import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.JInternalFrame;
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;
assertNotNull(
ColourSchemeProperty.getColourScheme(viewport,
viewport.getAlignment(),
- viewport.getGlobalColourScheme()
- .getSchemeName()),
+ viewport.getGlobalColourScheme().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;
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(
af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- Desktop.getAlignmentPanels(
- af.getViewport().getSequenceSetId()).length,
+ Assert.assertEquals(Desktop
+ .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
oldviews);
}
"Mismatch PDBEntry 'Type'");
Assert.assertNotNull(recov.getFile(),
"Recovered PDBEntry should have a non-null file entry");
+ Assert.assertEquals(
+ recov.getFile().toLowerCase(Locale.ENGLISH)
+ .lastIndexOf("pdb"),
+ recov.getFile().length() - 3,
+ "Recovered PDBEntry file should have PDB suffix");
}
}
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.");
/*
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
assertNotNull(af, "Didn't read in the example file correctly.");
-
+
AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
SequenceI pep = ap.getAlignment().getSequenceAt(0);
SequenceI cds = ap.getAlignment().getSequenceAt(1);
Assert.fail("Didn't save the state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
-
+
new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
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);
}