X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.cpp;h=00cd3f1948e009a86456e32bbcde2a40c6f889ac;hp=7e6154b6c5af1d69259223025d9da9f7f3f5d4df;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=4f8291bc0a482c68dc739ef5aa7a311fc74f5f43 diff --git a/ccode.cpp b/ccode.cpp index 7e6154b..00cd3f1 100644 --- a/ccode.cpp +++ b/ccode.cpp @@ -11,328 +11,414 @@ #include "ignoregaps.h" #include "eachgapdist.h" - -//*************************************************************************************************************** -Ccode::Ccode(string filename, string temp) { fastafile = filename; templateFile = temp; } //*************************************************************************************************************** +Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int numW, string o) : Chimera() { + try { + + fastafile = filename; + outputDir = o; + templateFileName = temp; templateSeqs = readSeqs(temp); + setMask(mask); + filter = f; + window = win; + numWanted = numW; + + distCalc = new eachGapDist(); + decalc = new DeCalculator(); + + mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo"; + + #ifdef USE_MPI + + //char* inFileName = new char[mapInfo.length()]; + //memcpy(inFileName, mapInfo.c_str(), mapInfo.length()); + + char inFileName[1024]; + strcpy(inFileName, mapInfo.c_str()); + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; -Ccode::~Ccode() { - try { - for (int i = 0; i < querySeqs.size(); i++) { delete querySeqs[i]; } - for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } - delete distCalc; + MPI_File_open(MPI_COMM_WORLD, inFileName, outMode, MPI_INFO_NULL, &outMap); //comm, filename, mode, info, filepointer + + //delete inFileName; + + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + string outString = "Place in masked, filtered and trimmed sequence\tPlace in original alignment\n"; + + MPI_Status status; + int length = outString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outString.c_str(), length); + + MPI_File_write_shared(outMap, buf2, length, MPI_CHAR, &status); + delete buf2; + } + #else + + ofstream out2; + m->openOutputFile(mapInfo, out2); + + out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl; + out2.close(); + #endif } catch(exception& e) { - errorOut(e, "Ccode", "~Ccode"); + m->errorOut(e, "Ccode", "Ccode"); exit(1); } +} +//*************************************************************************************************************** +Ccode::~Ccode() { + delete distCalc; + delete decalc; + + #ifdef USE_MPI + MPI_File_close(&outMap); + #endif } //*************************************************************************************************************** -void Ccode::print(ostream& out) { +Sequence Ccode::print(ostream& out, ostream& outAcc) { try { - mothurOutEndLine(); - - string mapInfo = getRootName(fastafile) + "mapinfo"; ofstream out2; - openOutputFile(mapInfo, out2); - - out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl; + m->openOutputFileAppend(mapInfo, out2); - for (int j = 0; j < querySeqs.size(); j++) { - out2 << querySeqs[j]->getName() << endl; - for (it = spotMap[j].begin(); it!= spotMap[j].end(); it++) { - out2 << it->first << '\t' << it->second << endl; - } + out2 << querySeq->getName() << endl; + for (it = spotMap.begin(); it!= spotMap.end(); it++) { + out2 << it->first << '\t' << it->second << endl; } out2.close(); + out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl; + + for (int j = 0; j < closest.size(); j++) { + out << closest[j].seq->getName() << '\t' << closest[j].dist << endl; + } + out << endl << endl; - out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); + //for each window + //window mapping info. + out << "Mapping information: "; + //you mask and did not filter + if ((seqMask != "") && (!filter)) { out << "mask and trim."; } + + //you filtered and did not mask + if ((seqMask == "") && (filter)) { out << "filter and trim."; } + + //you masked and filtered + if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; } + + out << endl << "Window\tStartPos\tEndPos" << endl; + it = trim.begin(); + for (int k = 0; k < windows.size()-1; k++) { + out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl; + } + + out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[it->second-it->first-1] << endl; + out << endl; + out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl; + for (int k = 0; k < windows.size(); k++) { + float ds = averageQuery[k] / averageRef[k]; + out << k+1 << '\t' << averageQuery[k] << '\t' << sdQuery[k] << '\t' << averageRef[k] << '\t'<< sdRef[k] << '\t' << ds << '\t' << anova[k] << endl; + } + out << endl; + + //varRef + //varQuery + /* F test for differences among variances. + * varQuery is expected to be higher or similar than varRef */ + //float fs = varQuery[query] / varRef[query]; /* F-Snedecor, test for differences of variances */ + + bool results = false; + + //confidence limit, t - Student, anova + out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl; + + for (int k = 0; k < windows.size(); k++) { + string temp = ""; + if (isChimericConfidence[k]) { temp += "*\t"; } + else { temp += "\t"; } + + if (isChimericTStudent[k]) { temp += "*\t"; } + else { temp += "\t"; } + + if (isChimericANOVA[k]) { temp += "*\t"; } + else { temp += "\t"; } + + out << k+1 << '\t' << temp << endl; + + if (temp == "*\t*\t*\t") { results = true; } + } + out << endl; + + if (results) { + m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine(); + outAcc << querySeq->getName() << endl; + } + + //free memory + for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; } + + return *querySeq; + } + catch(exception& e) { + m->errorOut(e, "Ccode", "print"); + exit(1); + } +} +#ifdef USE_MPI +//*************************************************************************************************************** +Sequence Ccode::print(MPI_File& out, MPI_File& outAcc) { + try { + + string outMapString = ""; - out << "For full window mapping info refer to " << mapInfo << endl << endl; + outMapString += querySeq->getName() + "\n"; + for (it = spotMap.begin(); it!