{
public static final String RESNUM_FEATURE = "RESNUM";
- /**
- * SequenceFeature group for PDB File features added to sequences
- */
- private static final String PDBFILEFEATURE = "PDBFile";
-
private static final String IEASTATUS = "IEA:jalview";
public String id;
public String pdbid = "";
- public PDBChain(String pdbid, String id)
+ public PDBChain(String thePdbid, String theId)
{
- this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
- this.id = id;
+ this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+ this.id = theId;
}
/**
}
/**
- * copy over the RESNUM seqfeatures from the internal chain sequence to the
+ * Copies over the RESNUM seqfeatures from the internal chain sequence to the
* mapped sequence
*
* @param seq
* @param status
* The Status of the transferred annotation
- * @return the features added to sq (or its dataset)
*/
- public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+ public void transferRESNUMFeatures(SequenceI seq,
String status)
{
SequenceI sq = seq;
sq = sq.getDatasetSequence();
if (sq == sequence)
{
- return null;
+ return;
}
}
- /**
+
+ /*
* Remove any existing features for this chain if they exist ?
* SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
* totfeat=seqsfeatures.length; // Remove any features for this exact chain
{
status = PDBChain.IEASTATUS;
}
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features == null)
- {
- return null;
- }
- for (int i = 0; i < features.length; i++)
+
+ List<SequenceFeature> features = sequence.getSequenceFeatures();
+ for (SequenceFeature feature : features)
{
- if (features[i].getFeatureGroup() != null
- && features[i].getFeatureGroup().equals(pdbid))
+ if (feature.getFeatureGroup() != null
+ && feature.getFeatureGroup().equals(pdbid))
{
- SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
- .elementAt(0).alignmentMapping);
- tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
- .elementAt(0).alignmentMapping);
+ int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping;
+ int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping;
+ SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
+ feature.getFeatureGroup(), feature.getScore());
tx.setStatus(status
- + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
+ + ((tx.getStatus() == null || tx.getStatus().length() == 0)
+ ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
{
}
}
}
- return features;
}
/**
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
- if (currAtom.insCode != ' '
- && !residues.isEmpty()
- && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
+ if (currAtom.insCode != ' ' && !residues.isEmpty()
+ && residues.lastElement().atoms
+ .get(0).resNumber == currAtom.resNumber)
{
- SequenceFeature sf = new SequenceFeature("INSERTION",
- currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
- + id, "", offset + count - 1, offset + count - 1,
- "PDB_INS");
+ String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ + pdbid + id;
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
+ + count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
else
{
-
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
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, tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
+ String desc = tmpat.resName
+ + ":" + tmpat.resNumIns + " " + pdbid + id;
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
+ offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
- if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
+ if ((symbol = ResidueProperties.getAA3Hash()
+ .get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
// use the aaIndex rather than call 'toLower' - which would take a bit
// more time.
deoxyn = nucname.length() == 2
- && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D'];
+ && ResidueProperties.aaIndex[nucname
+ .charAt(0)] == ResidueProperties.aaIndex['D'];
if (tmpat.name.equalsIgnoreCase("CA")
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- char r = ResidueProperties
- .getSingleCharacterCode(ResidueProperties
- .getCanonicalAminoAcid(tmpat.resName));
+ char r = ResidueProperties.getSingleCharacterCode(
+ ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
seq.append(r == '0' ? 'X' : r);
// System.err.println("PDBReader:Null aa3Hash for " +
// tmpat.resName);
{
if (nucleotide)
{
- System.err
- .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ System.err.println(
+ "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
}
seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0),
- 0, null, null, 0f);
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
for (AlignmentAnnotation ana : shadow.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
- ana.getCalcId(), ana.label);
+ List<AlignmentAnnotation> transfer = sq
+ .getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
// 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++)
{
int prn = mapping.getPDBResNum(k + 1);