+ System.out
+ .println("Per sequence (Group) colourscheme successfully applied and recovered.");
+ }
+
+ @Test
+ 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
+ public void viewRefPdbAnnotation() 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;
+ 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)
+ {
+ fail("Mismatch of alignment annotations at position " + p
+ + " Ref seq ann: " + refan.annotations[p]
+ + " alignment " + alaa.annotations[p]);
+ }
+ }
+ }
+ }
+
+ }
+
+ @Test
+ public void testCopyViewSettings() throws Exception
+ {
+ AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ Assert.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();
+ Assert.assertFalse(structureStyle.sameStyle(groupStyle));
+
+ groups.getAlignViewport().setViewStyle(structureStyle);
+ Assert.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+ Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
+ .getViewStyle()));
+