if (StructureImportSettings.getDefaultPDBFileParser()
.equals(StructureParser.JALVIEW_PARSER))
{
- assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+ assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
}
}
}
break;
}
}
- assertTrue(
- "Couldn't find sequence associated annotation "
- + aa.label
- + " on the sequence it is associated with.\nSequence associated editing will fail.",
+ assertTrue("Couldn't find sequence associated annotation "
+ + aa.label
+ + " on the sequence it is associated with.\nSequence associated editing will fail.",
found);
}
}
@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" });
}
/**
String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, DataSourceType.FILE);
+ 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,
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
- assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
- .size());
+ assertEquals("Expected only one PDB ID", 1,
+ sq.getAllPDBEntries().size());
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
- System.err.println("PDB Entry " + pdbentry.getId() + " "
- + pdbentry.getFile());
+ System.err.println(
+ "PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
boolean exists = false, found = false;
for (AlignmentAnnotation ana : sq.getAnnotation())
{
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;
}
}
if (exists)
{
- assertTrue("Couldn't find any annotation for " + pdbentry.getId()
- + " (file handle " + pdbentry.getFile() + ")", found);
+ assertTrue(
+ "Couldn't find any annotation for " + pdbentry.getId()
+ + " (file handle " + pdbentry.getFile() + ")",
+ found);
}
}
}