import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
-import jalview.structure.StructureViewSettings;
+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 = !StructureViewSettings
+ boolean isParseWithJMOL = !StructureImportSettings
.getCurrentDefaultFormat().equalsIgnoreCase("PDB");
if (isParseWithJMOL)
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
}
else
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
type);
}
else if (format.equals("mmCIF"))
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile, type);
boolean isParseWithJMOL = false;
if (isParseWithJMOL)
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
else
{
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
}
else if (format.equals("mmCIF"))
{
- StructureViewSettings.addSettings(annotFromStructure,
+ StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);