@BeforeClass
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+ jalview.bin.Jalview.main(new String[]
+ { "-props", "test/src/jalview/io/testProps.jvprops" });
}
/**
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
+
}
+
public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
- int numdsann=0;
- for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
+ int numdsann = 0;
+ for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+ {
if (sq.getAnnotation() != null)
{
for (AlignmentAnnotation dssa : sq.getAnnotation())
}
return numdsann;
}
+
@Test
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);
+ 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"));
+ 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);
+ 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
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);
+ 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()
jalview.schemes.ColourSchemeProperty.getColourName(af
.getViewport().getGlobalColourScheme())) != null);
- assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+ 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.");
+ 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
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);
+ 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);
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"));
+ 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);
-
+ 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);
+
+ 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());
+ 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++)
+ 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]))
+ 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);
+ 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++)
+ 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]))
+ 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.");
+ System.out
+ .println("Per sequence (Group) colourscheme successfully applied and recovered.");
}
+
@Test
public void gatherViewsHere() throws Exception
{
int origCount = 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);
-
+ 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);
+
}
}
git://source.jalview.org / jalview.git / blobdiff