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 jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
import java.awt.Color;
import java.io.File;
public class FeaturesFileTest
{
- private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
- exonerateOutput = "examples/testdata/exonerateoutput.gff",
- simpleGffFile = "examples/testdata/simpleGff3.gff";
+ private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@Test(groups = { "Functional" })
public void testParse() throws Exception
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", FormatAdapter.FILE);
*/
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("26 feature group colours not found", 26, colours.size());
- assertEquals(colours.get("Cath"), new Color(0x93b1d1));
- assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
+ assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
+ assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
/*
* verify (some) features on sequences
*/
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);
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
- String gffData = "METAL\tcc9900\n" + "GFF\n"
- + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n"
+ // 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);
// verify colours read or synthesized
colours = af.getFeatureRenderer().getFeatureColours();
assertEquals("1 feature group colours not found", 1, colours.size());
- assertEquals(colours.get("METAL"), new Color(0xcc9900));
+ 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("uniprot", sf.description);
+ assertEquals("Iron-sulfur,2Fe-2S", sf.description);
assertEquals(44, sf.begin);
assertEquals(45, sf.end);
assertEquals("uniprot", sf.featureGroup);
}
/**
- * Test various ways of describing a feature colour scheme
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testParseGraduatedColourScheme() throws Exception
- {
- FeaturesFile ff = new FeaturesFile();
-
- // colour by label:
- GraduatedColor gc = ff.parseGraduatedColourScheme(
- "BETA-TURN-IR\t9a6a94", "label");
- assertTrue(gc.isColourByLabel());
- assertEquals(Color.white, gc.getMinColor());
- assertEquals(Color.black, gc.getMaxColor());
- assertTrue(gc.isAutoScale());
-
- // using colour name, rgb, etc:
- String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertFalse(gc.isColourByLabel());
- assertEquals(Color.blue, gc.getMinColor());
- assertEquals(new Color(255, 0, 255), gc.getMaxColor());
- assertFalse(gc.isAutoScale());
- assertFalse(gc.getTolow());
- assertEquals(20.0f, gc.getMin(), 0.001f);
- assertEquals(95.0f, gc.getMax(), 0.001f);
- assertEquals(AnnotationColourGradient.BELOW_THRESHOLD,
- gc.getThreshType());
- assertEquals(66.0f, gc.getThresh(), 0.001f);
-
- // inverse gradient high to low:
- spec = "blue|255,0,255|95.0|20.0|below|66.0";
- gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
- assertTrue(gc.isAutoScale());
- assertTrue(gc.getTolow());
- }
-
- /**
* Test parsing a features file with GFF formatted content only
*
* @throws Exception
*/
@Test(groups = { "Functional" })
- public void testParse_pureGff() throws Exception
+ 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, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
- String gffData = "##gff-version 2\n"
+ // 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.";
+ + "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",
assertEquals(1, sfs.length);
SequenceFeature sf = sfs[0];
// description parsed from Note attribute
- assertEquals("Iron-sulfur (2Fe-2S); another note", sf.description);
+ assertEquals("Iron-sulfur (2Fe-2S),another note", sf.description);
assertEquals(39, sf.begin);
assertEquals(39, sf.end);
assertEquals("uniprot", sf.featureGroup);
sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
assertEquals(1, sfs.length);
sf = sfs[0];
- assertEquals("uniprot", sf.description);
+ // ID used for description if available
+ assertEquals("$23", sf.description);
assertEquals(55, sf.begin);
assertEquals(130, sf.end);
assertEquals("uniprot", sf.featureGroup);
File f = new File("examples/uniref50.fa");
AlignmentI al = readAlignmentFile(f);
AlignFrame af = new AlignFrame(al, 500, 500);
- Map<String, Object> colours = af.getFeatureRenderer()
+ Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
/*
{
assertEquals("no sequences extracted from GFF3 file", 2,
dataset.getHeight());
-
- SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
- .findName("seq2");
+
+ SequenceI seq1 = dataset.findName("seq1");
+ SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
assertNotNull(seq2);
assertFalse(
"Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0);
-
+
}
@Test(groups = { "Functional" })
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);
}
@Test(groups = { "Functional" })
- public void simpleGff3FileIdentify()
- {
- assertEquals("Didn't recognise file correctly.",
- IdentifyFile.FeaturesFile,
- new IdentifyFile().identify(simpleGffFile, FormatAdapter.FILE));
- }
-
- @Test(groups = { "Functional" })
public void simpleGff3FileLoader() throws IOException
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
- // FIXME codon mappings are on the alignment but not on the dataset
- checkDatasetfromSimpleGff3(af.getViewport().getAlignment()/* .getDataset() */);
+ 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);
-
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
+
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
parseResult);
}
@Test(groups = { "Functional" })
- public void testExonerateImport()
+ public void testPrintJalviewFormat() throws Exception
{
- // exonerate does not tag sequences after features, so we have a more
- // conventional annotation import test here
-
- FileLoader loader = new FileLoader(false);
-
- AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
- FormatAdapter.FILE);
-
- assertEquals("Unexpected number of DNA protein associations", 0, af
- .getViewport().getAlignment().getCodonFrames().size());
-
- af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
-
- assertTrue("Expected at least one DNA protein association", 0 != af
- .getViewport().getAlignment().getDataset().getCodonFrames()
- .size());
+ 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