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;
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);
.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));
/*
*/
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<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,
+ 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<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,
+ 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<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,
+ 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<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"
+ + "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,
+ FormatAdapter.PASTE);
+ featuresFile.parse(al.getDataset(), colours, false);
+
+ /*
+ * first with no features displayed
+ */
+ FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+ Map<String, FeatureColourI> 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"
+ + "<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";
+ assertEquals(expected, exported);
+ }
}
git://source.jalview.org / jalview.git / blobdiff