@Override
public NucSeq generateCompositeSequence(
ArrayList<Part> composition, Object additionalRequirements) {
StringBuffer sb = new StringBuffer();
for (Part p : composition) {
sb.append(p.getSeq().getSeq());
}
NucSeq outnuc = new NucSeq(sb.toString());
outnuc.setTransient();
int offset = 0;
for (Part p : composition) {
String parseq = p.getSeq().getSeq();
for (Annotation ann : p.getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = offset + ann.getStart();
int End = offset + ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
offset += parseq.length();
}
return outnuc;
}
@Override
public NucSeq generatePlasmidSequence(Plasmid p) {
String out = "";
out += p.getPart().getSeq().getSeq();
out += p.getVector().getSeq().getSeq();
NucSeq outnuc = new NucSeq(out);
outnuc.setTransient();
for (Annotation ann : p.getPart().getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = ann.getStart();
int End = ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
String parseq = p.getPart().getSeq().getSeq();
int offset = parseq.length();
for (Annotation ann : p.getVector().getSeq().getAnnotations()) {
Feature afeature = ann.getFeature();
String name = ann.getName();
Color forColor = ann.getForwardColor();
Color revColor = ann.getReverseColor();
int Start = offset + ann.getStart();
int End = offset + ann.getEnd();
Person user = ann.getAuthor();
boolean plusstrandtrue = ann.isForwardStrand();
String symbol = ann.getSymbol();
Annotation newann;
if (afeature == null) {
newann =
new Annotation(
name, outnuc, forColor, forColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
} else {
newann =
new Annotation(
afeature, outnuc, forColor, revColor, Start, End, user, plusstrandtrue, symbol);
newann.setTransient();
}
System.out.println("Generated annotation: " + newann.getName());
}
return outnuc;
}