@Test(groups = { "Functional" })
public void testMatrixToFloatsAndBack()
{
- int imax=2000;
- int i=imax;
- SequenceI sq = new Sequence("dummy","SEQ");
- while (sq.getLength()<i)
+ int imax = 2000;
+ int i = imax;
+ SequenceI sq = new Sequence("dummy", "SEQ");
+ while (sq.getLength() < i)
{
- sq.setSequence(sq.getSequenceAsString()+'Q');
+ sq.setSequence(sq.getSequenceAsString() + 'Q');
}
float[][] paevals = new float[i][i];
for (i = imax - 1; i >= 0; i--)
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
assertEquals(vals[4][3], paevals[4][3]);
-
+
// test recovery
- for (i=0;i<imax;i++)
+ for (i = 0; i < imax; i++)
{
- for (int j=0;j<imax;j++)
+ for (int j = 0; j < imax; j++)
{
- assertEquals(vals[i][j],paevals[i][j]);
+ assertEquals(vals[i][j], paevals[i][j]);
}
}
}
+
@Test(groups = { "Functional" })
public void testPAEsaveRestore() throws Exception
{
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
assertEquals(vals[4][3], paevals[4][3]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false, 0.5f, false));
Assert.assertNotSame(dummyMat.getNewick(), "");
AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
al.addAnnotation(paeCm);
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
// verify no duplicate PAE matrix data when new view created and saved
-
+
// add reference annotations to view first, then copy
- AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
-
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0),
+ newSeq.getAnnotation()[0], null);
+
AlignmentViewPanel newview = af.newView("copy of PAE", true);
-
+
// redundant asserts here check all is good with the new view firest...
AlignmentI newviewAl = newview.getAlignment();
SequenceI newviewSeq = newviewAl.getSequenceAt(0);
Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
// check we have just one contact matrix mapping
Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
-
+
// and can be found for the annotation on the sequence
ContactMatrixI newviewMat = newviewSeq
.getContactMatrixFor(newviewSeq.getAnnotation()[0]);
Assert.assertNotNull(newviewMat);
Assert.assertTrue(newviewMat == restoredMat);
-
- // save the two views and restore. Now look at visible annotation to check all views have shared refs.
-
+
+ // save the two views and restore. Now look at visible annotation to check
+ // all views have shared refs.
+
tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
".jvp");
new Jalview2XML(false).saveState(tfile);
AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
newviewAl = af.getAlignPanels().get(1).getAlignment();
- AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+ AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0)
+ .getAnnotation()[0];
- // annotations are shared across alignment views - so should still have an identical pair of annotations.
- Assert.assertTrue(view1aa==view2aa);
+ // annotations are shared across alignment views - so should still have an
+ // identical pair of annotations.
+ Assert.assertTrue(view1aa == view2aa);
// identical annotations means identical contact matrix mappings
- Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+ Assert.assertEquals(
+ newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
- // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+ // TODO Verify when distinct mappable PAEs are created, only one PAE dataset
+ // is actually held.
// Assert.assertTrue(view1aa!=view2aa);
// restoredMat = newAl.getContactMatrixFor(view1aa);
// newviewMat = newviewAl.getContactMatrixFor(view2aa);
// Assert.assertTrue(restoredMat!=newviewMat);
-
+
}
@Test(groups = "Functional")
- public void testStoreAndRestoreIDwidthAndAnnotationHeight() throws IOException
+ public void testStoreAndRestoreIDwidthAndAnnotationHeight()
+ throws IOException
{
Desktop.instance.closeAll_actionPerformed(null);
final String SECONDVIEW = "With Diffferent IDwidth";
// create a new tempfile
File tempfile = File.createTempFile("jvIdWidthStoreRestore", "jvp");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ // FIXME JAL-4281 test made platform dependent to pass, but probably
+ // shouldn't be platform dependent
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(),
+ Platform.isAMacAndNotJS() ? 144 : 138,
+ "Legacy project import should have fixed ID width");
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("examples/exampleFile.jvp",
- DataSourceType.FILE);
- assertNotNull(af, "Didn't read in the example file correctly.");
- // FIXME JAL-4281 test made platform dependent to pass, but probably shouldn't be platform dependent
- assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), Platform.isAMacAndNotJS() ? 144 : 138,
- "Legacy project import should have fixed ID width");
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
-
- af.alignPanel.getAlignViewport().setIdWidth(100);
- af.alignPanel.updateLayout();
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
- 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");
- af = null;
- // load again.
- Desktop.instance.closeAll_actionPerformed(null);
- af = new FileLoader().LoadFileWaitTillLoaded(
- tempfile.getCanonicalPath(), DataSourceType.FILE);
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas()
- .isManuallyAdjusted());
- assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
- "New project exported and import should have adjusted ID width");
-
- af.alignPanel.getAlignViewport().setIdWidth(100);
- af.alignPanel.updateLayout();
- assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
-
- // now make it autoadjusted
- af.alignPanel.getAlignViewport().setIdWidth(-1);
- af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
- af.alignPanel.updateLayout();
- assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
- "New project exported and import should have adjusted ID width");
-
- jv2xml = new jalview.project.Jalview2XML(false);
- tempfile.delete();
- jv2xml.saveState(tempfile);
- assertTrue(jv2xml.errorMessage == null,
- "Failed to save dummy project with PCA: test broken");
- af = null;
- // load again.
- Desktop.instance.closeAll_actionPerformed(null);
- af = new FileLoader().LoadFileWaitTillLoaded(
- tempfile.getCanonicalPath(), DataSourceType.FILE);
- assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
- assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
- "New project exported and import should have adjusted ID width");
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ 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");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
+ "New project exported and import should have adjusted ID width");
+
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ // now make it autoadjusted
+ af.alignPanel.getAlignViewport().setIdWidth(-1);
+ af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
+ af.alignPanel.updateLayout();
+ assertFalse(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+ "New project exported and import should have adjusted ID width");
+
+ jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertFalse(
+ af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+ "New project exported and import should have adjusted ID width");
}
}
git://source.jalview.org / jalview.git / blobdiff