* 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 Vector bonds = new Vector();
+
public Vector atoms = new Vector();
+
public Vector residues = new Vector();
+
public int offset;
+
public Sequence sequence;
+
public boolean isVisible = true;
+
public int pdbstart = 0;
+
public int pdbend = 0;
+
public int seqstart = 0;
+
public int seqend = 0;
+
public String pdbid = "";
+
public PDBChain(String pdbid, String id)
{
this.pdbid = pdbid.toLowerCase();
for (int i = 0; i < bonds.size(); i++)
{
- tmp = tmp + ( (Bond) bonds.elementAt(i)).at1.resName + " " +
- ( (Bond) bonds.elementAt(i)).at1.resNumber + " " + offset +
- "\n";
+ tmp = tmp + ((Bond) bonds.elementAt(i)).at1.resName + " "
+ + ((Bond) bonds.elementAt(i)).at1.resNumber + " " + offset
+ + "\n";
}
return tmp;
}
}
}
+
/**
- * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
+ * copy over the RESNUM seqfeatures from the internal chain sequence to the
+ * mapped sequence
+ *
* @param seq
- * @param status The Status of the transferred annotation
+ * @param status
+ * The Status of the transferred annotation
* @return the features added to sq (or its dataset)
*/
- public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
+ public SequenceFeature[] transferRESNUMFeatures(SequenceI seq,
+ String status)
{
SequenceI sq = seq;
- while (sq!=null && sq.getDatasetSequence()!=null)
+ while (sq != null && sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
if (sq == sequence)
}
/**
* 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 ?
- for (int i=0; i<seqsfeatures.length; i++) {
- } */
+ * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int
+ * totfeat=seqsfeatures.length; // Remove any features for this exact chain ?
+ * for (int i=0; i<seqsfeatures.length; i++) { }
+ */
if (status == null)
{
status = PDBChain.IEASTATUS;
if (features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 +
- ( (Atom) ( (Residue) residues.elementAt(tx.getBegin() - offset)).
- atoms.elementAt(0)).alignmentMapping);
- tx.setEnd(1 +
- ( (Atom) ( (Residue) residues.elementAt(tx.getEnd() - offset)).
- atoms.elementAt(0)).alignmentMapping);
- tx.setStatus(status +
- ( (tx.getStatus() == null || tx.getStatus().length() == 0) ?
- "" : ":" + tx.getStatus()));
- if (tx.begin!=0 && tx.end!=0)
+ tx.setBegin(1 + ((Atom) ((Residue) residues.elementAt(tx.getBegin()
+ - offset)).atoms.elementAt(0)).alignmentMapping);
+ tx.setEnd(1 + ((Atom) ((Residue) residues.elementAt(tx.getEnd()
+ - offset)).atoms.elementAt(0)).alignmentMapping);
+ tx
+ .setStatus(status
+ + ((tx.getStatus() == null || tx.getStatus()
+ .length() == 0) ? "" : ":" + tx.getStatus()));
+ if (tx.begin != 0 && tx.end != 0)
sq.addSequenceFeature(tx);
}
}
Atom at1 = tmpres.findAtom("CA");
Atom at2 = tmpres2.findAtom("CA");
- if ( (at1 != null) && (at2 != null))
+ if ((at1 != null) && (at2 != null))
{
if (at1.chain.equals(at2.chain))
{
}
Vector resAtoms = new Vector();
- //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()))
+ // 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()))
{
- resAtoms.addElement( (Atom) atoms.elementAt(i));
+ resAtoms.addElement((Atom) atoms.elementAt(i));
i++;
if (i < atoms.size())
{
- resNumber = ( (Atom) atoms.elementAt(i)).resNumber;
+ resNumber = ((Atom) atoms.elementAt(i)).resNumber;
}
else
{
}
}
- //We need this to keep in step with the outer for i = loop
+ // We need this to keep in step with the outer for i = loop
i--;
- //Make a new Residue object with the new atoms vector
+ // Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
Residue tmpres = (Residue) residues.lastElement();
Atom tmpat = (Atom) tmpres.atoms.elementAt(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);
+ 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 (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
{
seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
}
else
{
- seq.append(ResidueProperties.aa[ ( (Integer) ResidueProperties.
