@BeforeMethod(alwaysRun = true)
public void setup() throws Exception
{
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
if (StructureImportSettings.getDefaultPDBFileParser()
.equals(StructureParser.JALVIEW_PARSER))
{
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
@AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
}
AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
+ af.saveAlignment(tfile, FileFormat.Jalview);
assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, FileFormat.Jalview));
+ af.isSaveAlignmentSuccessful());
af.closeMenuItem_actionPerformed(true);
af = null;
af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
{
System.err.println("CalcId " + ana.getCalcId());
if (ana.getCalcId() != null
- && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+ && mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
{
exists = true;
- if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
+ if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
{
found = true;
}