- 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);