package jalview.ext.jmol;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
import java.util.Vector;
import org.jmol.c.STR;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import MCview.PDBfile;
+import mc_view.PDBfile;
/**
* @author jimp
*/
public class JmolParserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* 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/1xyz.pdb" };
+ 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.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_TEMPFACT_ANN",
+ Boolean.FALSE.toString());
+ Cache.setPropertyNoSave("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, AppletFormatAdapter.FILE);
+ AlignFrame af = fl.LoadFileWaitTillLoaded(f, DataSourceType.FILE);
validateSecStrRows(af.getViewport().getAlignment());
}
}
for (String pdbStr : testFile)
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
- AppletFormatAdapter.FILE);
- JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- jalview.io.AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
+ JmolParser jtest = new JmolParser(pdbStr, 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);
+ 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());
+ 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);
}
}
+
}
private void validateSecStrRows(AlignmentI al)
private void checkFirstAAIsAssoc(SequenceI sq)
{
- assertTrue("No secondary structure assigned for protein sequence.",
+ assertTrue(
+ "No secondary structure assigned for protein sequence for "
+ + sq.getName(),
sq.getAnnotation() != null && sq.getAnnotation().length >= 1
&& sq.getAnnotation()[0].hasIcons);
assertTrue(
"Secondary structure not associated for sequence "
- + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+ + sq.getName(),
+ sq.getAnnotation()[0].sequenceRef == sq);
}
/**
@Test(groups = { "Functional" })
public void testParse_missingResidues() throws Exception
{
- PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
- AppletFormatAdapter.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct,
- pdbWithChainBreak,
- jalview.io.AppletFormatAdapter.PASTE);
+ PDBfile mctest = new PDBfile(false, false, false,
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
+ JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
+ DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
public void testParse_alternativeResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
- AppletFormatAdapter.PASTE);
- boolean annotFromStructure = false;
- boolean localSecondaryStruct = false;
- boolean serviceSecondaryStruct = false;
- JmolParser jtest = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
- jalview.io.AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
+ JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
-
+
assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
assertEquals("ALC", seqs.get(0).getSequenceAsString());
assertEquals('H', structCode[4]);
assertEquals('E', structCode[5]);
}
+
+ @Test(groups = "Functional")
+ public void testLocalPDBId() throws Exception
+ {
+ JmolParser structureData;
+ /*
+ * reads a local structure
+ */
+ structureData = new JmolParser("examples/testdata/localstruct.pdb",
+ DataSourceType.FILE);
+ assertNotNull(structureData);
+ /*
+ * local structure files should yield a false ID based on the filename
+ */
+ assertNotNull(structureData.getId());
+ assertEquals(structureData.getId(), "localstruct");
+ assertNotNull(structureData.getSeqs());
+ /*
+ * the ID is also the group for features derived from structure data
+ */
+ String featureGroup = structureData.getSeqs().get(0)
+ .getSequenceFeatures().get(0).featureGroup;
+ assertNotNull(featureGroup);
+ assertEquals(featureGroup, "localstruct");
+ }
}
git://source.jalview.org / jalview.git / blobdiff