import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import MCview.PDBfile;
+import mc_view.PDBfile;
/**
* @author jimp
* 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",
+ String[] testFile = new String[] { "./examples/1gaq.txt",
"./test/jalview/ext/jmol/1xyz.pdb",
- "./test/jalview/ext/jmol/1qcf.pdb" };
+ "./test/jalview/ext/jmol/1QCF.pdb" };
//@formatter:off
// a modified and very cut-down extract of 4UJ4
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(pdbStr, 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 checkFirstAAIsAssoc(SequenceI sq)
{
- assertTrue("No secondary structure assigned for protein sequence for "
- + sq.getName(),
+ 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);
}
/**
public void testParse_missingResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false,
- pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
- AppletFormatAdapter.PASTE);
+ 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);
- JmolParser jtest = new JmolParser(pdbWithAltLoc,
- AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
+ JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();
* reads a local structure
*/
structureData = new JmolParser("examples/testdata/localstruct.pdb",
- AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
assertNotNull(structureData);
/*
* local structure files should yield a false ID based on the filename
*/
assertNotNull(structureData.getId());
- assertEquals(structureData.getId(), "localstruct.pdb");
+ assertEquals(structureData.getId(), "localstruct");
assertNotNull(structureData.getSeqs());
/*
* the ID is also the group for features derived from structure data
*/
- assertNotNull(structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup);
- assertEquals(
- structureData.getSeqs().get(0).getSequenceFeatures()[0].featureGroup,
- "localstruct.pdb");
-
+ String featureGroup = structureData.getSeqs().get(0)
+ .getSequenceFeatures().get(0).featureGroup;
+ assertNotNull(featureGroup);
+ assertEquals(featureGroup, "localstruct");
}
}