import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.PDBEntry.Type;
public AlignmentI readFile(File selectedFile, String file,
DataSourceType sourceType, FileFormatI fileFormat,
- AlignmentAnnotation.TFType tempfacType) throws IOException
+ StructureImportSettings.TFType tempfacType) throws IOException
{
this.selectedFile = selectedFile;
- if (selectedFile != null)
- {
- this.inFile = selectedFile.getPath();
- }
- this.inFile = file;
+ this.inFile = selectedFile != null ? selectedFile.getPath() : file;
try
{
if (fileFormat.isStructureFile())
.toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
+ if (tempfacType != null)
+ {
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+ }
if (isParseWithJMOL)
{
// needs a File option
alignFile = new JmolParser(
selectedFile == null ? inFile : selectedFile, sourceType,
- tempfacType);
+ StructureImportSettings.getTemperatureFactorType());
}
else
{