*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenSequences;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.AlignmentViewport;
import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+@Test(singleThreaded = true)
public class Jalview2xmlTests
{
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[]
- { "-props", "test/jalview/io/testProps.jvprops" });
+ jalview.bin.Jalview.main(new String[] { "-props",
+ "test/jalview/io/testProps.jvprops" });
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
}
- public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+ int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
{
int numdsann = 0;
for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
return numdsann;
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testRNAStructureRecovery() throws Exception
{
String inFile = "examples/RF00031_folded.stk";
af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testTCoffeeScores() throws Exception
{
String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
.println("T-Coffee score shading successfully recovered from project.");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testColourByAnnotScores() throws Exception
{
String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
.println("Per sequence (Group) colourscheme successfully applied and recovered.");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void gatherViewsHere() throws Exception
{
int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void viewRefPdbAnnotation() throws Exception
{
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
assertTrue("Couldn't find the structure view", sps != null);
SequenceI sq = sps.getAlignment().findName("1A70|");
AlignmentAnnotation refan = null;
- for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
+ for (AlignmentAnnotation ra : sps.getAlignment()
+ .getAlignmentAnnotation())
{
if (ra.graph != 0)
{
break;
}
}
- assertTrue("Annotation secondary structure not found.",refan!=null);
+ 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 (int p = 0; p < ala.annotations.length; p++)
{
sq.findPosition(p);
- try {
+ try
+ {
assertTrue(
"Mismatch at alignment position " + p,
- (alaa.annotations[p] == null && refan.annotations[p] == null)
+ (alaa.annotations[p] == null && refan.annotations[p] == null)
|| alaa.annotations[p].value == refan.annotations[p].value);
- }
- catch (NullPointerException q)
+ } catch (NullPointerException q)
{
- Assert.fail("Mismatch of alignment annotations at position " + p
- + " Ref seq ann: " + refan.annotations[p]
+ Assert.fail("Mismatch of alignment annotations at position "
+ + p + " Ref seq ann: " + refan.annotations[p]
+ " alignment " + alaa.annotations[p]);
}
- }
+ }
}
}
-
+
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testCopyViewSettings() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
.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 = true)
+ 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);
+ }
+
+ /**
+ * Test save and reload of a project with a different representative sequence
+ * in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverReferenceSeqSettings() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new 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();
+
+ /*
+ * remember representative and hidden sequences marked
+ * on each panel
+ */
+ Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+ Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+
+ /*
+ * mark sequence 2, 3, 4.. in panels 1, 2, 3...
+ * as reference sequence for itself and the preceding sequence
+ */
+ int n = 1;
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ int repIndex = n % alignment.getHeight();
+ SequenceI rep = alignment.getSequenceAt(repIndex);
+ refseqs.put(ap.getViewName(), rep);
+ List<String> hiddenNames = new ArrayList<String>();
+ hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+
+ /*
+ * hide rep sequence and the one before it
+ */
+ SequenceI seqToHide = alignment.getSequenceAt(repIndex);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(seqToHide, false);
+ SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+ sg.addSequence(precedingSeq, false);
+ av.setSelectionGroup(sg);
+ ((AlignmentViewport) av).hideSequences(seqToHide, true);
+
+ /*
+ * record names of hidden sequences
+ */
+ HiddenSequences hs = alignment.getHiddenSequences();
+ for (SequenceI seq : hs.hiddenSequences)
+ {
+ if (seq != null)
+ {
+ hiddenNames.add(seq.getName());
+ }
+ }
+ // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
+ // todo refactor this to an alignment view controller
+ av.setDisplayReferenceSeq(true);
+ av.setColourByReferenceSeq(true);
+ av.getAlignment().setSeqrep(rep);
+
+ n++;
+ }
+ File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
+ ".jvp");
+ try
+ {
+ new Jalview2XML(false).saveState(tfile);
+ } catch (Throwable 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 FileLoader().LoadFileWaitTillLoaded(
+ tfile.getAbsolutePath(), FormatAdapter.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ // check representative
+ AlignmentI alignment = ap.getAlignment();
+ SequenceI rep = alignment.getSeqrep();
+ Assert.assertNotNull(rep,
+ "Couldn't restore sequence representative from project");
+ // can't use a strong equals here, because by definition, the sequence IDs
+ // will be different.
+ // could set vamsas session save/restore flag to preserve IDs across
+ // load/saves.
+ Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
+ rep.toString(),
+ "Representative wasn't the same when recovered.");
+ Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
+ "Display reference sequence view setting not set.");
+ Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
+ "Colour By Reference Seq view setting not set.");
+
+ /*
+ * verify hidden sequences in restored panel
+ */
+ List<String> hidden = hiddenSeqNames.get(ap.getViewName());
+ HiddenSequences hs = alignment.getHiddenSequences();
+ assertEquals(
+ "wrong number of restored hidden sequences in "
+ + ap.getViewName(),
+ hidden.size(), hs.getSize());
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsVersionStringLaterThan()
+ {
+ /*
+ * No version / development / test / autobuild is leniently assumed to be
+ * compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+ "DEVELOPMENT BUILD"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Development Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
+ assertTrue(Jalview2XML
+ .isVersionStringLaterThan(null, "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "Automated Build"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+ "AUTOMATED BUILD"));
+
+ /*
+ * same version returns true i.e. compatible
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
+
+ /*
+ * later version returns true
+ */
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
+
+ /*
+ * earlier version returns false
+ */
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+ }
}
git://source.jalview.org / jalview.git / blobdiff