= spotMap.end(); it++) { + outMapString += toString(it->first) + "\t" + toString(it->second) + "\n"; + } + printMapping(outMapString); + outMapString = ""; - for (int i = 0; i < querySeqs.size(); i++) { + string outString = ""; + string outAccString = ""; - out << querySeqs[i]->getName() << endl << endl << "Reference sequences used and distance to query:" << endl; + outString += querySeq->getName() + "\n\nReference sequences used and distance to query:\n"; - for (int j = 0; j < closest[i].size(); j++) { - out << setprecision(3) << closest[i][j].seq->getName() << '\t' << closest[i][j].dist << endl; - } - out << endl << endl; + for (int j = 0; j < closest.size(); j++) { + outString += closest[j].seq->getName() + "\t" + toString(closest[j].dist) + "\n"; + } + outString += "\n\nMapping information: "; - //for each window - //window mapping info. - out << "Mapping information: "; - //you mask and did not filter - if ((seqMask != "") && (!filter)) { out << "mask and trim."; } + //for each window + //window mapping info. + //you mask and did not filter + if ((seqMask != "") && (!filter)) { outString += "mask and trim."; } - //you filtered and did not mask - if ((seqMask == "") && (filter)) { out << "filter and trim."; } + //you filtered and did not mask + if ((seqMask == "") && (filter)) { outString += "filter and trim."; } - //you masked and filtered - if ((seqMask != "") && (filter)) { out << "mask, filter and trim."; } + //you masked and filtered + if ((seqMask != "") && (filter)) { outString += "mask, filter and trim."; } - out << endl << "Window\tStartPos\tEndPos" << endl; - it = trim[i].begin(); - - for (int k = 0; k < windows[i].size()-1; k++) { - out << k+1 << '\t' << spotMap[i][windows[i][k]-it->first] << '\t' << spotMap[i][windows[i][k]-it->first+windowSizes[i]] << endl; - } - - out << windows[i].size() << '\t' << spotMap[i][windows[i][windows[i].size()-1]-it->first] << '\t' << spotMap[i][it->second-it->first-1] << endl; - out << endl; + outString += "\nWindow\tStartPos\tEndPos\n"; + it = trim.begin(); + for (int k = 0; k < windows.size()-1; k++) { + outString += toString(k+1) + "\t" + toString(spotMap[windows[k]-it->first]) + "\t" + toString(spotMap[windows[k]-it->first+windowSizes]) + "\n"; + } - out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl; - for (int k = 0; k < windows[i].size(); k++) { - float ds = averageQuery[i][k] / averageRef[i][k]; - out << k+1 << '\t' << averageQuery[i][k] << '\t' << sdQuery[i][k] << '\t' << averageRef[i][k] << '\t'<< sdRef[i][k] << '\t' << ds << '\t' << anova[i][k] << endl; - } - out << endl; + outString += toString(windows.size()) + "\t" + toString(spotMap[windows[windows.size()-1]-it->first]) + "\t" + toString(spotMap[it->second-it->first-1]) + "\n\n"; + + outString += "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova\n"; + for (int k = 0; k < windows.size(); k++) { + float ds = averageQuery[k] / averageRef[k]; + outString += toString(k+1) + "\t" + toString(averageQuery[k]) + "\t" + toString(sdQuery[k]) + "\t" + toString(averageRef[k]) + "\t" + toString(sdRef[k]) + "\t" + toString(ds) + "\t" + toString(anova[k]) + "\n"; + } - //varRef - //varQuery - /* F test for differences among variances. - * varQuery is expected to be higher or similar than varRef */ - //float fs = varQuery[query][i] / varRef[query][i]; /* F-Snedecor, test for differences of variances */ + //varRef + //varQuery + /* F test for differences among variances. + * varQuery is expected to be higher or similar than varRef */ + //float fs = varQuery[query] / varRef[query]; /* F-Snedecor, test for differences of variances */ - bool results = false; - - //confidence limit, t - Student, anova - out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl; + bool results = false; + + //confidence limit, t - Student, anova + outString += "\nWindow\tConfidenceLimit\tt-Student\tAnova\n"; - for (int k = 0; k < windows[i].size(); k++) { - string temp = ""; - if (isChimericConfidence[i][k]) { temp += "*\t"; } - else { temp += "\t"; } + for (int k = 0; k < windows.size(); k++) { + string temp = ""; + if (isChimericConfidence[k]) { temp += "*\t"; } + else { temp += "\t"; } - if (isChimericTStudent[i][k]) { temp += "*\t"; } - else { temp += "\t"; } + if (isChimericTStudent[k]) { temp += "*\t"; } + else { temp += "\t"; } - if (isChimericANOVA[i][k]) { temp += "*\t"; } - else { temp += "\t"; } + if (isChimericANOVA[k]) { temp += "*\t"; } + else { temp += "\t"; } - out << k+1 << '\t' << temp << endl; + outString += toString(k+1) + "\t" + temp + "\n"; - if (temp == "*\t*\t*\t") { results = true; } - } - out << endl; + if (temp == "*\t*\t*\t") { results = true; } + } + outString += "\n"; + + MPI_Status status; + int length = outString.length(); + char* buf2 = new char[length]; + memcpy(buf2, outString.c_str(), length); + + MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status); + delete buf2; + + if (results) { + m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine(); + outAccString += querySeq->getName() + "\n"; - if (results) { - mothurOut(querySeqs[i]->getName() + " was found have at least one chimeric window."); mothurOutEndLine(); - } + MPI_Status statusAcc; + length = outAccString.length(); + char* buf = new char[length]; + memcpy(buf, outAccString.c_str(), length); + + MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc); + delete buf; } + + //free memory + for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; } + + return *querySeq; } catch(exception& e) { - errorOut(e, "Ccode", "print"); + m->errorOut(e, "Ccode", "print"); exit(1); } } - //*************************************************************************************************************** -void Ccode::getChimeras() { +int Ccode::printMapping(string& output) { try { - - //read in query sequences and subject sequences - mothurOut("Reading sequences and template file... "); cout.flush(); - querySeqs = readSeqs(fastafile); - templateSeqs = readSeqs(templateFile); - mothurOut("Done."); mothurOutEndLine(); - - int numSeqs = querySeqs.size(); - - closest.resize(numSeqs); - - refCombo.resize(numSeqs, 0); - sumRef.resize(numSeqs); - varRef.resize(numSeqs); - varQuery.resize(numSeqs); - sdRef.resize(numSeqs); - sdQuery.resize(numSeqs); - sumQuery.resize(numSeqs); - sumSquaredRef.resize(numSeqs); - sumSquaredQuery.resize(numSeqs); - averageRef.resize(numSeqs); - averageQuery.resize(numSeqs); - anova.resize(numSeqs); - isChimericConfidence.resize(numSeqs); - isChimericTStudent.resize(numSeqs); - isChimericANOVA.resize(numSeqs); - trim.resize(numSeqs); - spotMap.resize(numSeqs); - windowSizes.resize(numSeqs, window); - windows.resize(numSeqs); - - //break up file if needed - int linesPerProcess = numSeqs / processors ; - - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - //find breakup of sequences for all times we will Parallelize - if (processors == 1) { lines.push_back(new linePair(0, numSeqs)); } - else { - //fill line pairs - for (int i = 0; i < (processors-1); i++) { - lines.push_back(new linePair((i*linesPerProcess), ((i*linesPerProcess) + linesPerProcess))); - } - //this is necessary to get remainder of processors / numSeqs so you don't miss any lines at the end - int i = processors - 1; - lines.push_back(new linePair((i*linesPerProcess), numSeqs)); - } + MPI_Status status; + int length = output.length(); + char* buf = new char[length]; + memcpy(buf, output.c_str(), length); + + MPI_File_write_shared(outMap, buf, length, MPI_CHAR, &status); + delete buf; - //find breakup of templatefile for quantiles - if (processors == 1) { templateLines.push_back(new linePair(0, templateSeqs.size())); } - else { - for (int i = 0; i < processors; i++) { - templateLines.push_back(new linePair()); - templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size()); - templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size()); - } - } - #else - lines.push_back(new linePair(0, numSeqs)); - templateLines.push_back(new linePair(0, templateSeqs.size())); - #endif + return 0; + + } + catch(exception& e) { + m->errorOut(e, "Ccode", "printMapping"); + exit(1); + } +} +#endif +//*************************************************************************************************************** +int Ccode::getChimeras(Sequence* query) { + try { - distCalc = new eachGapDist(); - decalc = new DeCalculator(); - - //find closest - if (processors == 1) { - mothurOut("Finding top matches for sequences... "); cout.flush(); - closest = findClosest(lines[0]->start, lines[0]->end, numWanted); - mothurOut("Done."); mothurOutEndLine(); - }else { createProcessesClosest(); } + closest.clear(); + refCombo = 0; + sumRef.clear(); + varRef.clear(); + varQuery.clear(); + sdRef.clear(); + sdQuery.clear(); + sumQuery.clear(); + sumSquaredRef.clear(); + sumSquaredQuery.clear(); + averageRef.clear(); + averageQuery.clear(); + anova.clear(); + isChimericConfidence.clear(); + isChimericTStudent.clear(); + isChimericANOVA.clear(); + trim.clear(); + spotMap.clear(); + windowSizes = window; + windows.clear(); - -for (int i = 0; i < closest.size(); i++) { - //cout << querySeqs[i]->getName() << ": "; - string file = querySeqs[i]->getName() + ".input"; - ofstream o; - openOutputFile(file, o); - querySeqs[i]->printSequence(o); - for (int j = 0; j < closest[i].size(); j++) { - //cout << closest[i][j].seq->getName() << '\t'; - closest[i][j].seq->printSequence(o); - } - //cout << endl; - o.close(); -} - for (int j = 0; j < numSeqs; j++) { - for (int i = 0; i < querySeqs[0]->getAligned().length(); i++) { - spotMap[j][i] = i; - } - } + querySeq = query; + + //find closest matches to query + closest = findClosest(query, numWanted); + if (m->control_pressed) { return 0; } + + //initialize spotMap + for (int i = 0; i < query->getAligned().length(); i++) { spotMap[i] = i; } + //mask sequences if the user wants to if (seqMask != "") { decalc->setMask(seqMask); - //mask querys - for (int i = 0; i < querySeqs.size(); i++) { - decalc->runMask(querySeqs[i]); - } - - //mask templates - for (int i = 0; i < templateSeqs.size(); i++) { - decalc->runMask(templateSeqs[i]); - } + decalc->runMask(query); - for (int i = 0; i < numSeqs; i++) { - spotMap[i] = decalc->getMaskMap(); - } + //mask closest + for (int i = 0; i < closest.size(); i++) { decalc->runMask(closest[i].seq); } + + spotMap = decalc->getMaskMap(); } if (filter) { - vector temp = templateSeqs; - for (int i = 0; i < querySeqs.size(); i++) { temp.push_back(querySeqs[i]); } + vector temp; + for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq); } + temp.push_back(query); - createFilter(temp); + createFilter(temp, 0.5); - runFilter(querySeqs); - runFilter(templateSeqs); + for (int i = 0; i < temp.size(); i++) { + if (m->control_pressed) { return 0; } + runFilter(temp[i]); + } //update spotMap map newMap; int spot = 0; - int j = 0; for (int i = 0; i < filterString.length(); i++) { if (filterString[i] == '1') { //add to newMap - newMap[spot] = spotMap[j][i]; + newMap[spot] = spotMap[i]; spot++; } } - - for (int i = 0; i < numSeqs; i++) { - spotMap[i] = newMap; - } + spotMap = newMap; } //trim sequences - this follows ccodes remove_extra_gaps - for (int i = 0; i < querySeqs.size(); i++) { - trimSequences(i); - } + trimSequences(query); + if (m->control_pressed) { return 0; } //windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length(). //Our default will be 10% and we will warn if user tries to use a window above or below these recommendations - for (int i = 0; i < querySeqs.size(); i++) { - windows[i] = findWindows(i); - } - - //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later - should be paralellized - for (int i = 0; i < closest.size(); i++) { - removeBadReferenceSeqs(closest[i], i); - } - - - //find the averages for each querys references - should be paralellized - for (int i = 0; i < numSeqs; i++) { - getAverageRef(closest[i], i); //fills sumRef[i], averageRef[i], sumSquaredRef[i] and refCombo[i]. - } - - //find the averages for the query - should be paralellized - for (int i = 0; i < numSeqs; i++) { - getAverageQuery(closest[i], i); //fills sumQuery[i], averageQuery[i], sumSquaredQuery[i]. - } - - //find the averages for each querys references - should be paralellized - for (int i = 0; i < numSeqs; i++) { - findVarianceRef(i); //fills varRef[i] and sdRef[i] also sets minimum error rate to 0.001 to avoid divide by 0. - } - - //find the averages for the query - should be paralellized - for (int i = 0; i < numSeqs; i++) { - findVarianceQuery(i); //fills varQuery[i] and sdQuery[i] also sets minimum error rate to 0.001 to avoid divide by 0. - } + windows = findWindows(); + if (m->control_pressed) { return 0; } - for (int i = 0; i < numSeqs; i++) { - determineChimeras(i); //fills anova, isChimericConfidence[i], isChimericTStudent[i] and isChimericANOVA[i]. - should be paralellized - } - - //free memory - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } - for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i]; } + //remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later + removeBadReferenceSeqs(closest); + if (m->control_pressed) { return 0; } + + //find the averages for each querys references + getAverageRef(closest); //fills sumRef, averageRef, sumSquaredRef and refCombo. + getAverageQuery(closest, query); //fills sumQuery, averageQuery, sumSquaredQuery. + if (m->control_pressed) { return 0; } + + //find the averages for each querys references + findVarianceRef(); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0. + if (m->control_pressed) { return 0; } + //find the averages for the query + findVarianceQuery(); //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0. + if (m->control_pressed) { return 0; } + + determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA. + if (m->control_pressed) { return 0; } + + return 0; } catch(exception& e) { - errorOut(e, "Ccode", "getChimeras"); + m->errorOut(e, "Ccode", "getChimeras"); exit(1); } } /***************************************************************************************************************/ //ccode algo says it does this to "Removes the initial and final gaps to avoid biases due to incomplete sequences." -void Ccode::trimSequences(int query) { +void Ccode::trimSequences(Sequence* query) { try { int frontPos = 0; //should contain first position in all seqs that is not a gap character - int rearPos = querySeqs[query]->getAligned().length(); + int rearPos = query->getAligned().length(); //********find first position in closest seqs that is a non gap character***********// //find first position all query seqs that is a non gap character - for (int i = 0; i < closest[query].size(); i++) { + for (int i = 0; i < closest.size(); i++) { - string aligned = closest[query][i].seq->getAligned(); + string aligned = closest[i].seq->getAligned(); int pos = 0; //find first spot in this seq @@ -348,7 +434,7 @@ void Ccode::trimSequences(int query) { } //find first position all querySeq[query] that is a non gap character - string aligned = querySeqs[query]->getAligned(); + string aligned = query->getAligned(); int pos = 0; //find first spot in this seq @@ -364,9 +450,9 @@ void Ccode::trimSequences(int query) { //********find last position in closest seqs that is a non gap character***********// - for (int i = 0; i < closest[query].size(); i++) { + for (int i = 0; i < closest.size(); i++) { - string aligned = closest[query][i].seq->getAligned(); + string aligned = closest[i].seq->getAligned(); int pos = aligned.length(); //find first spot in this seq @@ -382,7 +468,7 @@ void Ccode::trimSequences(int query) { } //find last position all querySeqs[query] that is a non gap character - aligned = querySeqs[query]->getAligned(); + aligned = query->getAligned(); pos = aligned.length(); //find first spot in this seq @@ -398,13 +484,13 @@ void Ccode::trimSequences(int query) { //check to make sure that is not whole seq - if ((rearPos - frontPos - 1) <= 0) { mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1); } + if ((rearPos - frontPos - 1) <= 0) { m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1); } map tempTrim; tempTrim[frontPos] = rearPos; //save trimmed locations - trim[query] = tempTrim; + trim = tempTrim; //update spotMask map newMap; @@ -412,59 +498,48 @@ void Ccode::trimSequences(int query) { for (int i = frontPos; i < rearPos; i++) { //add to newMap -//cout << query << '\t' << i << '\t' << spotMap[query][i] << endl; - newMap[spot] = spotMap[query][i]; + newMap[spot] = spotMap[i]; spot++; } - - //for (it = newMap.begin(); it!