+ 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
+ {
+ Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Boolean.TRUE.toString());
+ 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()));
+
+ }
+
+ /**
+ * test store and recovery of expanded views - currently this is disabled
+ * since the Desktop.explodeViews method doesn't seem to result in the views
+ * being expanded to distinct align frames when executed programmatically.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = false)
+ public void testStoreAndRecoverExpandedviews() 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);
+ String afid = af.getViewport().getSequenceSetId();
+ {
+ final AlignFrame xaf = af;
+ af = null;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Desktop.instance.explodeViews(xaf);
+ }
+ }).start();
+ Thread.sleep(1000);
+ }
+ // int times = 0;
+ // while (++times < 5 && Desktop.getAlignFrames().length < )
+ // {
+ // Thread.sleep(300);
+ // }
+ int oldviews = Desktop.getAlignFrames().length;
+ Assert.assertEquals(Desktop.getAlignFrames().length,
+ Desktop.getAlignmentPanels(afid).length);
+ File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Error e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ } catch (Exception e)
+ {
+ Assert.fail("Didn't save the expanded view state", e);
+ }
+ Desktop.instance.closeAll_actionPerformed(null);
+ if (Desktop.getAlignFrames() != null)
+ {
+ Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ }
+ af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ Assert.assertNotNull(af);
+ Assert.assertEquals(
+ Desktop.getAlignFrames().length,
+ Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+ Assert.assertEquals(
+ oldviews,
+ Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);