import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
import mc_view.PDBChain;
public abstract class StructureFile extends AlignFile
private boolean pdbIdAvailable;
+ private StructureImportSettings.TFType temperatureFactorType = TFType.DEFAULT;
+
+ private String paeMatrix = null;
+
+ private boolean alphaFoldModel;
+
+ public void setPAEMatrix(String paeFilename)
+ {
+ paeMatrix = paeFilename;
+ }
+
+ public String getPAEMatrix()
+ {
+ return paeMatrix;
+ }
+
+ public boolean hasPAEMatrix()
+ {
+ return paeMatrix != null;
+ }
+
+ public void setTemperatureFactorType(StructureImportSettings.TFType t)
+ {
+ this.temperatureFactorType = t;
+ }
+
+ public StructureImportSettings.TFType getTemperatureFactorType()
+ {
+ return temperatureFactorType;
+ }
+
+ public void setAlphafoldModel(boolean afm)
+ {
+ alphaFoldModel = afm;
+ }
+
+ public boolean isAlphafoldModel()
+ {
+ return alphaFoldModel;
+ }
+
public StructureFile(Object inFile, DataSourceType sourceType)
throws IOException
{
}
public StructureFile(Object inFile, DataSourceType sourceType,
- AlignmentAnnotation.TFType tempfacType) throws IOException
+ StructureImportSettings.TFType tempfacType) throws IOException
{
- super(inFile, sourceType, tempfacType);
+ super(false, inFile, sourceType);
+ this.setTemperatureFactorType(tempfacType);
+ doParse();
}
public StructureFile(FileParse fp) throws IOException
.isProcessSecondaryStructure();
this.externalSecondaryStructure = StructureImportSettings
.isExternalSecondaryStructure();
-
+ this.temperatureFactorType = StructureImportSettings
+ .getTemperatureFactorType();
}
public StructureFile(boolean parseImmediately, Object dataObject,
.setProcessSecondaryStructure(predictSecondaryStructure);
StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
+ StructureImportSettings
+ .setTemperatureFactorType(temperatureFactorType);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl
.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));