/*
* Constructs a new DNAStrand which contains a given Nucleotide.
* This nucleotide should be able to be ANY of the many nucleotides in a strand
* (i.e. you will need to calculate the threeEnd and fiveEnd from any Nucleotide.)
*/
public DNAStrand(Nucleotide any) {
if (any == null) {
throw new IllegalArgumentException();
} else {
threeEnd = any.getThree();
fiveEnd = any.getFive();
}
}
public String toStringPlainReversed() {
StringBuilder sb = new StringBuilder();
Nucleotide now = fiveEnd;
while (now != null) {
sb.append(now.toString());
now = now.getPrev();
}
return sb.toString();
}
public String toStringPlain() {
StringBuilder sb = new StringBuilder();
Nucleotide now = threeEnd;
while (now != null) {
sb.append(now.toString());
now = now.getNext();
}
return sb.toString();
}
private void selectFocus() {
Point3D p = new Point3D(0, 0, 0);
Nucleotide n =
selectionModel
.getItems()[
selectionModel
.getSelectedIndices()
.get(selectionModel.getSelectedIndices().size() - 1)];
p = p.add(utils.fx3d.computeCenter(n.getNucleotideCoordinates()));
p = p.add(utils.fx3d.computeCenter(n.getBaseCoordinates()));
p = p.multiply(1 / ((double) 2));
// fx3d.transiteFromTOo(tertiaryRoom.getCamera(), p);
tertiaryRoom.setCameraCenter(p);
}
public String toStringReversed() {
StringBuilder sb = new StringBuilder();
sb.append("(5) ");
Nucleotide now = fiveEnd;
while (true) {
sb.append(now.toString());
now = now.getPrev();
if (now != null) {
sb.append("=");
} else {
break;
}
}
sb.append(" (3)");
return sb.toString();
}
/*
* Constructs a new DNAStrand from a given sequence (in the three to five ordering)
*/
public DNAStrand(String sequence) {
if (sequence.length() > 0) {
fiveEnd = threeEnd = new Nucleotide(sequence.charAt(0));
for (int i = 1; i < sequence.length(); i++) {
Nucleotide now = new Nucleotide(sequence.charAt(i));
fiveEnd.append(now);
fiveEnd = now;
}
} else {
throw new IllegalArgumentException();
}
}