X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=602ce9fb29aa7d53618ac749d65149742653a4c6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=56305dabe8c5567d0a6cdb85ec982dc81cb9624d;hpb=bf0d052fef43e9809b7170dbfd372b3ea116391b;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index 56305da..602ce9f 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -75,53 +75,63 @@ 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); @@ -143,7 +153,8 @@ public class FeaturesFileTest 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, @@ -294,7 +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); @@ -325,7 +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" }) @@ -342,9 +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); @@ -365,9 +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); @@ -388,7 +397,7 @@ public class FeaturesFileTest + "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" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\n" + "ENDGROUP\tuniprot\n"; FeaturesFile featuresFile = new FeaturesFile(features, FormatAdapter.PASTE); @@ -398,8 +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"; @@ -438,7 +446,7 @@ public class FeaturesFileTest + "\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" + + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" + "ENDGROUP\tuniprot\n"; assertEquals(expected, exported); }