import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.io.IOException;
public void xferSettings()
{
- this.visibleChainAnnotation = StructureViewSettings
+ this.visibleChainAnnotation = StructureImportSettings
.isVisibleChainAnnotation();
- this.predictSecondaryStructure = StructureViewSettings
+ this.predictSecondaryStructure = StructureImportSettings
.isPredictSecondaryStructure();
- this.externalSecondaryStructure = StructureViewSettings
+ this.externalSecondaryStructure = StructureImportSettings
.isExternalSecondaryStructure();
}
- public StructureFile(boolean parseImmediately, String inFile, String type)
+ public StructureFile(boolean parseImmediately, String dataObject, String type)
throws IOException
{
- super(parseImmediately, inFile, type);
+ super(parseImmediately, dataObject, type);
}
public StructureFile(boolean a, FileParse fp) throws IOException
predictSecondaryStructure, externalSecondaryStructure,
new FileParse(getDataName(), type) };
- StructureViewSettings.setShowSeqFeatures(false);
- StructureViewSettings.setVisibleChainAnnotation(false);
- StructureViewSettings
+ StructureImportSettings.setShowSeqFeatures(false);
+ StructureImportSettings.setVisibleChainAnnotation(false);
+ StructureImportSettings
.setPredictSecondaryStructure(predictSecondaryStructure);
- StructureViewSettings
+ StructureImportSettings
.setExternalSecondaryStructure(externalSecondaryStructure);
Object jmf = constructor.newInstance(args);
AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
} catch (ClassNotFoundException q)
{
}
- StructureViewSettings.setShowSeqFeatures(true);
+ StructureImportSettings.setShowSeqFeatures(true);
}
public PDBChain findChain(String id) throws Exception