X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayer.cpp;h=102db7478223d0027e676304288552a2148966fb;hp=3f45e17ed5aad1e5007b530b5cb7025688b3b164;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=43835751a12097ea9d46a4ce68e2671ba7aff9d4 diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp index 3f45e17..102db74 100644 --- a/chimeraslayer.cpp +++ b/chimeraslayer.cpp @@ -14,7 +14,7 @@ //*************************************************************************************************************** ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div, -int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() { +int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera() { try { fastafile = file; templateFileName = temp; templateSeqs = readSeqs(temp); @@ -34,9 +34,10 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num numWanted = numw; realign = r; trimChimera = trim; + numNoParents = 0; + blastlocation = blas; + threadID = tid; - decalc = new DeCalculator(); - doPrep(); } catch(exception& e) { @@ -45,8 +46,59 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num } } //*************************************************************************************************************** +//template=self, byGroup parameter used for mpienabled version to read the template as MPI_COMM_SELF instead of MPI_COMM_WORLD +ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map& prior, string mode, int k, int ms, int mms, int win, float div, + int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid, bool bg) : Chimera() { + try { + byGroup = bg; + fastafile = file; templateSeqs = readSeqs(fastafile); + templateFileName = temp; + searchMethod = mode; + kmerSize = k; + match = ms; + misMatch = mms; + window = win; + divR = div; + minSim = minsim; + minCov = mincov; + minBS = minbs; + minSNP = minsnp; + parents = par; + iters = it; + increment = inc; + numWanted = numw; + realign = r; + trimChimera = trim; + priority = prior; + numNoParents = 0; + blastlocation = blas; + threadID = tid; + + + createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap + + if (searchMethod == "distance") { + //createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap + + //run filter on template copying templateSeqs into filteredTemplateSeqs + for (int i = 0; i < templateSeqs.size(); i++) { + if (m->control_pressed) { break; } + + Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned()); + runFilter(newSeq); + filteredTemplateSeqs.push_back(newSeq); + } + } + } + catch(exception& e) { + m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer"); + exit(1); + } +} +//*************************************************************************************************************** +//template=self ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map& prior, string mode, int k, int ms, int mms, int win, float div, - int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera() { + int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera() { try { fastafile = file; templateSeqs = readSeqs(fastafile); templateFileName = temp; @@ -67,13 +119,15 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, mapgetRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3); + databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation, threadID); if (m->control_pressed) { return 0; } @@ -235,14 +289,14 @@ int ChimeraSlayer::doPrep() { } } //*************************************************************************************************************** -vector ChimeraSlayer::getTemplate(Sequence* q, vector& userTemplateFiltered) { +vector ChimeraSlayer::getTemplate(Sequence q, vector& userTemplateFiltered) { try { //when template=self, the query file is sorted from most abundance to least abundant //userTemplate grows as the query file is processed by adding sequences that are not chimeric and more abundant vector userTemplate; - int myAbund = priority[q->getName()]; + int myAbund = priority[q.getName()]; for (int i = 0; i < templateSeqs.size(); i++) { @@ -258,6 +312,11 @@ vector ChimeraSlayer::getTemplate(Sequence* q, vector& use } } + //avoids nuisance error from formatdb for making blank blast database + if (userTemplate.size() == 0) { + return userTemplate; + } + string kmerDBNameLeft; string kmerDBNameRight; @@ -326,7 +385,7 @@ vector ChimeraSlayer::getTemplate(Sequence* q, vector& use }else if (searchMethod == "blast") { //generate blastdb - databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3); + databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation, threadID); if (m->control_pressed) { return userTemplate; } @@ -346,7 +405,6 @@ vector ChimeraSlayer::getTemplate(Sequence* q, vector& use //*************************************************************************************************************** ChimeraSlayer::~ChimeraSlayer() { - delete