import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.structure.StructureViewSettings;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.File;
{
// TODO obtain config value from preference settings.
// Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = false;
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
if (isParseWithJMOL)
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
}
else
{
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
type);
}
+ ((StructureFile) alignFile).setDbRefType(format);
}
- else if (format.equals("mmCIF"))
+ else if (format.equalsIgnoreCase("mmCIF"))
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+ alignFile = new jalview.ext.jmol.JmolParser(inFile, type);
+ ((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
{
boolean isParseWithJMOL = false;
if (isParseWithJMOL)
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
}
- else if (format.equals("mmCIF"))
+ else if (format.equalsIgnoreCase("mmCIF"))
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
+ ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
{