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 java.awt.Color;
import java.util.List;
public class PDBChain
{
+ public static final String RESNUM_FEATURE = "RESNUM";
+
/**
* SequenceFeature group for PDB File features added to sequences
*/
public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
this.id = id;
}
pdbpos++;
}
- if (as.astr1.charAt(i) == as.astr2.charAt(i))
+ boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
+ as.astr2.charAt(i), false);
+ if (sameResidue)
{
if (pdbpos >= residues.size())
{
status = PDBChain.IEASTATUS;
}
SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features == null)
+ {
+ return null;
+ }
for (int i = 0; i < features.length; i++)
{
- if (features[i].getFeatureGroup().equals(pdbid))
+ if (features[i].getFeatureGroup() != null
+ && features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
.elementAt(0).alignmentMapping);
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)
{
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
- if (currAtom.insCode != ' '
- && 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");
+ + id,
+ "", 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", tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
- + count, offset + count, pdbid);
- // MCview.PDBChain.PDBFILEFEATURE);
- resFeatures.addElement(sf);
- resAnnotation.addElement(new Annotation(tmpat.tfactor));
- // Keep totting up the sequence
- 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'];
- if (tmpat.name.equalsIgnoreCase("CA")
- || ResidueProperties.nucleotideIndex[nucname
- .charAt((deoxyn ? 1 : 0))] == -1)
+ // 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);
+ resFeatures.addElement(sf);
+ resAnnotation.addElement(new Annotation(tmpat.tfactor));
+ // Keep totting up the sequence
+
+ if ((symbol = ResidueProperties.getAA3Hash()
+ .get(tmpat.resName)) == null)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ 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'];
+ if (tmpat.name.equalsIgnoreCase("CA")
+ || ResidueProperties.nucleotideIndex[nucname
+ .charAt((deoxyn ? 1 : 0))] == -1)
+ {
+ char r = ResidueProperties.getSingleCharacterCode(
+ ResidueProperties.getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
+ }
+ else
+ {
+ // nucleotide flag
+ nucleotide = true;
+ seq.append(nucname.charAt((deoxyn ? 1 : 0)));
+ }
}
else
{
- // nucleotide flag
- nucleotide = true;
- seq.append(nucname.charAt((deoxyn ? 1 : 0)));
- }
- }
- else
- {
- if (nucleotide)
- {
- System.err
- .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ if (nucleotide)
+ {
+ System.err.println(
+ "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!");
+ }
+ seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
- seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
- }
count++;
}
}
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
- for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+
+ if (StructureImportSettings.isShowSeqFeatures())
{
- sequence.addSequenceFeature(resFeatures.elementAt(i));
- resFeatures.setElementAt(null, i);
+ for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+ {
+ sequence.addSequenceFeature(resFeatures.elementAt(i));
+ resFeatures.setElementAt(null, i);
+ }
}
if (visibleChainAnnotation)
{
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ 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));
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
} catch (Exception e)
{
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);
{
for (AlignmentAnnotation ana : sequence.getAnnotation())
{
- List<AlignmentAnnotation> transfer = sq
+ List<AlignmentAnnotation> transfer = dsq
.getAlignmentAnnotations(ana.getCalcId(), ana.label);
if (transfer == null || transfer.size() == 0)
{
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
+ dsq.addAlignmentAnnotation(ana);
// mapping.transfer(ana);
}
else
// 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);
git://source.jalview.org / jalview.git / blobdiff