+ isNa = nucleotide;
+ sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note:
+ // resNumber-offset
+ // ~=
+ // seq.size()
+ // Add normalised feature scores to RESNUM indicating start/end of sequence
+ // sf.setScore(offset+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++)
+ {
+ 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++)
+ {
+ annots[i] = (Annotation) resAnnotation.elementAt(i);
+ if (annots[i].value > max)
+ max = annots[i].value;
+ resAnnotation.setElementAt(null, i);
+ }
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+ "PDB.TempFactor", "Temperature Factor for "
+ + sequence.getName(), annots, 0, max,
+ AlignmentAnnotation.LINE_GRAPH);
+ tfactorann.setSequenceRef(sequence);
+ sequence.addAlignmentAnnotation(tfactorann);
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < bonds.size(); i++)
+ {
+ try
+ {
+ Bond b = (Bond) bonds.elementAt(i);