=newMap.end(); it++) { - //cout << query << '\t' << it->first << '\t' << it->second << endl; - //} - - spotMap[query] = newMap; - - + spotMap = newMap; } catch(exception& e) { - errorOut(e, "Ccode", "trimSequences"); + m->errorOut(e, "Ccode", "trimSequences"); exit(1); } - } /***************************************************************************************************************/ -vector Ccode::findWindows(int query) { +vector Ccode::findWindows() { try { vector win; - it = trim[query].begin(); + it = trim.begin(); int length = it->second - it->first; - + //default is wanted = 10% of total length - if (windowSizes[query] > length) { - mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length."); - windowSizes[query] = length / 10; - }else if (windowSizes[query] == 0) { windowSizes[query] = length / 10; } - else if (windowSizes[query] > (length / 20)) { - mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine(); - }else if (windowSizes[query] < (length / 5)) { - mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine(); + if (windowSizes > length) { + m->mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length."); + windowSizes = length / 10; + }else if (windowSizes == 0) { windowSizes = length / 10; } + else if (windowSizes > (length * 0.20)) { + m->mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine(); + }else if (windowSizes < (length * 0.05)) { + m->mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine(); } //save starting points of each window - for (int m = it->first; m < (it->second-windowSizes[query]); m+=windowSizes[query]) { win.push_back(m); } + for (int m = it->first; m < (it->second-windowSizes); m+=windowSizes) { win.push_back(m); } //save last window if (win[win.size()-1] < (it->first+length)) { - win.push_back(win[win.size()-1]+windowSizes[query]); // ex. string length is 115, window is 25, without this you would get 0, 25, 50, 75 + win.push_back(win[win.size()-1]+windowSizes); // ex. string length is 115, window is 25, without this you would get 0, 25, 50, 75 } //with this you would get 1,25,50,75,100 - return win; - } catch(exception& e) { - errorOut(e, "Ccode", "findWindows"); + m->errorOut(e, "Ccode", "findWindows"); exit(1); } } @@ -519,13 +594,13 @@ int Ccode::getDiff(string seqA, string seqB) { } catch(exception& e) { - errorOut(e, "Ccode", "getDiff"); + m->errorOut(e, "Ccode", "getDiff"); exit(1); } } //*************************************************************************************************************** //tried to make this look most like ccode original implementation -void Ccode::removeBadReferenceSeqs(vector& seqs, int query) { +void Ccode::removeBadReferenceSeqs(vector& seqs) { try { vector< vector > numDiffBases; @@ -533,7 +608,7 @@ void Ccode::removeBadReferenceSeqs(vector& seqs, int query) { //initialize to 0 for (int i = 0; i < numDiffBases.size(); i++) { numDiffBases[i].resize(seqs.size(),0); } - it = trim[query].begin(); + it = trim.begin(); int length = it->second - it->first; //calc differences from each sequence to everyother seq in the set @@ -589,82 +664,72 @@ void Ccode::removeBadReferenceSeqs(vector& seqs, int query) { seqs = goodSeqs; }else { //warn, but dont remove any - mothurOut(querySeqs[query]->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); mothurOutEndLine(); + m->mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); m->mothurOutEndLine(); } - } catch(exception& e) { - errorOut(e, "Ccode", "removeBadReferenceSeqs"); + m->errorOut(e, "Ccode", "removeBadReferenceSeqs"); exit(1); } } //*************************************************************************************************************** -vector< vector > Ccode::findClosest(int start, int end, int numWanted) { +//makes copy of templateseq for filter +vector Ccode::findClosest(Sequence* q, int numWanted) { try{ - vector< vector > topMatches; topMatches.resize(querySeqs.size()); - - float smallestOverall, smallestLeft, smallestRight; - smallestOverall = 1000; smallestLeft = 1000; smallestRight = 1000; + vector topMatches; - //for each sequence in querySeqs - find top matches to use as reference - for(int j = start; j < end; j++){ - - Sequence query = *(querySeqs[j]); + Sequence query = *(q); - vector distances; + //calc distance to each sequence in template seqs + for (int i = 0; i < templateSeqs.size(); i++) { - //calc distance to each sequence in template seqs - for (int i = 0; i < templateSeqs.size(); i++) { - - Sequence ref = *(templateSeqs[i]); + Sequence ref = *(templateSeqs[i]); - //find overall dist - distCalc->calcDist(query, ref); - float dist = distCalc->getDist(); + //find overall dist + distCalc->calcDist(query, ref); + float dist = distCalc->getDist(); - //save distance - SeqDist temp; - temp.seq = templateSeqs[i]; - temp.dist = dist; + //save distance + SeqDist temp; + temp.seq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned()); + temp.dist = dist; - distances.push_back(temp); - } - - sort(distances.begin(), distances.end(), compareSeqDist); - - //save the number of top matches wanted - for (int h = 0; h < numWanted; h++) { - topMatches[j].push_back(distances[h]); - } + topMatches.push_back(temp); } + sort(topMatches.begin(), topMatches.end(), compareSeqDist); + + for (int i = numWanted; i < topMatches.size(); i++) { delete topMatches[i].seq; } + + topMatches.resize(numWanted); + return topMatches; } catch(exception& e) { - errorOut(e, "Ccode", "findClosestSides"); + m->errorOut(e, "Ccode", "findClosestSides"); exit(1); } } /**************************************************************************************************/ //find the distances from each reference sequence to every other reference sequence for each window for this query -void Ccode::getAverageRef(vector ref, int query) { +void Ccode::getAverageRef(vector ref) { try { - vector< vector< vector > > diffs; //diffs[0][1][2] is the number of differences between ref seq 0 and ref seq 1 at window 2. + vector< vector< vector > > diffs; //diffs[0][1][2] is the number of differences between ref seq 0 and ref seq 1 at window 2. //initialize