import jalview.gui.AlignFrame;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
+import jalview.structure.StructureImportSettings;
import java.util.Vector;
* 1GAQ has been reduced to alpha carbons only
* 1QCF is the full PDB file including headers, HETATM etc
*/
- // String[] testFile = new String[] { "./examples/1GAQ.txt",
- // "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
- String[] testFile = new String[] { "./examples/testdata/1qcf.cif" }; // ,
+ String[] testFile = new String[] { "./examples/1GAQ.txt",
+ "./test/jalview/ext/jmol/1xyz.pdb",
+ "./test/jalview/ext/jmol/1qcf.pdb" };
//@formatter:off
// a modified and very cut-down extract of 4UJ4
- String pdbWithChainBreak =
+ String pastePDBDataWithChainBreak =
"HEADER TRANSPORT PROTEIN 08-APR-15 4UJ4\n" +
// chain B has missing residues; these should all go in the same sequence:
"ATOM 1909 CA VAL B 358 21.329 -19.739 -67.740 1.00201.05 C\n" +
@BeforeMethod(alwaysRun = true)
public void setUp()
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+ Boolean.FALSE.toString());
Cache.applicationProperties.setProperty("ADD_SS_ANN",
Boolean.TRUE.toString());
+ StructureImportSettings.setDefaultStructureFileFormat("PDB");
}
@Test(groups = { "Functional" })
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
AppletFormatAdapter.FILE);
- JmolParser jtest = new JmolParser(pdbStr,
+ JmolParser jtest = new JmolParser(false, false, false, pdbStr,
jalview.io.AppletFormatAdapter.FILE);
Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
validateSecStrRows(al);
}
}
+
}
private void validateSecStrRows(AlignmentI al)
@Test(groups = { "Functional" })
public void testParse_missingResidues() throws Exception
{
- PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
+ PDBfile mctest = new PDBfile(false, false, false,
+ pastePDBDataWithChainBreak,
AppletFormatAdapter.PASTE);
- JmolParser jtest = new JmolParser(pdbWithChainBreak,
+ boolean annotFromStructure = false;
+ boolean localSecondaryStruct = false;
+ boolean serviceSecondaryStruct = false;
+ JmolParser jtest = new JmolParser(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct,
+ pastePDBDataWithChainBreak,
jalview.io.AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
{
PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
AppletFormatAdapter.PASTE);
- JmolParser jtest = new JmolParser(pdbWithAltLoc,
+ boolean annotFromStructure = false;
+ boolean localSecondaryStruct = false;
+ boolean serviceSecondaryStruct = false;
+ JmolParser jtest = new JmolParser(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
jalview.io.AppletFormatAdapter.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();