*/
package jalview.io;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertSame;
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.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
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
{
/**
* @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())
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
+ inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
int olddsann = countDsAnn(af.getViewport());
assertTrue("Didn't find any dataset annotations", olddsann > 0);
"Couldn't apply RNA helices colourscheme",
af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue("Failed to import new project", af != null);
int newdsann = countDsAnn(af.getViewport());
assertTrue(
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
+ inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
assertTrue(
"Didn't set T-coffee colourscheme",
af.getViewport().getGlobalColourScheme().getClass()
.getViewport().getGlobalColourScheme())) != null);
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue("Failed to import new project", af != null);
assertTrue(
"Didn't set T-coffee colourscheme for imported project.",
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
+ inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+ af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
AlignmentAnnotation[] aa = af.getViewport().getAlignment()
.getSequenceAt(0).getAnnotation("IUPredWS (Short)");
assertTrue(
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
+ af.saveAlignment(tfile, FileFormat.Jalview));
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
assertTrue("Failed to import new project", af != null);
// check for group and alignment colourschemes
int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
.getAlignFrames().length;
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.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);
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
AlignmentViewPanel sps = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
public void testCopyViewSettings() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
AlignmentViewPanel sps = null, groups = null;
for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = false)
+ @Test(groups = { "Functional" }, enabled = true)
public void testStoreAndRecoverExpandedviews() throws Exception
{
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+ "examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertTrue("Didn't read in the example file correctly.", af != null);
String afid = af.getViewport().getSequenceSetId();
{
Assert.assertEquals(Desktop.getAlignFrames().length, 0);
}
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- tfile.getAbsolutePath(), FormatAdapter.FILE);
+ tfile.getAbsolutePath(), DataSourceType.FILE);
Assert.assertNotNull(af);
Assert.assertEquals(
Desktop.getAlignFrames().length,
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", DataSourceType.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+
+ // remember reference sequence for each panel
+ Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+
+ /*
+ * 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);
+
+ // 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(), DataSourceType.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.");
+ }
+ }
+
@Test(groups = { "Functional" })
public void testIsVersionStringLaterThan()
{
*/
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,
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
}
+
+ /**
+ * Test save and reload of a project with a different sequence group (and
+ * representative sequence) in each view.
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" })
+ public void testStoreAndRecoverGroupRepSeqs() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ String afid = af.getViewport().getSequenceSetId();
+ // make a second view of the alignment
+ af.newView_actionPerformed(null);
+
+ /*
+ * remember representative and hidden sequences marked
+ * on each panel
+ */
+ Map<String, SequenceI> repSeqs = 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();
+ // ensure at least one preceding sequence i.e. index >= 1
+ repIndex = Math.max(repIndex, 1);
+ SequenceI repSeq = alignment.getSequenceAt(repIndex);
+ repSeqs.put(ap.getViewName(), repSeq);
+ List<String> hiddenNames = new ArrayList<String>();
+ hiddenSeqNames.put(ap.getViewName(), hiddenNames);
+
+ /*
+ * have rep sequence represent itself and the one before it
+ * this hides the group (except for the rep seq)
+ */
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(repSeq, false);
+ SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
+ sg.addSequence(precedingSeq, false);
+ sg.setSeqrep(repSeq);
+ assertTrue(sg.getSequences().contains(repSeq));
+ assertTrue(sg.getSequences().contains(precedingSeq));
+ av.setSelectionGroup(sg);
+ assertSame(repSeq, sg.getSeqrep());
+
+ /*
+ * represent group with sequence adds to a map of hidden rep sequences
+ * (it does not create a group on the alignment)
+ */
+ ((AlignmentViewport) av).hideSequences(repSeq, true);
+ assertSame(repSeq, sg.getSeqrep());
+ assertTrue(sg.getSequences().contains(repSeq));
+ assertTrue(sg.getSequences().contains(precedingSeq));
+ assertTrue("alignment has groups", alignment.getGroups().isEmpty());
+ Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av.getHiddenRepSequences();
+ assertNotNull(hiddenRepSeqsMap);
+ assertEquals(1, hiddenRepSeqsMap.size());
+ assertSame(sg, hiddenRepSeqsMap.get(repSeq));
+ assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
+ assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
+ hiddenNames.add(precedingSeq.getName());
+
+ n++;
+ }
+ File tfile = File
+ .createTempFile("testStoreAndRecoverGroupReps",
+ ".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(), DataSourceType.FILE);
+ afid = af.getViewport().getSequenceSetId();
+
+ for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ {
+ String viewName = ap.getViewName();
+ AlignViewportI av = ap.getAlignViewport();
+ AlignmentI alignment = ap.getAlignment();
+ List<SequenceGroup> groups = alignment.getGroups();
+ assertNotNull(groups);
+ assertTrue("Alignment has groups", groups.isEmpty());
+ Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+ .getHiddenRepSequences();
+ assertNotNull("No hidden represented sequences", hiddenRepSeqsMap);
+ assertEquals(1, hiddenRepSeqsMap.size());
+ assertEquals(repSeqs.get(viewName).getDisplayId(true),
+ hiddenRepSeqsMap.keySet().iterator().next()
+ .getDisplayId(true));
+
+ /*
+ * 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());
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff