/** Generation of new BioBricks primers for parts * */
public static String[] generateVectorPrimers(
RVector vector,
Collector coll,
Double meltingTemp,
Integer targetLength,
Integer maxPrimerLength,
Integer minPCRLength) {
// initialize primer parameters
String[] oligos = new String[2];
String vectorPrimerPrefix = "gaattcgcggccgcttctagag";
String vectorPrimerSuffix = "tactagtagcggccgctgcag";
Vector currentVector = coll.getVector(vector.getUUID(), true);
String seq = currentVector.getSeq();
String fwdHomology;
String revHomology;
if (seq.equals("")) {
fwdHomology = "[ VECTOR " + currentVector.getName() + " HOMOLOGY REGION ]";
revHomology = "[ VECTOR " + currentVector.getName() + " HOMOLOGY REGION ]";
} else {
fwdHomology =
seq.substring(
0,
Math.min(
seq.length(),
PrimerDesign.getPrimerHomologyLength(
meltingTemp, targetLength, maxPrimerLength - 23, minPCRLength, seq, true)));
revHomology =
PrimerDesign.reverseComplement(
currentVector
.getSeq()
.substring(
Math.max(
0,
seq.length()
- PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 22,
minPCRLength,
PrimerDesign.reverseComplement(seq),
true))));
}
String forwardOligoSequence = vectorPrimerPrefix + fwdHomology;
String reverseOligoSequence = PrimerDesign.reverseComplement(vectorPrimerSuffix) + revHomology;
oligos[0] = forwardOligoSequence;
oligos[1] = reverseOligoSequence;
return oligos;
}
/** Generation of new BioBricks primers for parts * */
public static String[] generatePartPrimers(
RNode node,
Collector coll,
Double meltingTemp,
Integer targetLength,
Integer minPCRLength,
Integer maxPrimerLength) {
// initialize primer parameters
String[] oligos = new String[2];
String partPrimerPrefix = "gaattcgcggccgcttctagag";
String partPrimerSuffix = "tactagtagcggccgctgcag";
String partPrimerPrefixAlt = "gaattcgcggccgcttctag";
String forwardOligoSequence;
String reverseOligoSequence;
Part currentPart = coll.getPart(node.getUUID(), true);
String seq = currentPart.getSeq();
ArrayList<String> type = node.getType();
String fwdHomology;
String revHomology;
// If the part is sufficiently large
if (seq.length() > minPCRLength) {
// Special case primers for coding sequences
if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {
fwdHomology =
seq.substring(
0,
Math.min(
seq.length(),
PrimerDesign.getPrimerHomologyLength(
meltingTemp, targetLength, maxPrimerLength - 20, minPCRLength, seq, true)));
revHomology =
seq.substring(
Math.max(
0,
currentPart.getSeq().length()
- PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 21,
minPCRLength,
PrimerDesign.reverseComplement(seq),
true)));
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);
} else {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
} else {
fwdHomology =
seq.substring(
0,
Math.min(
seq.length(),
PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 22,
minPCRLength,
seq,
true)));
revHomology =
seq.substring(
Math.max(
0,
currentPart.getSeq().length()
- PrimerDesign.getPrimerHomologyLength(
meltingTemp,
targetLength,
maxPrimerLength - 21,
minPCRLength,
PrimerDesign.reverseComplement(seq),
true)));
}
forwardOligoSequence = partPrimerPrefix + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(revHomology + partPrimerSuffix);
}
// Otherwise make annealing primers or synthesize
} else {
if (type.get(0).equals("gene") || type.get(0).equals("reporter")) {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
} else {
fwdHomology = seq;
forwardOligoSequence = partPrimerPrefixAlt + fwdHomology + partPrimerSuffix;
reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
}
} else {
if (seq.equals("")) {
fwdHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
revHomology = "[ PART " + currentPart.getName() + " HOMOLOGY REGION ]";
forwardOligoSequence = partPrimerPrefix + fwdHomology;
reverseOligoSequence = PrimerDesign.reverseComplement(partPrimerSuffix) + revHomology;
} else {
fwdHomology = seq;
forwardOligoSequence = partPrimerPrefix + fwdHomology + partPrimerSuffix;
reverseOligoSequence = PrimerDesign.reverseComplement(forwardOligoSequence);
}
}
}
oligos[0] = forwardOligoSequence;
oligos[1] = reverseOligoSequence;
return oligos;
}