diffs vector diffs.resize(ref.size()); for (int i = 0; i < diffs.size(); i++) { diffs[i].resize(ref.size()); for (int j = 0; j < diffs[i].size(); j++) { - diffs[i][j].resize(windows[query].size(), 0); + diffs[i][j].resize(windows.size(), 0); } } - it = trim[query].begin(); + it = trim.begin(); //find the distances from each reference sequence to every other reference sequence for each window for this query for (int i = 0; i < ref.size(); i++) { @@ -676,23 +741,23 @@ void Ccode::getAverageRef(vector ref, int query) { string refJ = ref[j].seq->getAligned(); - for (int k = 0; k < windows[query].size(); k++) { + for (int k = 0; k < windows.size(); k++) { string refIWindowk, refJWindowk; - if (k < windows[query].size()-1) { + if (k < windows.size()-1) { //get window strings - refIWindowk = refI.substr(windows[query][k], windowSizes[query]); - refJWindowk = refJ.substr(windows[query][k], windowSizes[query]); + refIWindowk = refI.substr(windows[k], windowSizes); + refJWindowk = refJ.substr(windows[k], windowSizes); }else { //last window may be smaller than rest - see findwindows //get window strings - refIWindowk = refI.substr(windows[query][k], (it->second-windows[query][k])); - refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k])); + refIWindowk = refI.substr(windows[k], (it->second-windows[k])); + refJWindowk = refJ.substr(windows[k], (it->second-windows[k])); } //find differences int diff = getDiff(refIWindowk, refJWindowk); -//cout << i << '\t' << j << '\t' << k << '\t' << diff << endl; + //save differences in [i][j][k] and [j][i][k] since they are the same diffs[i][j][k] = diff; diffs[j][i][k] = diff; @@ -704,20 +769,20 @@ void Ccode::getAverageRef(vector ref, int query) { }//i //initialize sumRef for this query - sumRef[query].resize(windows[query].size(), 0); - sumSquaredRef[query].resize(windows[query].size(), 0); - averageRef[query].resize(windows[query].size(), 0); + sumRef.resize(windows.size(), 0); + sumSquaredRef.resize(windows.size(), 0); + averageRef.resize(windows.size(), 0); //find the sum of the differences for hte reference sequences for (int i = 0; i < diffs.size(); i++) { for (int j = 0; j < i; j++) { //increment this querys reference sequences combos - refCombo[query]++; + refCombo++; for (int k = 0; k < diffs[i][j].size(); k++) { - sumRef[query][k] += diffs[i][j][k]; - sumSquaredRef[query][k] += (diffs[i][j][k]*diffs[i][j][k]); + sumRef[k] += diffs[i][j][k]; + sumSquaredRef[k] += (diffs[i][j][k]*diffs[i][j][k]); }//k }//j @@ -725,18 +790,18 @@ void Ccode::getAverageRef(vector ref, int query) { //find the average of the differences for the references for each window - for (int i = 0; i < windows[query].size(); i++) { - averageRef[query][i] = sumRef[query][i] / (float) refCombo[query]; + for (int i = 0; i < windows.size(); i++) { + averageRef[i] = sumRef[i] / (float) refCombo; } } catch(exception& e) { - errorOut(e, "Ccode", "getAverageRef"); + m->errorOut(e, "Ccode", "getAverageRef"); exit(1); } } /**************************************************************************************************/ -void Ccode::getAverageQuery (vector ref, int query) { +void Ccode::getAverageQuery (vector ref, Sequence* query) { try { vector< vector > diffs; //diffs[1][2] is the number of differences between querySeqs[query] and ref seq 1 at window 2. @@ -744,35 +809,35 @@ void Ccode::getAverageQuery (vector ref, int query) { //initialize diffs vector diffs.resize(ref.size()); for (int j = 0; j < diffs.size(); j++) { - diffs[j].resize(windows[query].size(), 0); + diffs[j].resize(windows.size(), 0); } - it = trim[query].begin(); + it = trim.begin(); - string refQuery = querySeqs[query]->getAligned(); + string refQuery = query->getAligned(); //jgetAligned(); - for (int k = 0; k < windows[query].size(); k++) { + for (int k = 0; k < windows.size(); k++) { string QueryWindowk, refJWindowk; - if (k < windows[query].size()-1) { + if (k < windows.size()-1) { //get window strings - QueryWindowk = refQuery.substr(windows[query][k], windowSizes[query]); - refJWindowk = refJ.substr(windows[query][k], windowSizes[query]); + QueryWindowk = refQuery.substr(windows[k], windowSizes); + refJWindowk = refJ.substr(windows[k], windowSizes); }else { //last window may be smaller than rest - see findwindows //get window strings - QueryWindowk = refQuery.substr(windows[query][k], (it->second-windows[query][k])); - refJWindowk = refJ.substr(windows[query][k], (it->second-windows[query][k])); + QueryWindowk = refQuery.substr(windows[k], (it->second-windows[k])); + refJWindowk = refJ.substr(windows[k], (it->second-windows[k])); } //find differences int diff = getDiff(QueryWindowk, refJWindowk); -//cout << j << '\t' << k << '\t' << diff << endl; + //save differences diffs[j][k] = diff; @@ -781,121 +846,119 @@ void Ccode::getAverageQuery (vector ref, int query) { //initialize sumRef for this query - sumQuery[query].resize(windows[query].size(), 0); - sumSquaredQuery[query].resize(windows[query].size(), 0); - averageQuery[query].resize(windows[query].size(), 0); + sumQuery.resize(windows.size(), 0); + sumSquaredQuery.resize(windows.size(), 0); + averageQuery.resize(windows.size(), 0); //find the sum of the differences for (int j = 0; j < diffs.size(); j++) { for (int k = 0; k < diffs[j].size(); k++) { - sumQuery[query][k] += diffs[j][k]; - sumSquaredQuery[query][k] += (diffs[j][k]*diffs[j][k]); + sumQuery[k] += diffs[j][k]; + sumSquaredQuery[k] += (diffs[j][k]*diffs[j][k]); }//k }//j //find the average of the differences for the references for each window - for (int i = 0; i < windows[query].size(); i++) { - averageQuery[query][i] = sumQuery[query][i] / (float) ref.size(); + for (int i = 0; i < windows.size(); i++) { + averageQuery[i] = sumQuery[i] / (float) ref.size(); } - - } catch(exception& e) { - errorOut(e, "Ccode", "getAverageQuery"); + m->errorOut(e, "Ccode", "getAverageQuery"); exit(1); } } /**************************************************************************************************/ -void Ccode::findVarianceRef (int query) { +void Ccode::findVarianceRef() { try { - varRef[query].resize(windows[query].size(), 0); - sdRef[query].resize(windows[query].size(), 0); + varRef.resize(windows.size(), 0); + sdRef.resize(windows.size(), 0); //for each window - for (int i = 0; i < windows[query].size(); i++) { - varRef[query][i] = (sumSquaredRef[query][i] - ((sumRef[query][i]*sumRef[query][i])/(float)refCombo[query])) / (float)(refCombo[query]-1); - sdRef[query][i] = sqrt(varRef[query][i]); + for (int i = 0; i < windows.size(); i++) { + varRef[i] = (sumSquaredRef[i] - ((sumRef[i]*sumRef[i])/(float)refCombo)) / (float)(refCombo-1); + sdRef[i] = sqrt(varRef[i]); //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation - if (averageRef[query][i] < 0.001) { averageRef[query][i] = 0.001; } - if (sumRef[query][i] < 0.001) { sumRef[query][i] = 0.001; } - if (varRef[query][i] < 0.001) { varRef[query][i] = 0.001; } - if (sumSquaredRef[query][i] < 0.001) { sumSquaredRef[query][i] = 0.001; } - if (sdRef[query][i] < 0.001) { sdRef[query][i] = 0.001; } + if (averageRef[i] < 0.001) { averageRef[i] = 0.001; } + if (sumRef[i] < 0.001) { sumRef[i] = 0.001; } + if (varRef[i] < 0.001) { varRef[i] = 0.001; } + if (sumSquaredRef[i] < 0.001) { sumSquaredRef[i] = 0.001; } + if (sdRef[i] < 0.001) { sdRef[i] = 0.001; } } } catch(exception& e) { - errorOut(e, "Ccode", "findVarianceRef"); + m->errorOut(e, "Ccode", "findVarianceRef"); exit(1); } } /**************************************************************************************************/ -void Ccode::findVarianceQuery (int query) { +void Ccode::findVarianceQuery() { try { - varQuery[query].resize(windows[query].size(), 0); - sdQuery[query].resize(windows[query].size(), 0); + varQuery.resize(windows.size(), 0); + sdQuery.resize(windows.size(), 0); //for each window - for (int i = 0; i < windows[query].size(); i++) { - varQuery[query][i] = (sumSquaredQuery[query][i] - ((sumQuery[query][i]*sumQuery[query][i])/(float) closest[query].size())) / (float) (closest[query].size()-1); - sdQuery[query][i] = sqrt(varQuery[query][i]); + for (int i = 0; i < windows.size(); i++) { + varQuery[i] = (sumSquaredQuery[i] - ((sumQuery[i]*sumQuery[i])/(float) closest.size())) / (float) (closest.size()-1); + sdQuery[i] = sqrt(varQuery[i]); //set minimum error rate to 0.001 - to avoid potential divide by zero - not sure if this is necessary but it follows ccode implementation - if (averageQuery[query][i] < 0.001) { averageQuery[query][i] = 0.001; } - if (sumQuery[query][i] < 0.001) { sumQuery[query][i] = 0.001; } - if (varQuery[query][i] < 0.001) { varQuery[query][i] = 0.001; } - if (sumSquaredQuery[query][i] < 0.001) { sumSquaredQuery[query][i] = 0.001; } - if (sdQuery[query][i] < 0.001) { sdQuery[query][i] = 0.001; } + if (averageQuery[i] < 0.001) { averageQuery[i] = 0.001; } + if (sumQuery[i] < 0.001) { sumQuery[i] = 0.001; } + if (varQuery[i] < 0.001) { varQuery[i] = 0.001; } + if (sumSquaredQuery[i] < 0.001) { sumSquaredQuery[i] = 0.001; } + if (sdQuery[i] < 0.001) { sdQuery[i] = 0.001; } } } catch(exception& e) { - errorOut(e, "Ccode", "findVarianceQuery"); + m->errorOut(e, "Ccode", "findVarianceQuery"); exit(1); } } /**************************************************************************************************/ -void Ccode::determineChimeras (int query) { +void Ccode::determineChimeras() { try { - isChimericConfidence[query].resize(windows[query].size(), false); - isChimericTStudent[query].resize(windows[query].size(), false); - isChimericANOVA[query].resize(windows[query].size(), false); - anova[query].resize(windows[query].size()); + isChimericConfidence.resize(windows.size(), false); + isChimericTStudent.resize(windows.size(), false); + isChimericANOVA.resize(windows.size(), false); + anova.resize(windows.size()); //for each window - for (int i = 0; i < windows[query].size(); i++) { + for (int i = 0; i < windows.size(); i++) { //get confidence limits - float t = getT(closest[query].size()-1); //how many seqs you are comparing to this querySeq - float dsUpper = (averageQuery[query][i] + (t * sdQuery[query][i])) / averageRef[query][i]; - float dsLower = (averageQuery[query][i] - (t * sdQuery[query][i])) / averageRef[query][i]; -//cout << t << '\t' << "ds upper = " << dsUpper << " dsLower = " << dsLower << endl; - if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[query][i] > averageRef[query][i])) { /* range does not include 1 */ - isChimericConfidence[query][i] = true; /* significantly higher at P<0.05 */ -//cout << i << " made it here" << endl; + float t = getT(closest.size()-1); //how many seqs you are comparing to this querySeq + float dsUpper = (averageQuery[i] + (t * sdQuery[i])) / averageRef[i]; + float dsLower = (averageQuery[i] - (t * sdQuery[i])) / averageRef[i]; + + if ((dsUpper > 1.0) && (dsLower > 1.0) && (averageQuery[i] > averageRef[i])) { /* range does not include 1 */ + isChimericConfidence[i] = true; /* significantly higher at P<0.05 */ + } //student t test - int degreeOfFreedom = refCombo[query] + closest[query].size() - 2; - float denomForT = (((refCombo[query]-1) * varQuery[query][i] + (closest[query].size() - 1) * varRef[query][i]) / (float) degreeOfFreedom) * ((refCombo[query] + closest[query].size()) / (float) (refCombo[query] * closest[query].size())); /* denominator, without sqrt(), for ts calculations */ + int degreeOfFreedom = refCombo + closest.size() - 2; + float denomForT = (((refCombo-1) * varQuery[i] + (closest.size() - 