import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.util.Vector;
Boolean.TRUE.toString());
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
+ StructureImportSettings
+ .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
}
@Test(groups = { "Functional" })
for (String f : testFile)
{
FileLoader fl = new jalview.io.FileLoader(false);
- AlignFrame af = fl
- .LoadFileWaitTillLoaded(f, DataSourceType.FILE);
+ AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE);
validateSecStrRows(af.getViewport().getAlignment());
}
}
@Test(groups = { "Functional" })
public void testFileParser() throws Exception
{
- StructureImportSettings.setProcessHETATMs(false);
for (String pdbStr : testFile)
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
DataSourceType.FILE);
JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- jalview.io.DataSourceType.FILE);
- Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
-
- assertTrue(
- "No sequences extracted from testfile\n"
- + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
- : "(No warnings raised)"), seqs != null
- && seqs.size() > 0);
- for (SequenceI sq : seqs)
- {
- assertEquals("JMol didn't process " + pdbStr
- + " to the same sequence as MCView",
- sq.getSequenceAsString(), mcseqs.remove(0)
- .getSequenceAsString());
- AlignmentI al = new Alignment(new SequenceI[] { sq });
- validateSecStrRows(al);
- }
- }
- StructureImportSettings.setProcessHETATMs(true);
- for (String pdbStr : testFile)
- {
- PDBfile mctest = new PDBfile(false, false, false, pdbStr,
DataSourceType.FILE);
- JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- jalview.io.DataSourceType.FILE);
Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
assertTrue(
validateSecStrRows(al);
}
}
+
}
private void validateSecStrRows(AlignmentI al)
public void testParse_missingResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false,
- pastePDBDataWithChainBreak,
- DataSourceType.PASTE);
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
boolean annotFromStructure = false;
boolean localSecondaryStruct = false;
boolean serviceSecondaryStruct = false;
JmolParser jtest = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct,
- pastePDBDataWithChainBreak,
- jalview.io.DataSourceType.PASTE);
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
boolean serviceSecondaryStruct = false;
JmolParser jtest = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
- jalview.io.DataSourceType.PASTE);
+ DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();