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.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
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.datamodel.features.FeatureMatcher;
+import jalview.datamodel.features.FeatureMatcherI;
+import jalview.datamodel.features.FeatureMatcherSet;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.schemes.FeatureColour;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.matcher.Condition;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
+import java.util.HashMap;
+import java.util.Iterator;
+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";
- static String TestFiles[][] = { { "Test example features import/export",
- "examples/uniref50.fa", "examples/exampleFeatures.txt" } };
-
- @Test(groups = { "Functional" })
- public void testParse() throws Exception
+ @AfterClass(alwaysRun = true)
+ public void tearDownAfterClass()
{
- testFeaturesFileIO("Features file test");
+ /*
+ * remove any sequence mappings created so they don't pollute other tests
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.resetAll();
}
- public static AlignmentI readAlignmentFile(File f) throws IOException
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- 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;
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- /**
- * 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
+ @Test(groups = { "Functional" })
+ public void testParse() throws Exception
{
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
- "examples/exampleFeatures.txt", FormatAdapter.FILE);
- assertTrue("Test " + testname + "\nFailed to parse features file.",
+ "examples/exampleFeatures.txt", DataSourceType.FILE);
+ assertTrue("Test " + "Features file test"
+ + "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
/*
* 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<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
.getSequenceFeatures(); // FER_CAPAA
- assertEquals(7, 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);
+ 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.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[1];
+
+ 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[2];
+
+ 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[3];
+
+ 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[4];
- 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(8, sf.begin);
- assertEquals(83, sf.end);
- assertEquals("uniprot", sf.featureGroup);
- assertEquals("Pfam", sf.type);
- sf = sfs[5];
- 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.get(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<String, FeatureColourI> 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,
+ DataSourceType.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
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(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.size());
+ sf = sfs.get(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, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.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<String, FeatureColourI> 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,
+ DataSourceType.PASTE);
+ assertTrue("Failed to parse features file",
+ featuresFile.parse(al.getDataset(), colours, true));
+
+ // verify feature on FER_CAPAA
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceFeatures();
+ 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);
+ 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.size());
+ sf = sfs.get(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<String, FeatureColourI> 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,
+ DataSourceType.PASTE);
+ assertTrue("Failed to parse features file",
+ featuresFile.parse(al.getDataset(), colours, true));
+
+ // verify FER_CAPAA feature
+ List<SequenceFeature> sfs = al.getSequenceAt(0).getDatasetSequence()
+ .getSequenceFeatures();
+ assertEquals(1, sfs.size());
+ SequenceFeature sf = sfs.get(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.size());
+ sf = sfs.get(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()
+ .size());
+ assertTrue(seq2.getSequenceFeatures().isEmpty());
+ assertEquals(
+ "Wrong number of features",
+ 0,
+ seq2.getSequenceFeatures() == null ? 0 : seq2
+ .getSequenceFeatures().size());
+ 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,
+ DataSourceType.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,
+ DataSourceType.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, DataSourceType.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,
+ DataSourceType.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<String, FeatureColourI> 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"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ + "ENDGROUP\tuniprot\n";
+ FeaturesFile featuresFile = new FeaturesFile(features,
+ DataSourceType.PASTE);
+ 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();
+ String exported = featuresFile
+ .printJalviewFormat(al.getSequencesArray(), fr, false);
+ String expected = "No Features Visible";
+ assertEquals(expected, exported);
+
+ /*
+ * include non-positional features, but still no positional features
+ */
+ fr.setGroupVisibility("uniprot", true);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ true);
