- @Test(groups = { "Functional" })
- public void testRNAStructureRecovery() throws Exception
- {
- String inFile = "examples/RF00031_folded.stk";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- int olddsann = countDsAnn(af.getViewport());
- assertTrue("Didn't find any dataset annotations", olddsann > 0);
- af.rnahelicesColour_actionPerformed(null);
- assertTrue(
- "Couldn't apply RNA helices colourscheme",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
- int newdsann = countDsAnn(af.getViewport());
- assertTrue(
- "Differing numbers of dataset sequence annotation\nOriginally "
- + olddsann + " and now " + newdsann,
- olddsann == newdsann);
- System.out
- .println("Read in same number of annotations as originally present ("
- + olddsann + ")");
- assertTrue(
- "RNA helices colourscheme was not applied on import.",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- }
-
- @Test(groups = { "Functional" })
- public void testTCoffeeScores() throws Exception
- {
- String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
- assertTrue(
- "Didn't set T-coffee colourscheme",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
- assertTrue(
- "Recognise T-Coffee score from string",
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(),
- jalview.schemes.ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())) != null);
-
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
- assertTrue(
- "Didn't set T-coffee colourscheme for imported project.",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
- System.out
- .println("T-Coffee score shading successfully recovered from project.");
- }
-
- @Test(groups = { "Functional" })
- public void testColourByAnnotScores() throws Exception
- {
- String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
- AlignmentAnnotation[] aa = af.getViewport().getAlignment()
- .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
- assertTrue(
- "Didn't find any IUPred annotation to use to shade alignment.",
- aa != null && aa.length > 0);
- AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
- aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
- AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
- aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
- cs.setSeqAssociated(true);
- gcs.setSeqAssociated(true);
- af.changeColour(cs);
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(57);
- sg.setEndRes(92);
- sg.cs = gcs;
- af.getViewport().getAlignment().addGroup(sg);
- sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
- sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
- af.alignPanel.alignmentChanged();
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
-
- // check for group and alignment colourschemes
-
- ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
- ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
- .get(0).cs;
- assertTrue("Didn't recover global colourscheme", _rcs != null);
- assertTrue("Didn't recover annotation colour global scheme",
- _rcs instanceof AnnotationColourGradient);
- AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
- assertTrue("Annotation colourscheme wasn't sequence associated",
- __rcs.isSeqAssociated());
-
- boolean diffseqcols = false, diffgseqcols = false;
- SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
- {
- if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
- .findColour(sqs[5].getCharAt(p), p, sqs[5]))
- {
- diffseqcols = true;
- }
- }
- assertTrue("Got Different sequence colours", diffseqcols);
- System.out
- .println("Per sequence colourscheme (Background) successfully applied and recovered.");
-
- assertTrue("Didn't recover group colourscheme", _rgcs != null);
- assertTrue("Didn't recover annotation colour group colourscheme",
- _rgcs instanceof AnnotationColourGradient);
- __rcs = (AnnotationColourGradient) _rgcs;
- assertTrue("Group Annotation colourscheme wasn't sequence associated",
- __rcs.isSeqAssociated());
-
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
- {
- if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
- .findColour(sqs[2].getCharAt(p), p, sqs[2]))
- {
- diffgseqcols = true;
- }
- }
- assertTrue("Got Different group sequence colours", diffgseqcols);
- System.out
- .println("Per sequence (Group) colourscheme successfully applied and recovered.");
- }
-
- @Test(groups = { "Functional" })
- public void gatherViewsHere() throws Exception
- {
- int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
- .getAlignFrames().length;
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- assertTrue("Didn't gather the views in the example file.",
- Desktop.getAlignFrames().length == 1 + origCount);
-
- }
-
- @Test(groups = { "Functional" })
- public void viewRefPdbAnnotation() throws Exception
- {
- // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
- // StructureImportSettings
- // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
- StructureImportSettings.setProcessSecondaryStructure(true);
- StructureImportSettings.setVisibleChainAnnotation(true);
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- AlignmentViewPanel sps = null;
- for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
- {
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- break;
- }
- }
- assertTrue("Couldn't find the structure view", sps != null);
- SequenceI sq = sps.getAlignment().findName("1A70|");
- AlignmentAnnotation refan = null;
- for (AlignmentAnnotation ra : sps.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ra.graph != 0)
- {
- refan = ra;
- break;
- }
- }
- assertTrue("Annotation secondary structure not found.", refan != null);
- assertTrue("Couldn't find 1a70 null chain", sq != null);
- // compare the manually added temperature factor annotation
- // to the track automatically transferred from the pdb structure on load
- for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
- {
- AlignmentAnnotation alaa;
- sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
- alaa.adjustForAlignment();
- if (ala.graph == refan.graph)
- {
- for (int p = 0; p < ala.annotations.length; p++)
- {
- sq.findPosition(p);
- try
- {
- assertTrue(
- "Mismatch at alignment position " + p,
- (alaa.annotations[p] == null && refan.annotations[p] == null)
- || alaa.annotations[p].value == refan.annotations[p].value);
- } catch (NullPointerException q)
- {
- Assert.fail("Mismatch of alignment annotations at position "
- + p + " Ref seq ann: " + refan.annotations[p]
- + " alignment " + alaa.annotations[p]);
- }
- }
- }
- }
-
- }
-
- @Test(groups = { "Functional" })
- public void testCopyViewSettings() throws Exception
- {
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- AlignmentViewPanel sps = null, groups = null;
- for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
- {
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- }
- if (ap.getViewName().contains("MAFFT"))
- {
- groups = ap;
- }
- }
- assertTrue("Couldn't find the structure view", sps != null);
- assertTrue("Couldn't find the MAFFT view", groups != null);
-
- ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
- ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
- AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
-
- groups.getAlignViewport().setViewStyle(structureStyle);
- AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
- Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
-
- }
-