquals(45, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("METAL", sf.type); + assertEquals(4f, sf.getScore(), 0.001f); + + // verify feature on FER1_SOLLC + sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); + assertEquals(1, sfs.length); + sf = sfs[0]; + assertEquals("uniprot", sf.description); + assertEquals(55, sf.begin); + assertEquals(130, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("Pfam", sf.type); + assertEquals(2f, sf.getScore(), 0.001f); + } + + public static AlignmentI readAlignmentFile(File f) throws IOException + { + System.out.println("Reading file: " + f); + String ff = f.getPath(); + FormatAdapter rf = new FormatAdapter(); + + AlignmentI al = rf.readFile(ff, FormatAdapter.FILE, + new IdentifyFile().identify(ff, FormatAdapter.FILE)); + + al.setDataset(null); // creates dataset sequences + assertNotNull("Couldn't read supplied alignment data.", al); + return al; + } + + /** + * Test parsing a features file with GFF formatted content only + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + 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(); + // 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.\tID=$23"; + FeaturesFile featuresFile = new FeaturesFile(gffData, + FormatAdapter.PASTE); + assertTrue("Failed to parse features file", + featuresFile.parse(al.getDataset(), colours, true)); + + // verify feature on FER_CAPAA + SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + .getSequenceFeatures(); + assertEquals(1, sfs.length); + SequenceFeature sf = sfs[0]; + // description parsed from Note attribute + assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description); + assertEquals(39, sf.begin); + assertEquals(39, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("METAL", sf.type); + assertEquals( + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465", + sf.getValue("ATTRIBUTES")); + + // verify feature on FER1_SOLLC1 + sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); + assertEquals(1, sfs.length); + sf = sfs[0]; + // ID used for description if available + assertEquals("$23", sf.description); + assertEquals(55, sf.begin); + assertEquals(130, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("Pfam", sf.type); + assertEquals(3f, sf.getScore(), 0.001f); + } + + /** + * Test parsing a features file with Jalview format features (but no colour + * descriptors or startgroup to give the hint not to parse as GFF) + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testParse_jalviewFeaturesOnly() 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(); + + /* + * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC + */ + 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); + assertTrue("Failed to parse features file", + featuresFile.parse(al.getDataset(), colours, true)); + + // verify FER_CAPAA feature + SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + .getSequenceFeatures(); + assertEquals(1, sfs.length); + SequenceFeature sf = sfs[0]; + assertEquals("Iron-sulfur (2Fe-2S)", sf.description); + assertEquals(39, sf.begin); + assertEquals(39, sf.end); + assertEquals("METAL", sf.type); + + // verify FER1_SOLLC feature + sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); + assertEquals(1, sfs.length); + sf = sfs[0]; + assertEquals("Iron-phosphorus (2Fe-P)", sf.description); + assertEquals(86, sf.begin); + assertEquals(87, sf.end); + assertEquals("METALLIC", sf.type); + } + + private void checkDatasetfromSimpleGff3(AlignmentI dataset) + { + assertEquals("no sequences extracted from GFF3 file", 2, + dataset.getHeight()); + + SequenceI seq1 = dataset.findName("seq1"); + SequenceI seq2 = dataset.findName("seq2"); + assertNotNull(seq1); + assertNotNull(seq2); + assertFalse( + "Failed to replace dummy seq1 with real sequence", + seq1 instanceof SequenceDummy + && ((SequenceDummy) seq1).isDummy()); + assertFalse( + "Failed to replace dummy seq2 with real sequence", + seq2 instanceof SequenceDummy + && ((SequenceDummy) seq2).isDummy()); + String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); + assertFalse("dummy replacement buggy for seq1", + placeholderseq.equals(seq1.getSequenceAsString())); + assertFalse("dummy replacement buggy for seq2", + placeholderseq.equals(seq2.getSequenceAsString())); + assertNotNull("No features added to seq1", seq1.getSequenceFeatures()); + assertEquals("Wrong number of features", 3, + seq1.getSequenceFeatures().length); + assertNull(seq2.getSequenceFeatures()); + assertEquals( + "Wrong number of features", + 0, + seq2.getSequenceFeatures() == null ? 0 : seq2 + .getSequenceFeatures().length); + assertTrue( + "Expected at least one CDNA/Protein mapping for seq1", + dataset.getCodonFrame(seq1) != null + && dataset.getCodonFrame(seq1).size() > 0); + + } + + @Test(groups = { "Functional" }) + public void readGff3File() throws IOException + { + FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile, + FormatAdapter.FILE); + Alignment dataset = new Alignment(gffreader.getSeqsAsArray()); + gffreader.addProperties(dataset); + checkDatasetfromSimpleGff3(dataset); + } + + @Test(groups = { "Functional" }) + public void simpleGff3FileClass() throws IOException + { + AlignmentI dataset = new Alignment(new SequenceI[] {}); + FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE); + + boolean parseResult = ffile.parse(dataset, null, false, false); + assertTrue("return result should be true", parseResult); + checkDatasetfromSimpleGff3(dataset); + } + + @Test(groups = { "Functional" }) + public void simpleGff3FileLoader() throws IOException + { + AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( + simpleGffFile, FormatAdapter.FILE); + assertTrue( + "Didn't read the alignment into an alignframe from Gff3 File", + af != null); + checkDatasetfromSimpleGff3(af.getViewport().getAlignment()); + } + + @Test(groups = { "Functional" }) + public void simpleGff3RelaxedIdMatching() throws IOException + { + AlignmentI dataset = new Alignment(new SequenceI[] {}); + 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); + } }