+ expected = "\nSTARTGROUP\tuniprot\n"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+ + "ENDGROUP\tuniprot\n\n"
+ + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n\n"
+ + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"; // NaN is not output
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "METAL\tcc9900\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "ENDGROUP\tuniprot\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ /*
+ * features are output within group, ordered by sequence and type
+ */
+ expected = "METAL\tcc9900\n"
+ + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ + "ENDGROUP\tuniprot\n"
+ // null / empty group features are output after named groups
+ + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ assertEquals(expected, exported);
+
+ /*
+ * hide uniprot group
+ */
+ fr.setGroupVisibility("uniprot", false);
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ assertEquals(expected, exported);
+
+ /*
+ * include non-positional (overrides group not shown)
+ */
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ true);
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ + "\nSTARTGROUP\tuniprot\n"
+ + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+ + "ENDGROUP\tuniprot\n"
+ + "\ndesc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+ + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+ + "\ndesc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n"
+ + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
+ assertEquals(expected, exported);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPrintGffFormat() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+
+ /*
+ * no features
+ */
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
+ .getFeatureRenderer();
+ String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+ fr, false);
+ String gffHeader = "##gff-version 2\n";
+ assertEquals(gffHeader, exported);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ true);
+ assertEquals(gffHeader, exported);
+
+ /*
+ * add some features
+ */
+ al.getSequenceAt(0).addSequenceFeature(
+ new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
+ al.getSequenceAt(0).addSequenceFeature(
+ new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
+ al.getSequenceAt(1)
+ .addSequenceFeature(
+ new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
+ "s3dm"));
+ SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
+ "Uniprot");
+ sf.setAttributes("x=y;black=white");
+ sf.setStrand("+");
+ sf.setPhase("2");
+ al.getSequenceAt(1).addSequenceFeature(sf);
+
+ /*
+ * 'discover' features then hide all feature types
+ */
+ fr.findAllFeatures(true);
+ FeatureSettingsBean[] data = new FeatureSettingsBean[4];
+ FeatureColourI fc = new FeatureColour(Color.PINK);
+ data[0] = new FeatureSettingsBean("Domain", fc, null, false);
+ data[1] = new FeatureSettingsBean("METAL", fc, null, false);
+ data[2] = new FeatureSettingsBean("GAMMA-TURN", fc, null, false);
+ data[3] = new FeatureSettingsBean("Pfam", fc, null, false);
+ fr.setFeaturePriority(data);
+
+ /*
+ * with no features displayed, exclude non-positional features
+ */
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ assertEquals(gffHeader, exported);
+
+ /*
+ * include non-positional features
+ */
+ fr.setGroupVisibility("Uniprot", true);
+ fr.setGroupVisibility("s3dm", false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ true);
+ String expected = gffHeader
+ + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+ * only Uniprot group visible here...
+ */
+ fr.setVisible("METAL");
+ fr.setVisible("GAMMA-TURN");
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ // METAL feature has null group: description used for column 2
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * set s3dm group visible
+ */
+ fr.setGroupVisibility("s3dm", true);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ // METAL feature has null group: description used for column 2
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now set Pfam visible
+ */
+ fr.setVisible("Pfam");
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ // Pfam feature columns include strand(+), phase(2), attributes
+ expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n"
+ + "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white\n";
+ assertEquals(expected, exported);
+ }
+
+ /**
+ * Test for parsing of feature filters as represented in a Jalview features
+ * file
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testParseFilters() throws Exception
+ {
+ Map<String, FeatureMatcherSetI> filters = new HashMap<>();
+ String text = "sequence_variant\tCSQ:PolyPhen NotContains 'damaging'\n"
+ + "missense_variant\t(label contains foobar) and (Score lt 1.3)";
+ FeaturesFile featuresFile = new FeaturesFile(text,
+ DataSourceType.PASTE);
+ featuresFile.parseFilters(filters);
+ assertEquals(filters.size(), 2);
+
+ FeatureMatcherSetI fm = filters.get("sequence_variant");
+ assertNotNull(fm);
+ Iterator<FeatureMatcherI> matchers = fm.getMatchers().iterator();
+ FeatureMatcherI matcher = matchers.next();
+ assertFalse(matchers.hasNext());
+ String[] attributes = matcher.getAttribute();
+ assertArrayEquals(attributes, new String[] { "CSQ", "PolyPhen" });
+ assertSame(matcher.getMatcher().getCondition(), Condition.NotContains);
+ assertEquals(matcher.getMatcher().getPattern(), "damaging");
+
