//Print the probes - description;ID;type;upStream;downStream;target;group number;quality;messageCountArms;messageCountProbe;;5'seq;Tm;3'seq;Tm;tag 1 lib;tag 1 pos;...;...;tag n lib;tag n pos;
p.println(TITLE_DESCRIPTOR + PROBES);
DefiniteSequenceDB<Probe> probes = proj.getProbes();
for (Iterator<Probe> i = probes.iterator(); i.hasNext(); ) {
Probe pr = i.next();
PropertyAcceptorNucleotideSequence fivePrime;
PropertyAcceptorNucleotideSequence threePrime;
try {
fivePrime = (PropertyAcceptorNucleotideSequence) pr.getTSSPair().getSequence(TSSPair.KEY_FIVE_PRIME);
}
catch (ClusterException e) {
fivePrime = null;
}
try {
threePrime = (PropertyAcceptorNucleotideSequence) pr.getTSSPair().getSequence(TSSPair.KEY_THREE_PRIME);
}
catch (ClusterException e) {
threePrime = null;
}
int targetNo = -1;
try {
targetNo = pr.getTarget() == null ? -1 : proj.getTargets().indexOfSequence(proj.getTargets().getSequenceByID(pr.getTarget().getID()));
}
catch (IDNotFoundException ix) {
//let targetNo be -1
}
Group<?> pg = DesignUtils.getGroupWithType(pr,ProbeGroup.GROUP_TYPE);
String outStr = tio.getOutString(new String[] {
pr.getName().replace(VALUE_SEPARATOR, VALUE_SEPARATOR_REPLACEMENT),
pr.getID() != null ? pr.getID().replace(VALUE_SEPARATOR, VALUE_SEPARATOR_REPLACEMENT) : "No ID", //$NON-NLS-1$
String.valueOf(pr.getType()),
String.valueOf(pr.getUpstreamBlockCount()),
String.valueOf(pr.getDownstreamBlockCount()),
String.valueOf(targetNo),
String.valueOf(pg == null ? -1 : p_groups.indexOf(pg)),
String.valueOf(ProbeMakerPropertyUtils.getRank(pr)),
String.valueOf(fivePrime == null ? 0 : ProbeMakerPropertyUtils.getAllMessages(fivePrime).size()),
String.valueOf(threePrime == null ? 0 : ProbeMakerPropertyUtils.getAllMessages(threePrime).size()),
String.valueOf(ProbeMakerPropertyUtils.getOwnMessages(pr.getTSSPair()).size()),
String.valueOf(ProbeMakerPropertyUtils.getOwnMessages(pr).size()),
fivePrime == null ? "" : fivePrime.seqString(), //$NON-NLS-1$
String.valueOf(fivePrime == null ? 0 : ProbeMakerPropertyUtils.getHybridizationTemp(fivePrime)),
threePrime == null ? "" : threePrime.seqString(), //$NON-NLS-1$
String.valueOf(threePrime == null ? 0 : ProbeMakerPropertyUtils.getHybridizationTemp(threePrime))
});
for (int t = 0; t < pr.getTags().size(); t++) {
outStr += VALUE_SEPARATOR;
NucleotideSequence tag = pr.getTagAt(t);