import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
IProgressIndicator progress)
{
return computeMapping(true, sequence, targetChains, pdbFile, protocol,
- progress);
+ progress, null, null);
}
/**
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
+ String pdbFile, DataSourceType sourceType, TFType tft,
+ String paeFilename)
{
return computeMapping(forStructureView, sequenceArray, targetChainIds,
- pdbFile, sourceType, null);
+ pdbFile, sourceType, null, tft, paeFilename);
}
/**
synchronized public StructureFile computeMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
String pdbFile, DataSourceType sourceType,
- IProgressIndicator progress)
+ IProgressIndicator progress, TFType tft, String paeFilename)
{
long progressSessionId = System.currentTimeMillis() * 3;
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(false, pdbFile, sourceType);
+ if (paeFilename != null)
+ {
+ pdb.setPAEMatrix(paeFilename);
+ }
+ pdb.setTemperatureFactorType(tft);
pdb.addSettings(parseSecStr && processSecondaryStructure,
parseSecStr && addTempFacAnnot,
parseSecStr && secStructServices);