import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
public PDBChain(String thePdbid, String theId,
AnnotationRowBuilder template)
public PDBChain(String thePdbid, String theId,
AnnotationRowBuilder template)
? tfacTemplate.getDescription()
: tfacTemplate.getName()) + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
? tfacTemplate.getDescription()
: tfacTemplate.getName()) + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
ana.getCalcId(), ana.label, ana.description);
if (transfer == null || transfer.size() == 0)
{
ana.getCalcId(), ana.label, ana.description);
if (transfer == null || transfer.size() == 0)
{
ana.liftOver(sequence, shadowMap);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
ana.liftOver(sequence, shadowMap);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
- // mapping.transfer(ana);
+ if (cm != null && cm instanceof MappableContactMatrixI)
+ {
+ dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+ .liftOver(dsq, sqmpping));
+ }
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
// Useful for debugging mappings - adds annotation for mapped position
float min = -1, max = 0;
Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
- for (int i = sq.getStart(), j = sq.getEnd(),
- k = 0; i <= j; i++, k++)
+ for (int i = sq.getStart(), j = sq
+ .getEnd(), k = 0; i <= j; i++, k++)