import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureViewSettings;
import jalview.util.MessageManager;
import java.io.IOException;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String inFile, String type) throws IOException
+ public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String inFile, String type)
+ throws IOException
{
super(inFile, type);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
}
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- FileParse fp) throws IOException
+ public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse fp) throws IOException
{
super(fp);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
- }
-
- public JmolParser(FileParse fp) throws IOException
- {
- super(fp);
- }
-
- public JmolParser(String inFile, String type) throws IOException
- {
- super(inFile, type);
+ // addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
}
public JmolParser()
@Override
public void parse() throws IOException
{
-
+ String dataName = getDataName();
+ if (dataName.endsWith(".cif"))
+ {
+ setDbRefType(DBRefSource.MMCIF);
+ }
+ else
+ {
+ setDbRefType(DBRefSource.PDB);
+ }
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
- createAnnotation(chainseq, chain, ms.at);
if (isRNA(chainseq))
{
rna.add(chainseq);
{
prot.add(chainseq);
}
+
+ if (StructureViewSettings.isPredictSecondaryStructure())
+ {
+ createAnnotation(chainseq, chain, ms.at);
+ }
}
} catch (OutOfMemoryError er)
{