import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureViewSettings;
import java.awt.Color;
import java.util.List;
// 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",
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));
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();
// 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()];