.getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
+ return new JmolParser(inFile, sourceType);
}
else
{
.getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
else
{
public AlignmentFileI getAlignmentFile(String inFile,
DataSourceType sourceType) throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile, sourceType);
+ return new JmolParser(inFile, sourceType);
}
@Override
public AlignmentFileI getAlignmentFile(FileParse source)
throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
@Override