*/
package MCview;
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureViewSettings;
+
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
public class PDBChain
{
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))
{
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);
+ tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping);
+ tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping);
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
* If > 99% 'P', flag as nucleotide; note the count doesn't include the last
* residue
*/
- if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99))
+ if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
{
isNa = true;
}
Vector<Annotation> resAnnotation = new Vector<Annotation>();
int i, iSize = atoms.size() - 1;
int resNumber = -1;
+ char insCode = ' ';
for (i = 0; i <= iSize; i++)
{
Atom tmp = atoms.elementAt(i);
resNumber = tmp.resNumber;
+ insCode = tmp.insCode;
+
int res = resNumber;
+ char ins = insCode;
if (i == 0)
{
Vector<Atom> resAtoms = new Vector<Atom>();
// Add atoms to a vector while the residue number
// remains the same as the first atom's resNumber (res)
- while ((resNumber == res) && (i < atoms.size()))
+ while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
{
resAtoms.add(atoms.elementAt(i));
i++;
if (i < atoms.size())
{
resNumber = atoms.elementAt(i).resNumber;
+ insCode = atoms.elementAt(i).insCode;
}
else
{
// We need this to keep in step with the outer for i = loop
i--;
+ // 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",
+ currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid
+ + id, "", offset + count - 1, offset + count - 1,
+ "PDB_INS");
+ resFeatures.addElement(sf);
+ residues.lastElement().atoms.addAll(resAtoms);
+ }
+ else
+ {
+
+ // boolean baseDetected = false;
+ // for (Atom resAtom : resAtoms)
+ // {
+ // if (resAtom.insCode == ' ')
+ // {
+ // baseDetected = true;
+ // }
+ // }
+ // if (!baseDetected)
+ // {
+ // continue;
+ // }
// 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
+ 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
{
}
seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
}
- count++;
+ count++;
+ }
}
if (id.length() < 1)
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
+
+ if (StructureViewSettings.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()];
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
"Temperature Factor", "Temperature Factor for " + pdbid + id,
- annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
+ annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
{
try
{
- index = ResidueProperties.aa3Hash.get(b.at1.resName)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- index = ResidueProperties.aa3Hash.get(b.at2.resName)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
} catch (Exception e)
* @param sqmpping
* - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(
- StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
+ public void transferResidueAnnotation(StructureMapping mapping,
+ jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;
git://source.jalview.org / jalview.git / blobdiff