decalc; if (templateFileName != "self") { if (searchMethod == "kmer") { delete databaseRight; delete databaseLeft; } else if (searchMethod == "blast") { delete databaseLeft; } @@ -361,10 +419,10 @@ void ChimeraSlayer::printHeader(ostream& out) { out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n"; } //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { +Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc) { try { - Sequence* trim = NULL; - if (trimChimera) { trim = new Sequence(trimQuery.getName(), trimQuery.getAligned()); } + Sequence trim; + if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); } if (chimeraFlags == "yes") { string chimeraFlag = "no"; @@ -375,23 +433,23 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { if (chimeraFlag == "yes") { if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { - m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine(); - outAcc << querySeq->getName() << endl; + m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine(); + outAcc << querySeq.getName() << endl; - if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); } + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } if (trimChimera) { int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart; int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart; - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); if (lengthLeft > lengthRight) { //trim right for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } }else { //trim left for (int i = 0; i < chimeraResults[0].winLEnd; i++) { newAligned[i] = '.'; } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } } } @@ -399,7 +457,7 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { printBlock(chimeraResults[0], chimeraFlag, out); out << endl; }else { - out << querySeq->getName() << "\tno" << endl; + out << querySeq.getName() << "\tno" << endl; } return trim; @@ -411,13 +469,13 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) { } } //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) { +Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) { try { - Sequence* trim = NULL; + Sequence trim; if (trimChimera) { string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned(); - trim = new Sequence(leftPiece.trimQuery.getName(), aligned); + trim.setName(leftPiece.trimQuery.getName()); trim.setAligned(aligned); } if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) { @@ -445,13 +503,13 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftP if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } } if (rightChimeric || leftChimeric) { - m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine(); - outAcc << querySeq->getName() << endl; + m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine(); + outAcc << querySeq.getName() << endl; - if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); } + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } if (trimChimera) { - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); //right side is fine so keep that if ((leftChimeric) && (!rightChimeric)) { @@ -493,7 +551,7 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftP } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } } @@ -502,7 +560,7 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftP printBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag, out); out << endl; }else { - out << querySeq->getName() << "\tno" << endl; + out << querySeq.getName() << "\tno" << endl; } return trim; @@ -516,18 +574,19 @@ Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftP #ifdef USE_MPI //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) { +Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece, bool& chimFlag) { try { MPI_Status status; bool results = false; string outAccString = ""; string outputString = ""; + chimFlag = false; - Sequence* trim = NULL; + Sequence trim; if (trimChimera) { string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned(); - trim = new Sequence(leftPiece.trimQuery.getName(), aligned); + trim.setName(leftPiece.trimQuery.getName()); trim.setAligned(aligned); } @@ -558,11 +617,11 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } } if (rightChimeric || leftChimeric) { - cout << querySeq->getName() << "\tyes" << endl; - outAccString += querySeq->getName() + "\n"; + cout << querySeq.getName() << "\tyes" << endl; + outAccString += querySeq.getName() + "\n"; results = true; - if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); } + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } //write to accnos file int length = outAccString.length(); @@ -570,10 +629,11 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef memcpy(buf2, outAccString.c_str(), length); MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status); + chimFlag = true; delete buf2; if (trimChimera) { - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); //right side is fine so keep that if ((leftChimeric) && (!rightChimeric)) { @@ -615,7 +675,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } } @@ -633,7 +693,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef delete buf; }else { - outputString += querySeq->getName() + "\tno\n"; + outputString += querySeq.getName() + "\tno\n"; //write to output file int length = outputString.length(); @@ -653,15 +713,15 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef } } //*************************************************************************************************************** -Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { +Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { try { MPI_Status status; bool results = false; string outAccString = ""; string outputString = ""; - Sequence* trim = NULL; - if (trimChimera) { trim = new Sequence(trimQuery.getName(), trimQuery.getAligned()); } + Sequence trim; + if (trimChimera) { trim.setName(trimQuery.getName()); trim.setAligned(trimQuery.getAligned()); } if (chimeraFlags == "yes") { string chimeraFlag = "no"; @@ -672,11 +732,11 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { if (chimeraFlag == "yes") { if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) { - cout << querySeq->getName() << "\tyes" << endl; - outAccString += querySeq->getName() + "\n"; + cout << querySeq.getName() << "\tyes" << endl; + outAccString += querySeq.getName() + "\n"; results = true; - if (templateFileName == "self") { chimericSeqs.insert(querySeq->getName()); } + if (templateFileName == "self") { chimericSeqs.insert(querySeq.getName()); } //write to accnos file int length = outAccString.length(); @@ -690,13 +750,13 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { int lengthLeft = chimeraResults[0].winLEnd - chimeraResults[0].winLStart; int lengthRight = chimeraResults[0].winREnd - chimeraResults[0].winRStart; - string newAligned = trim->getAligned(); + string newAligned = trim.getAligned(); if (lengthLeft > lengthRight) { //trim right for (int i = (chimeraResults[0].winRStart-1); i < newAligned.length(); i++) { newAligned[i] = '.'; } }else { //trim left for (int i = 0; i < (chimeraResults[0].winLEnd-1); i++) { newAligned[i] = '.'; } } - trim->setAligned(newAligned); + trim.setAligned(newAligned); } } } @@ -713,7 +773,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) { delete buf; }else { - outputString += querySeq->getName() + "\tno\n"; + outputString += querySeq.getName() + "\tno\n"; //write to output file int length = outputString.length(); @@ -743,20 +803,19 @@ int ChimeraSlayer::getChimeras(Sequence* query) { chimeraFlags = "no"; printResults.flag = "no"; - querySeq = query; + querySeq = *query; //you must create a template vector thisTemplate; vector thisFilteredTemplate; if (templateFileName != "self") { thisTemplate = templateSeqs; thisFilteredTemplate = filteredTemplateSeqs; } - else { thisTemplate = getTemplate(query, thisFilteredTemplate); } //fills this template and creates the databases + else { thisTemplate = getTemplate(*query, thisFilteredTemplate); } //fills this template and creates the databases if (m->control_pressed) { return 0; } - if (thisTemplate.size() == 0) { return 0; } //not chimeric //moved this out of maligner - 4/29/11 - vector refSeqs = getRefSeqs(query, thisTemplate, thisFilteredTemplate); + vector refSeqs = getRefSeqs(*query, thisTemplate, thisFilteredTemplate); Maligner maligner(refSeqs, match, misMatch, divR, minSim, minCov); Slayer slayer(window, increment, minSim, divR, iters, minSNP, minBS); @@ -768,13 +827,13 @@ int ChimeraSlayer::getChimeras(Sequence* query) { if (m->control_pressed) { return 0; } - string chimeraFlag = maligner.getResults(query, decalc); + string chimeraFlag = maligner.getResults(*query, decalc); if (m->control_pressed) { return 0; } vector Results = maligner.getOutput(); - for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } + //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } if (chimeraFlag == "yes") { @@ -791,7 +850,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) { // cout << query->getAligned() << endl; //get sequence that were given from maligner results - vector seqs; + vector seqs; map removeDups; map::iterator itDup; map parentNameSeq; @@ -820,9 +879,9 @@ int ChimeraSlayer::getChimeras(Sequence* query) { for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) { itSeq = parentNameSeq.find(itDup->first); - Sequence* seq = new Sequence(itDup->first, itSeq->second); + Sequence seq(itDup->first, itSeq->second); - SeqDist member; + SeqCompare member; member.seq = seq; member.dist = itDup->second; seqs.push_back(member); @@ -831,30 +890,30 @@ int ChimeraSlayer::getChimeras(Sequence* query) { //limit number of parents to explore - default 