}
//***************************************************************************************************************
-Pintail::Pintail(string filename, string temp) { fastafile = filename; templateFile = temp; }
+Pintail::Pintail(string filename, string temp, string o) { fastafile = filename; templateFile = temp; outputDir = o; }
//***************************************************************************************************************
Pintail::~Pintail() {
}
//***************************************************************************************************************
-void Pintail::getChimeras() {
+int Pintail::getChimeras() {
try {
//read in query sequences and subject sequences
int numSeqs = querySeqs.size();
+ if (unaligned) { mothurOut("Your sequences need to be aligned when you use the pintail method."); mothurOutEndLine(); return 1; }
+
obsDistance.resize(numSeqs);
expectedDistance.resize(numSeqs);
seqCoef.resize(numSeqs);
mothurOut("Done."); mothurOutEndLine();
}else { createProcessesPairs(); }
-/*string o = "foronlinepintailpairs-eachgap";
-ofstream out7;
-openOutputFile(o, out7);
+//string o = "closestmatch.eachgap.fasta";
+//ofstream out7;
+//openOutputFile(o, out7);
-for (int i = 0; i < bestfit.size(); i++) {
- out7 << querySeqs[i]->getName() << endl;
- out7 << querySeqs[i]->getUnaligned() << endl << endl;
-
- out7 << bestfit[i]->getName() << endl;
- out7 << bestfit[i]->getUnaligned() << endl << endl << endl;
-}
-out7.close();/*/
+//for (int i = 0; i < bestfit.size(); i++) {
+ //out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+ //out7 << bestfit[i]->getAligned() << endl;
+//}
+//out7.close();
//find P
mothurOut("Getting conservation... "); cout.flush();
if (consfile == "") {
mothurOut("Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. "); cout.flush();
- probabilityProfile = decalc->calcFreq(templateSeqs, templateFile);
+ probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFile));
mothurOut("Done."); mothurOutEndLine();
}else { probabilityProfile = readFreq(); }
string noOutliers, outliers;
if ((!filter) && (seqMask == "")) {
- noOutliers = getRootName(templateFile) + "pintail.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.quan";
}else if ((filter) && (seqMask == "")) {
- noOutliers = getRootName(templateFile) + "pintail.filtered.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.quan";
}else if ((!filter) && (seqMask != "")) {
- noOutliers = getRootName(templateFile) + "pintail.masked.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.masked.quan";
}else if ((filter) && (seqMask != "")) {
- noOutliers = getRootName(templateFile) + "pintail.filtered.masked.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.masked.quan";
}
//outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";
delete distcalculator;
delete decalc;
+
+ return 0;
}
catch(exception& e) {
errorOut(e, "Pintail", "getChimeras");
vector<Sequence*> seqsMatches;
for(int i = start; i < end; i++){
-
- float smallest = 10000.0;
- Sequence query = *(querySeqs[i]);
- Sequence* match;
-
- for(int j = 0; j < templateSeqs.size(); j++){
-
- Sequence temp = *(templateSeqs[j]);
-
- distcalculator->calcDist(query, temp);
- float dist = distcalculator->getDist();
-
- if (dist < smallest) {
- match = templateSeqs[j];
- smallest = dist;
- }
- }
-
- //make copy so trimSeqs doesn't overtrim
- Sequence* copy = new Sequence(match->getName(), match->getAligned());
- seqsMatches.push_back(copy);
+ vector<Sequence*> copy = decalc->findClosest(querySeqs[i], templateSeqs, 1);
+ seqsMatches.push_back(copy[0]);
}
return seqsMatches;