X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=152ab8461b8816fe0524214f6a4211841dfa4772;hb=8d3aefef72e993e55c0f6b5c26e3979ae7269e0f;hp=d59c6bbc86bc969fed036b562583bbdd54c25d36;hpb=60e252f7e0084336b0a85620842ce3db8f63e5b0;p=jalview.git diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java index d59c6bb..152ab84 100644 --- a/test/jalview/io/FeaturesFileTest.java +++ b/test/jalview/io/FeaturesFileTest.java @@ -23,7 +23,6 @@ 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; @@ -33,8 +32,11 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.gui.AlignFrame; +import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.structure.StructureSelectionManager; import java.awt.Color; import java.io.File; @@ -45,11 +47,24 @@ import java.util.HashMap; import java.util.List; import java.util.Map; +import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class FeaturesFileTest { + private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; + + @AfterClass(alwaysRun = true) + public void tearDownAfterClass() + { + /* + * remove any sequence mappings created so they don't pollute other tests + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); + } @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() @@ -58,8 +73,6 @@ public class FeaturesFileTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - private static String simpleGffFile = "examples/testdata/simpleGff3.gff"; - @Test(groups = { "Functional" }) public void testParse() throws Exception { @@ -79,17 +92,26 @@ public class FeaturesFileTest * updated - JAL-1904), and verify (some) feature group colours */ colours = af.getFeatureRenderer().getFeatureColours(); - assertEquals("26 feature group colours not found", 26, colours.size()); + assertEquals("27 feature group colours not found", 27, colours.size()); assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1)); assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb)); + FeatureColourI kdColour = colours.get("kdHydrophobicity"); + assertTrue(kdColour.isGraduatedColour()); + assertTrue(kdColour.isAboveThreshold()); + assertEquals(-2f, kdColour.getThreshold()); /* * verify (some) features on sequences */ - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); // FER_CAPAA - assertEquals(8, sfs.length); - SequenceFeature sf = sfs[0]; + SequenceFeatures.sortFeatures(sfs, true); + assertEquals(8, sfs.size()); + + /* + * verify (in ascending start position order) + */ + SequenceFeature sf = sfs.get(0); assertEquals("Pfam family%LINK%", sf.description); assertEquals(0, sf.begin); assertEquals(0, sf.end); @@ -99,46 +121,52 @@ public class FeaturesFileTest assertEquals("Pfam family|http://pfam.xfam.org/family/PF00111", sf.links.get(0)); - sf = sfs[1]; + sf = sfs.get(1); + 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.get(2); + 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)); + assertEquals(8, sf.begin); + assertEquals(83, sf.end); + assertEquals("uniprot", sf.featureGroup); + assertEquals("Pfam", sf.type); + + sf = sfs.get(3); 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[2]; + + sf = sfs.get(4); 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[3]; + + sf = sfs.get(5); 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[4]; + + sf = sfs.get(6); 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[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)); - assertEquals(8, sf.begin); - assertEquals(83, sf.end); - assertEquals("uniprot", sf.featureGroup); - assertEquals("Pfam", sf.type); - 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[7]; + + sf = sfs.get(7); assertEquals( "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%", sf.description); @@ -181,10 +209,10 @@ public class FeaturesFileTest assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900)); // verify feature on FER_CAPAA - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + assertEquals(1, sfs.size()); + SequenceFeature sf = sfs.get(0); assertEquals("Iron-sulfur,2Fe-2S", sf.description); assertEquals(44, sf.begin); assertEquals(45, sf.end); @@ -194,8 +222,8 @@ public class FeaturesFileTest // verify feature on FER1_SOLLC sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); assertEquals("uniprot", sf.description); assertEquals(55, sf.begin); assertEquals(130, sf.end); @@ -242,10 +270,10 @@ public class FeaturesFileTest featuresFile.parse(al.getDataset(), colours, true)); // verify feature on FER_CAPAA - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + assertEquals(1, sfs.size()); + SequenceFeature sf = sfs.get(0); // description parsed from Note attribute assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description); assertEquals(39, sf.begin); @@ -258,8 +286,8 @@ public class FeaturesFileTest // verify feature on FER1_SOLLC1 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); // ID used for description if available assertEquals("$23", sf.description); assertEquals(55, sf.begin); @@ -295,10 +323,10 @@ public class FeaturesFileTest featuresFile.parse(al.getDataset(), colours, true)); // verify FER_CAPAA feature - SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence() + List sfs = al.getSequenceAt(0).getDatasetSequence() .getSequenceFeatures(); - assertEquals(1, sfs.length); - SequenceFeature sf = sfs[0]; + assertEquals(1, sfs.size()); + SequenceFeature sf = sfs.get(0); assertEquals("Iron-sulfur (2Fe-2S)", sf.description); assertEquals(39, sf.begin); assertEquals(39, sf.end); @@ -306,8 +334,8 @@ public class FeaturesFileTest // verify FER1_SOLLC feature sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures(); - assertEquals(1, sfs.length); - sf = sfs[0]; + assertEquals(1, sfs.size()); + sf = sfs.get(0); assertEquals("Iron-phosphorus (2Fe-P)", sf.description); assertEquals(86, sf.begin); assertEquals(87, sf.end); @@ -337,14 +365,14 @@ public class FeaturesFileTest 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", 3, seq1.getSequenceFeatures() + .size()); + assertTrue(seq2.getSequenceFeatures().isEmpty()); assertEquals( "Wrong number of features", 0, seq2.getSequenceFeatures() == null ? 0 : seq2 - .getSequenceFeatures().length); + .getSequenceFeatures().size()); assertTrue( "Expected at least one CDNA/Protein mapping for seq1", dataset.getCodonFrame(seq1) != null @@ -420,6 +448,21 @@ public class FeaturesFileTest featuresFile.parse(al.getDataset(), colours, false); /* + * add positional and non-positional features with null and + * empty feature group to check handled correctly + */ + SequenceI seq = al.getSequenceAt(1); // FER_CAPAN + seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, + null)); + seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9, + Float.NaN, null)); + seq = al.getSequenceAt(2); // FER1_SOLLC + seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0, + Float.NaN, "")); + seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8, + -2.6f, "")); + + /* * first with no features displayed, exclude non-positional features */ FeatureRenderer fr = af.alignPanel.getFeatureRenderer(); @@ -437,7 +480,10 @@ public class FeaturesFileTest visibleGroups.add("uniprot"); exported = featuresFile.printJalviewFormat(al.getSequencesArray(), visible, visibleGroups, true); - expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n"; + expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n" + + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n" + + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output + + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n"; assertEquals(expected, exported); /* @@ -473,7 +519,11 @@ public class FeaturesFileTest + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n" + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n" + "Pfam domainPfam_3_4\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n" - + "ENDGROUP\tuniprot\n"; + + "ENDGROUP\tuniprot\n" + // null / empty group features output after features in named + // groups: + + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n" + + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n"; assertEquals(expected, exported); }