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, String tempFactorColumnName)
+ public PDBChain(String thePdbid, String theId,
+ AnnotationRowBuilder template)
- boolean sameResidue = Comparison.isSameResidue(
- seqchar, strchar, false);
+ boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
+ false);
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
- SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
- + count - 1, offset + count - 1, "PDB_INS");
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc,
+ offset + count - 1, offset + count - 1, "PDB_INS");
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
max = Math.max(max, annots[i].value);
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
max = Math.max(max, annots[i].value);
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
- tfacName, tfacName + " for " + pdbid + id,
+ tfacTemplate.getName(),
+ (tfacTemplate.isHasDescription()
+ ? tfacTemplate.getDescription()
+ : tfacTemplate.getName()) + " for " + pdbid + id,
annots, min, max, AlignmentAnnotation.LINE_GRAPH);
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);
// 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++)