package jalview.io;
+import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
{
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = !StructureImportSettings
- .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
return new JmolParser(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
inFile,
sourceType);
StructureImportSettings.setShowSeqFeatures(true);
return new MCview.PDBfile(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
inFile,
sourceType);
public AlignmentFileI getAlignmentFile(FileParse source)
throws IOException
{
- boolean isParseWithJMOL = !StructureImportSettings
- .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
return new JmolParser(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
source);
}
StructureImportSettings.setShowSeqFeatures(true);
return new MCview.PDBfile(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
source);
}
{
return new JmolParser(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
inFile, sourceType);
}
{
return new JmolParser(
StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isPredictSecondaryStructure(),
+ StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
source);
}