3 if (Results.size() > parents) { //sort by distance - sort(seqs.begin(), seqs.end(), compareSeqDist); + sort(seqs.begin(), seqs.end(), compareSeqCompare); //prioritize larger more similiar sequence fragments reverse(seqs.begin(), seqs.end()); - for (int k = seqs.size()-1; k > (parents-1); k--) { - delete seqs[k].seq; - seqs.pop_back(); - } + //for (int k = seqs.size()-1; k > (parents-1); k--) { + // delete seqs[k].seq; + //seqs.pop_back(); + //} } //put seqs into vector to send to slayer // cout << query->getAligned() << endl; - vector seqsForSlayer; + vector seqsForSlayer; for (int k = 0; k < seqs.size(); k++) { // cout << seqs[k].seq->getAligned() << endl; seqsForSlayer.push_back(seqs[k].seq); // cout << seqs[k].seq->getName() << endl; } - if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; } + if (m->control_pressed) { return 0; } //send to slayer - chimeraFlags = slayer.getResults(query, seqsForSlayer); + chimeraFlags = slayer.getResults(*query, seqsForSlayer); if (m->control_pressed) { return 0; } chimeraResults = slayer.getOutput(); @@ -862,7 +921,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) { printResults.results = chimeraResults; //free memory - for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } + //for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } } //cout << endl << endl; return 0; @@ -875,7 +934,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) { //*************************************************************************************************************** void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){ try { - out << querySeq->getName() << '\t'; + out << querySeq.getName() << '\t'; out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t'; out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t'; @@ -894,7 +953,7 @@ void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bo try { if ((leftChimeric) && (!rightChimeric)) { //print left - out << querySeq->getName() << '\t'; + out << querySeq.getName() << '\t'; out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t'; out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t'; @@ -903,7 +962,7 @@ void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bo out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t'; }else if ((!leftChimeric) && (rightChimeric)) { //print right - out << querySeq->getName() << '\t'; + out << querySeq.getName() << '\t'; out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t'; out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t'; @@ -913,7 +972,7 @@ void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bo }else { //print both results if (leftdata.flag == "yes") { - out << querySeq->getName() + "_LEFT" << '\t'; + out << querySeq.getName() + "_LEFT" << '\t'; out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t'; out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t'; @@ -925,7 +984,7 @@ void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bo if (rightdata.flag == "yes") { if (leftdata.flag == "yes") { out << endl; } - out << querySeq->getName() + "_RIGHT"<< '\t'; + out << querySeq.getName() + "_RIGHT"<< '\t'; out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t'; out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t'; @@ -948,7 +1007,7 @@ string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bo string out = ""; if ((leftChimeric) && (!rightChimeric)) { //get left - out += querySeq->getName() + "\t"; + out += querySeq.getName() + "\t"; out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t"; out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t"; @@ -957,7 +1016,7 @@ string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bo out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t"; }else if ((!leftChimeric) && (rightChimeric)) { //print right - out += querySeq->getName() + "\t"; + out += querySeq.getName() + "\t"; out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t"; out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t"; @@ -968,7 +1027,7 @@ string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bo }else { //print both results if (leftdata.flag == "yes") { - out += querySeq->getName() + "_LEFT\t"; + out += querySeq.getName() + "_LEFT\t"; out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t"; out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t"; @@ -979,7 +1038,7 @@ string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bo if (rightdata.flag == "yes") { if (leftdata.flag == "yes") { out += "\n"; } - out += querySeq->getName() + "_RIGHT\t"; + out += querySeq.getName() + "_RIGHT\t"; out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t"; out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t"; @@ -1003,7 +1062,7 @@ string ChimeraSlayer::getBlock(data_struct data, string flag){ string outputString = ""; - outputString += querySeq->getName() + "\t"; + outputString += querySeq.getName() + "\t"; outputString += data.parentA.getName() + "\t" + data.parentB.getName() + "\t"; outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t"; @@ -1019,16 +1078,16 @@ string ChimeraSlayer::getBlock(data_struct data, string flag){ } } //*************************************************************************************************************** -vector ChimeraSlayer::getRefSeqs(Sequence* q, vector& thisTemplate, vector& thisFilteredTemplate){ +vector ChimeraSlayer::getRefSeqs(Sequence q, vector& thisTemplate, vector& thisFilteredTemplate){ try { - vector refSeqs; + vector refSeqs; if (searchMethod == "distance") { //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate - Sequence* newSeq = new Sequence(q->getName(), q->getAligned()); + Sequence* newSeq = new Sequence(q.getName(), q.getAligned()); runFilter(newSeq); - refSeqs = decalc->findClosest(newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim); + refSeqs = decalc.findClosest(*newSeq, thisTemplate, thisFilteredTemplate, numWanted, minSim); delete newSeq; }else if (searchMethod == "blast") { refSeqs = getBlastSeqs(q, thisTemplate, numWanted); //fills indexes @@ -1044,18 +1103,18 @@ vector ChimeraSlayer::getRefSeqs(Sequence* q, vector& this } } //***************************************************************************************************************/ -vector ChimeraSlayer::getBlastSeqs(Sequence* q, vector& db, int num) { +vector ChimeraSlayer::getBlastSeqs(Sequence q, vector& db, int num) { try { - vector refResults; + vector refResults; //get parts of query - string queryUnAligned = q->getUnaligned(); + string queryUnAligned = q.getUnaligned(); string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence //cout << "whole length = " << queryUnAligned.length() << '\t' << "left length = " << leftQuery.length() << '\t' << "right length = "<< rightQuery.length() << endl; - Sequence* queryLeft = new Sequence(q->getName(), leftQuery); - Sequence* queryRight = new Sequence(q->getName(), rightQuery); + Sequence* queryLeft = new Sequence(q.getName(), leftQuery); + Sequence* queryRight = new Sequence(q.getName(), rightQuery); vector tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim); vector tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim); @@ -1120,12 +1179,13 @@ vector ChimeraSlayer::getBlastSeqs(Sequence* q, vector& db //string qname = q->getName().substr(0, q->getName().find_last_of('_')); //cout << qname << endl; + if (mergedResults.size() == 0) { numNoParents++; } + for (int i = 0; i < mergedResults.size(); i++) { //cout << q->getName() << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl; - if (db[mergedResults[i]]->getName() != q->getName()) { - Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); + if (db[mergedResults[i]]->getName() != q.getName()) { + Sequence temp(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); refResults.push_back(temp); - } } //cout << endl << endl; @@ -1133,8 +1193,6 @@ vector ChimeraSlayer::getBlastSeqs(Sequence* q, vector& db delete queryRight; delete queryLeft; - if (refResults.size() == 0) { m->mothurOut("[WARNING]: mothur found 0 potential parents, so we are not able to check " + q->getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); } - return refResults; } catch(exception& e) { @@ -1143,17 +1201,17 @@ vector ChimeraSlayer::getBlastSeqs(Sequence* q, vector& db } } //*************************************************************************************************************** -vector ChimeraSlayer::getKmerSeqs(Sequence* q, vector& db, int num) { +vector ChimeraSlayer::getKmerSeqs(Sequence q, vector& db, int num) { try { - vector refResults; + vector refResults; //get parts of query - string queryUnAligned = q->getUnaligned(); + string queryUnAligned = q.getUnaligned(); string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence - Sequence* queryLeft = new Sequence(q->getName(), leftQuery); - Sequence* queryRight = new Sequence(q->getName(), rightQuery); + Sequence* queryLeft = new Sequence(q.getName(), leftQuery); + Sequence* queryRight = new Sequence(q.getName(), rightQuery); vector tempIndexesLeft = databaseLeft->findClosestSequences(queryLeft, num); vector tempIndexesRight = databaseRight->findClosestSequences(queryRight, num); @@ -1210,8 +1268,8 @@ vector ChimeraSlayer::getKmerSeqs(Sequence* q, vector& db, for (int i = 0; i < mergedResults.size(); i++) { //cout << mergedResults[i] << '\t' << db[mergedResults[i]]->getName() << endl; - if (db[mergedResults[i]]->getName() != q->getName()) { - Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); + if (db[mergedResults[i]]->getName() != q.getName()) { + Sequence temp(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned()); refResults.push_back(temp); }