- getAA3Hash()
- .get(tmpat.resName)).intValue()]);
+ seq.append(ResidueProperties.aa[((Integer) ResidueProperties
+ .getAA3Hash().get(tmpat.resName)).intValue()]);
}
count++;
}
id = " ";
}
- sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()
- // System.out.println("PDB Sequence is :\nSequence = " + seq);
- // System.out.println("No of residues = " + residues.size());
+ sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
+ // resNumber-offset
+ // ~=
+ // seq.size()
+ // 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++)
{
- sequence.addSequenceFeature( (SequenceFeature) resFeatures.elementAt(i));
+ sequence.addSequenceFeature((SequenceFeature) resFeatures
+ .elementAt(i));
resFeatures.setElementAt(null, i);
}
Annotation[] annots = new Annotation[resAnnotation.size()];
- float max=0;
- for (i=0,iSize=annots.length; i<iSize; i++)
+ float max = 0;
+ for (i = 0, iSize = annots.length; i < iSize; i++)
{
annots[i] = (Annotation) resAnnotation.elementAt(i);
- if (annots[i].value>max)
+ if (annots[i].value > max)
max = annots[i].value;
resAnnotation.setElementAt(null, i);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(),
- annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "PDB.CATempFactor", "CA Temperature Factor for "
+ + sequence.getName(), annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
{
Bond b = (Bond) bonds.elementAt(i);
- if (b.at1.resName.equalsIgnoreCase("ASP") ||
- b.at1.resName.equalsIgnoreCase("GLU"))
+ if (b.at1.resName.equalsIgnoreCase("ASP")
+ || b.at1.resName.equalsIgnoreCase("GLU"))
{
b.startCol = Color.red;
}
- else if (b.at1.resName.equalsIgnoreCase("LYS") ||
- b.at1.resName.equalsIgnoreCase("ARG"))
+ else if (b.at1.resName.equalsIgnoreCase("LYS")
+ || b.at1.resName.equalsIgnoreCase("ARG"))
{
b.startCol = Color.blue;
}
b.startCol = Color.lightGray;
}
- if (b.at2.resName.equalsIgnoreCase("ASP") ||
- b.at2.resName.equalsIgnoreCase("GLU"))
+ if (b.at2.resName.equalsIgnoreCase("ASP")
+ || b.at2.resName.equalsIgnoreCase("GLU"))
{
b.endCol = Color.red;
}
- else if (b.at2.resName.equalsIgnoreCase("LYS") ||
- b.at2.resName.equalsIgnoreCase("ARG"))
+ else if (b.at2.resName.equalsIgnoreCase("LYS")
+ || b.at2.resName.equalsIgnoreCase("ARG"))
{
b.endCol = Color.blue;
}
{
b.endCol = Color.lightGray;
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
Bond b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
{
b = (Bond) bonds.elementAt(i);
- index = ( (Integer) ResidueProperties.aa3Hash.get(b.at1.
- resName)).intValue();
+ index = ((Integer) ResidueProperties.aa3Hash.get(b.at1.resName))
+ .intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- index = ( (Integer) ResidueProperties.aa3Hash.get(b.at2.resName)).
- intValue();
+ index = ((Integer) ResidueProperties.aa3Hash.get(b.at2.resName))
+ .intValue();
b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- }
- catch (Exception e)
+ } catch (Exception e)
{
b = (Bond) bonds.elementAt(i);
b.startCol = Color.gray;
}
}
- public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, String status)
+ public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq,
+ String status)
{
AlignmentAnnotation[] transferred = null;
}
/**
- * copy any sequence annotation onto the sequence mapped using the provided StructureMapping
+ * copy any sequence annotation onto the sequence mapped using the provided
+ * StructureMapping
+ *
* @param mapping
*/
public void transferResidueAnnotation(StructureMapping mapping)
{
SequenceI sq = mapping.getSequence();
- if (sq!=null)
+ if (sq != null)
{
- if (sequence!=null && sequence.getAnnotation()!=null)
+ if (sequence != null && sequence.getAnnotation() != null)
{
}
- 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++)
+ 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++)
{
- int prn = mapping.getPDBResNum(k+1);
+ int prn = mapping.getPDBResNum(k + 1);
- an[k] = new Annotation((float)prn);
- if (min==-1)
+ an[k] = new Annotation((float) prn);
+ if (min == -1)
{
- min=k;
- max=k;
- } else {
- if (min>k)
+ min = k;
+ max = k;
+ }
+ else
+ {
+ if (min > k)
+ {
+ min = k;
+ }
+ else if (max < k)
{
- min=k;
- } else
- if (max<k)
- {
- max=k;
- }
+ max = k;
+ }
}
}
- sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", "PDB Residue Numbering for "+this.pdbid+":"+this.id, an, (float)min,(float)max, AlignmentAnnotation.LINE_GRAPH));
+ sq
+ .addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+ "PDB Residue Numbering for " + this.pdbid + ":"
+ + this.id, an, (float) min, (float) max,
+ AlignmentAnnotation.LINE_GRAPH));
}
}
}
git://source.jalview.org / jalview.git / blobdiff