+ fm = filters.get("missense_variant");
+ assertNotNull(fm);
+ matchers = fm.getMatchers().iterator();
+ matcher = matchers.next();
+ assertTrue(matcher.isByLabel());
+ assertSame(matcher.getMatcher().getCondition(), Condition.Contains);
+ assertEquals(matcher.getMatcher().getPattern(), "foobar");
+ matcher = matchers.next();
+ assertTrue(matcher.isByScore());
+ assertSame(matcher.getMatcher().getCondition(), Condition.LT);
+ assertEquals(matcher.getMatcher().getPattern(), "1.3");
+ assertEquals(matcher.getMatcher().getFloatValue(), 1.3f);
+
+ assertFalse(matchers.hasNext());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testOutputFeatureFilters()
+ {
+ FeaturesFile ff = new FeaturesFile();
+ StringBuilder sb = new StringBuilder();
+ Map<String, FeatureColourI> visible = new HashMap<>();
+ visible.put("pfam", new FeatureColour(Color.red));
+ Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
+
+ // with no filters, nothing is output
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ assertEquals("", sb.toString());
+
+ // with filter for not visible features only, nothing is output
+ FeatureMatcherSet filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byLabel(Condition.Present, null));
+ featureFilters.put("foobar", filter);
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ assertEquals("", sb.toString());
+
+ // with filters for visible feature types
+ FeatureMatcherSet filter2 = new FeatureMatcherSet();
+ filter2.and(FeatureMatcher.byAttribute(Condition.Present, null, "CSQ",
+ "PolyPhen"));
+ filter2.and(FeatureMatcher.byScore(Condition.LE, "-2.4"));
+ featureFilters.put("pfam", filter2);
+ visible.put("foobar", new FeatureColour(Color.blue));
+ ff.outputFeatureFilters(sb, visible, featureFilters);
+ String expected = "\nSTARTFILTERS\nfoobar\tLabel Present\npfam\t(CSQ:PolyPhen Present) AND (Score LE -2.4)\nENDFILTERS\n";
+ assertEquals(expected, sb.toString());
+ }
+
+ /**
+ * Output as GFF should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintGffFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ null);
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ null);
+ sf2.setValue("clin_sig", "Benign");
+ sf2.setValue("AF", "46");
+ al.getSequenceAt(0).addSequenceFeature(sf2);
+
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ final String gffHeader = "##gff-version 2\n";
+
+ fr.setVisible("METAL");
+ fr.setColour("METAL", new FeatureColour(Color.PINK));
+ String exported = featuresFile.printGffFormat(al.getSequencesArray(),
+ fr, false);
+ String expected = gffHeader
+ + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now threshold to Score > 1.1 - should exclude sf2
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
+ false);
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ assertEquals(expected, exported);
+ }
+
+ /**
+ * Output as Jalview should not include features which are not visible due to
+ * colour threshold or feature filter settings
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testPrintJalviewFormat_withFilters() throws Exception
+ {
+ File f = new File("examples/uniref50.fa");
+ AlignmentI al = readAlignmentFile(f);
+ AlignFrame af = new AlignFrame(al, 500, 500);
+ SequenceFeature sf1 = new SequenceFeature("METAL", "Cath", 39, 39, 1.2f,
+ "grp1");
+ sf1.setValue("clin_sig", "Likely Pathogenic");
+ sf1.setValue("AF", "24");
+ al.getSequenceAt(0).addSequenceFeature(sf1);
+ SequenceFeature sf2 = new SequenceFeature("METAL", "Cath", 41, 41, 0.6f,
+ "grp2");
+ sf2.setValue("clin_sig", "Benign");
+ sf2.setValue("AF", "46");
+ al.getSequenceAt(0).addSequenceFeature(sf2);
+
+ FeaturesFile featuresFile = new FeaturesFile();
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ fr.findAllFeatures(true);
+
+ fr.setVisible("METAL");
+ fr.setColour("METAL", new FeatureColour(Color.PINK));
+ String exported = featuresFile.printJalviewFormat(
+ al.getSequencesArray(),
+ fr, false);
+ String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+
+ /*
+ * now threshold to Score > 1.1 - should exclude sf2
+ * (and there should be no empty STARTGROUP/ENDGROUP output)
+ */
+ FeatureColourI fc = new FeatureColour(null, Color.white, Color.BLACK,
+ Color.white, 0f, 2f);
+ fc.setAboveThreshold(true);
+ fc.setThreshold(1.1f);
+ fr.setColour("METAL", fc);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
+ + "STARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n";
+ assertEquals(expected, exported);
+
+ /*
+ * remove threshold and check sf2 is exported
+ */
+ fc.setAboveThreshold(false);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTGROUP\tgrp1\n"
+ + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+
+ /*
+ * filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
+ */
+ FeatureMatcherSetI filter = new FeatureMatcherSet();
+ filter.and(FeatureMatcher.byAttribute(Condition.Contains, "benign",
+ "clin_sig"));
+ fr.setFeatureFilter("METAL", filter);
+ exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
+ false);
+ expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
+ expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
+ + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"
+ + "STARTGROUP\tgrp2\n"
+ + "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ + "ENDGROUP\tgrp2\n";
+ assertEquals(expected, exported);
+ }
}
git://source.jalview.org / jalview.git / blobdiff