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;
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(
public void testParse_missingResidues() throws Exception
{
PDBfile mctest = new PDBfile(false, false, false,
- pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
- JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
- AppletFormatAdapter.PASTE);
+ 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);
+ DataSourceType.PASTE);
JmolParser jtest = new JmolParser(pdbWithAltLoc,
- AppletFormatAdapter.PASTE);
+ 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");
}
}