+
+ /**
+ * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
+ * view (JAL-3171) this test ensures we can import and merge those views
+ */
+ @Test(groups = { "Functional" })
+ public void testMergeDatasetsforViews() throws IOException
+ {
+ // simple project - two views on one alignment
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
+ assertNotNull(af);
+ assertTrue(af.getAlignPanels().size() > 1);
+ verifyDs(af);
+ }
+
+ /**
+ * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
+ * view (JAL-3171) this test ensures we can import and merge those views This
+ * is a more complex project
+ */
+ @Test(groups = { "Functional" })
+ public void testMergeDatasetsforManyViews() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ // complex project - one dataset, several views on several alignments
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ "examples/testdata/projects/manyViews.jvp",
+ DataSourceType.FILE);
+ assertNotNull(af);
+
+ AlignmentI ds = null;
+ for (AlignFrame alignFrame : Desktop.getAlignFrames())
+ {
+ if (ds == null)
+ {
+ ds = verifyDs(alignFrame);
+ }
+ else
+ {
+ // check that this frame's dataset matches the last
+ assertTrue(ds == verifyDs(alignFrame));
+ }
+ }
+ }
+
+ private AlignmentI verifyDs(AlignFrame af)
+ {
+ AlignmentI ds = null;
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ if (ds == null)
+ {
+ ds = ap.getAlignment().getDataset();
+ }
+ else
+ {
+ assertTrue(ap.getAlignment().getDataset() == ds,
+ "Dataset was not the same for imported 2.10.5 project with several alignment views");
+ }
+ }
+ return ds;
+ }
+
+ @Test(groups = "Functional")
+ public void testPcaViewAssociation() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ final String PCAVIEWNAME = "With PCA";
+ // create a new tempfile
+ File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
+
+ {
+ String exampleFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
+ AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
+ // create another for good measure
+ af.newView("Not the PCA View", true);
+ PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
+ new SimilarityParams(true, true, true, false));
+ // we're in the test exec thread, so we can just run synchronously here
+ pcaPanel.run();
+
+ // now switch the linked view
+ pcaPanel.selectAssociatedView(newview);
+
+ assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
+ "PCA should be associated with 'With PCA' view: test is broken");
+
+ // now save and reload project
+ Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ }
+
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ // PCA and the tabbed alignment view should be the only two windows on the
+ // desktop
+ assertEquals(frames.length, 2,
+ "PCA and the tabbed alignment view should be the only two windows on the desktop");
+ PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
+
+ AlignmentViewPanel restoredNewView = null;
+ for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
+ {
+ if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
+ {
+ restoredNewView = alignpanel;
+ }
+ }
+ assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
+ assertTrue(
+ restoredNewView.getAlignViewport() == pcaPanel
+ .getAlignViewport(),
+ "Didn't restore correct view association for the PCA view");
+ }