import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
af.getViewport()
.getGlobalColourScheme() instanceof RNAHelicesColour,
"Couldn't apply RNA helices colourscheme");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
.getSchemeName()),
"Recognise T-Coffee score from string");
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
af.alignPanel.alignmentChanged();
- assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+ af.saveAlignment(tfile, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
af.closeMenuItem_actionPerformed(true);
af = null;
File tfile = File.createTempFile("JalviewTest", ".jvp");
tfile.deleteOnExit();
String filePath = tfile.getAbsolutePath();
- assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+ af.saveAlignment(filePath, FileFormat.Jalview);
+ assertTrue(af.isSaveAlignmentSuccessful(),
"Failed to store as a project.");
/*
DataSourceType.FILE);
AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+ DBModList<DBRefEntry> dbrefs = rpep.getDBRefs();
assertEquals(rpep.getName(), "P30419");
- DBRefEntry[] dbrefs = rpep.getDBRefs();
- assertEquals(dbrefs.length, 3);
- DBRefEntry dbRef = dbrefs[0];
+ assertEquals(dbrefs.size(), 3);
+ DBRefEntry dbRef = dbrefs.get(0);
assertFalse(dbRef instanceof GeneLocus);
assertNull(dbRef.getMap());
assertEquals(dbRef, dbref1);
* restored dbrefs with mapping have a different 'map to'
* sequence but otherwise match the original dbrefs
*/
- dbRef = dbrefs[1];
+ dbRef = dbrefs.get(1);
assertFalse(dbRef instanceof GeneLocus);
assertTrue(dbRef.equalRef(dbref2));
assertNotNull(dbRef.getMap());
/*
* GeneLocus map.to is null so can compare Mapping objects
*/
- dbRef = dbrefs[2];
+ dbRef = dbrefs.get(2);
assertTrue(dbRef instanceof GeneLocus);
assertEquals(dbRef, dbref3);
}