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;
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);
+ DataSourceType.FILE);
JmolParser jtest = new JmolParser(false, false, false, pdbStr,
- jalview.io.AppletFormatAdapter.FILE);
+ 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);
+ pastePDBDataWithChainBreak, DataSourceType.PASTE);
boolean annotFromStructure = false;
boolean localSecondaryStruct = false;
boolean serviceSecondaryStruct = false;
JmolParser jtest = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct,
- pastePDBDataWithChainBreak,
- jalview.io.AppletFormatAdapter.PASTE);
+ 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);
boolean annotFromStructure = false;
boolean localSecondaryStruct = false;
boolean serviceSecondaryStruct = false;
JmolParser jtest = new JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
- jalview.io.AppletFormatAdapter.PASTE);
+ DataSourceType.PASTE);
Vector<SequenceI> seqs = jtest.getSeqs();
Vector<SequenceI> mcseqs = mctest.getSeqs();