1) * varRef[i]) / (float) degreeOfFreedom) * ((refCombo + closest.size()) / (float) (refCombo * closest.size())); /* denominator, without sqrt(), for ts calculations */ - float ts = fabs((averageQuery[query][i] - averageRef[query][i]) / (sqrt(denomForT))); /* value of ts for t-student test */ + float ts = fabs((averageQuery[i] - averageRef[i]) / (sqrt(denomForT))); /* value of ts for t-student test */ t = getT(degreeOfFreedom); -//cout << i << '\t' << t << '\t' << ts << endl; - if ((ts >= t) && (averageQuery[query][i] > averageRef[query][i])) { - isChimericTStudent[query][i] = true; /* significantly higher at P<0.05 */ + + if ((ts >= t) && (averageQuery[i] > averageRef[i])) { + isChimericTStudent[i] = true; /* significantly higher at P<0.05 */ } //anova test - float value1 = sumQuery[query][i] + sumRef[query][i]; - float value2 = sumSquaredQuery[query][i] + sumSquaredRef[query][i]; - float value3 = ((sumQuery[query][i]*sumQuery[query][i]) / (float) (closest[query].size())) + ((sumRef[query][i] * sumRef[query][i]) / (float) refCombo[query]); - float value4 = (value1 * value1) / ( (float) (closest[query].size() + refCombo[query]) ); + float value1 = sumQuery[i] + sumRef[i]; + float value2 = sumSquaredQuery[i] + sumSquaredRef[i]; + float value3 = ((sumQuery[i]*sumQuery[i]) / (float) (closest.size())) + ((sumRef[i] * sumRef[i]) / (float) refCombo); + float value4 = (value1 * value1) / ( (float) (closest.size() + refCombo) ); float value5 = value2 - value4; float value6 = value3 - value4; float value7 = value5 - value6; @@ -904,16 +967,18 @@ void Ccode::determineChimeras (int query) { float f = getF(degreeOfFreedom); - if ((anovaValue >= f) && (averageQuery[query][i] > averageRef[query][i])) { - isChimericANOVA[query][i] = true; /* significant P<0.05 */ + if ((anovaValue >= f) && (averageQuery[i] > averageRef[i])) { + isChimericANOVA[i] = true; /* significant P<0.05 */ } - anova[query][i] = anovaValue; + if (isnan(anovaValue) || isinf(anovaValue)) { anovaValue = 0.0; } + + anova[i] = anovaValue; } } catch(exception& e) { - errorOut(e, "Ccode", "determineChimeras"); + m->errorOut(e, "Ccode", "determineChimeras"); exit(1); } } @@ -958,13 +1023,13 @@ float Ccode::getT(int numseq) { else if (numseq > 2) tvalue = 2.353; else if (numseq > 1) tvalue = 2.920; else if (numseq <= 1) { - mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine(); + m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine(); } return tvalue; } catch(exception& e) { - errorOut(e, "Ccode", "getT"); + m->errorOut(e, "Ccode", "getT"); exit(1); } } @@ -1010,126 +1075,17 @@ float Ccode::getF(int numseq) { else if (numseq > 1) fvalue = 18.5; else if (numseq > 0) fvalue = 161; else if (numseq <= 0) { - mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine(); + m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine(); } return fvalue; } catch(exception& e) { - errorOut(e, "Ccode", "getF"); + m->errorOut(e, "Ccode", "getF"); exit(1); } } +//*************************************************************************************************************** -/**************************************************************************************************/ -void Ccode::createProcessesClosest() { - try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; - vector processIDS; - - //loop through and create all the processes you want - while (process != processors) { - int pid = fork(); - - if (pid > 0) { - processIDS.push_back(pid); - process++; - }else if (pid == 0){ - - mothurOut("Finding top matches for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine(); - closest = findClosest(lines[process]->start, lines[process]->end, numWanted); - mothurOut("Done finding top matches for sequences " + toString(lines[process]->start) + " to " + toString(lines[process]->end)); mothurOutEndLine(); - - //write out data to file so parent can read it - ofstream out; - string s = toString(getpid()) + ".temp"; - openOutputFile(s, out); - - //output pairs - for (int i = lines[process]->start; i < lines[process]->end; i++) { - for (int j = 0; j < closest[i].size(); j++) { - closest[i][j].seq->printSequence(out); - } - } - out << ">" << endl; //to stop sequence read - - for (int i = lines[process]->start; i < lines[process]->end; i++) { - for (int j = 0; j < closest[i].size(); j++) { - out << closest[i][j].dist << '\t'; - } - out << endl; - } - - out.close(); - - exit(0); - }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); } - } - - //force parent to wait until all the processes are done - for (int i=0;i > tempClosest; tempClosest.resize(querySeqs.size()); - //get pairs - for (int k = lines[i]->start; k < lines[i]->end; k++) { - vector tempVector; - - for (int j = 0; j < numWanted; j++) { - - Sequence* temp = new Sequence(in); - gobble(in); - - tempVector.push_back(temp); - } - - tempClosest[k] = tempVector; - } - - string junk; - in >> junk; gobble(in); // to get ">" - - vector< vector > dists; dists.resize(querySeqs.size()); - - for (int i = lines[process]->start; i < lines[process]->end; i++) { - dists[i].resize(closest[i].size()); - for (int j = 0; j < closest[i].size(); j++) { - in >> dists[i][j]; - } - gobble(in); - } - - for (int i = lines[process]->start; i < lines[process]->end; i++) { - for (int j = 0; j < closest[i].size(); j++) { - closest[i][j].seq = tempClosest[i][j]; - closest[i][j].dist = dists[i][j]; - } - } - - in.close(); - remove(s.c_str()); - } - - -#else - closest = findClosest(lines[0]->start, lines[0]->end, numWanted); -#endif - - } - catch(exception& e) { - errorOut(e, "Ccode", "createProcessesClosest"); - exit(1); - } -} -//***************************************************************************************************************