import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import java.awt.Color;
public PDBChain(String pdbid, String id)
{
- this.pdbid = pdbid.toLowerCase();
+ this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
this.id = id;
}
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
+ if (pdbpos >= residues.size())
+ {
+ continue;
+ }
Residue res = residues.elementAt(pdbpos);
for (Atom atom : res.atoms)
{
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))
// 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)
{
SequenceFeature sf = new SequenceFeature("INSERTION",
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();
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // 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);
}
else
{
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
+
+ if (StructureImportSettings.isShowSeqFeatures())
+ {
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
{
sequence.addSequenceFeature(resFeatures.elementAt(i));
resFeatures.setElementAt(null, i);
}
+ }
if (visibleChainAnnotation)
{
Annotation[] annots = new Annotation[resAnnotation.size()];
{
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