X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=3d1d1c9fa5ac995a65265b62ed4c59f25ed6679d;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=f4c4a9821350c38a9bde8ca7a4fcd6ae01d6b3c3;hpb=d945488119ad368b180537f36ed40298ff170f39;p=mothur.git diff --git a/maligner.cpp b/maligner.cpp index f4c4a98..3d1d1c9 100644 --- a/maligner.cpp +++ b/maligner.cpp @@ -10,33 +10,33 @@ #include "maligner.h" /***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight -Maligner::Maligner(vector temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) { +Maligner::Maligner(vector temp, int match, int misMatch, float div, int ms, int minCov) : db(temp), matchScore(match), misMatchPenalty(misMatch), minDivR(div), minSimilarity(ms), minCoverage(minCov) { //numWanted(num), , searchMethod(mode), databaseLeft(dataLeft), databaseRight(dataRight) m = MothurOut::getInstance(); } /***********************************************************************/ -string Maligner::getResults(Sequence* q, DeCalculator* decalc) { +string Maligner::getResults(Sequence q, DeCalculator decalc) { try { outputResults.clear(); //make copy so trimming doesn't destroy query from calling class - remember to deallocate - query = new Sequence(q->getName(), q->getAligned()); + query.setName(q.getName()); query.setAligned(q.getAligned()); string chimera; //copy refSeqs so that filter does not effect original for(int i = 0; i < db.size(); i++) { - Sequence* newSeq = new Sequence(db[i]->getName(), db[i]->getAligned()); + Sequence newSeq(db[i].getName(), db[i].getAligned()); refSeqs.push_back(newSeq); } refSeqs = minCoverageFilter(refSeqs); if (refSeqs.size() < 2) { - for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } + //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } percentIdenticalQueryChimera = 0.0; return "unknown"; } @@ -49,9 +49,9 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { if (m->control_pressed) { return chimera; } //free memory - delete query; + //delete query; - for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } + //for (int i = 0; i < refSeqs.size(); i++) { delete refSeqs[i]; } return chimera; } @@ -61,30 +61,26 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) { } } /***********************************************************************/ -string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { +string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator decalc) { try { string chimera; - //trims seqs to first non gap char in all seqs and last non gap char in all seqs - spotMap = decalc->trimSeqs(query, refSeqs); - + spotMap = decalc.trimSeqs(query, refSeqs); + //you trimmed the whole sequence, skip - if (query->getAligned() == "") { return "no"; } + if (query.getAligned() == "") { return "no"; } - vector temp = refSeqs; - -// for(int i=0;igetName() << endl; -// } - + vector temp = refSeqs; temp.push_back(query); - verticalFilter(temp); + temp = verticalFilter(temp); + query = temp[temp.size()-1]; + for (int i = 0; i < temp.size()-1; i++) { refSeqs[i] = temp[i]; } //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl ; }//<< refSeqs[i]->getAligned() << endl - vector< vector > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes + vector< vector > matrix = buildScoreMatrix(query.getAligned().length(), refSeqs.size()); //builds and initializes if (m->control_pressed) { return chimera; } @@ -94,14 +90,14 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { if (m->control_pressed) { return chimera; } - vector trace = mapTraceRegionsToAlignment(path, refSeqs); + vector trace = mapTraceRegionsToAlignment(path); if (trace.size() > 1) { chimera = "yes"; } else { chimera = "no"; return chimera; } int traceStart = path[0].col; int traceEnd = path[path.size()-1].col; - string queryInRange = query->getAligned(); + string queryInRange = query.getAligned(); queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1)); // cout << queryInRange << endl; string chimeraSeq = constructChimericSeq(trace, refSeqs); @@ -140,23 +136,23 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { // cout << regionStart << '\t' << regionEnd << '\t' << seqIndex << endl; results temp; - temp.parent = refSeqs[seqIndex]->getName(); - temp.parentAligned = db[seqIndex]->getAligned(); + temp.parent = refSeqs[seqIndex].getName(); + temp.parentAligned = db[seqIndex].getAligned(); temp.nastRegionStart = spotMap[regionStart]; temp.nastRegionEnd = spotMap[regionEnd]; temp.regionStart = unalignedMap[regionStart]; temp.regionEnd = unalignedMap[regionEnd]; - string parentInRange = refSeqs[seqIndex]->getAligned(); + string parentInRange = refSeqs[seqIndex].getAligned(); parentInRange = parentInRange.substr(traceStart, (traceEnd-traceStart+1)); temp.queryToParent = computePercentID(queryInRange, parentInRange); temp.divR = (percentIdenticalQueryChimera / temp.queryToParent); - string queryInRegion = query->getAligned(); + string queryInRegion = query.getAligned(); queryInRegion = queryInRegion.substr(regionStart, (regionEnd-regionStart+1)); - string parentInRegion = refSeqs[seqIndex]->getAligned(); + string parentInRegion = refSeqs[seqIndex].getAligned(); parentInRegion = parentInRegion.substr(regionStart, (regionEnd-regionStart+1)); temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion); @@ -175,15 +171,15 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) { } /***********************************************************************/ //removes top matches that do not have minimum coverage with query. -vector Maligner::minCoverageFilter(vector ref){ +vector Maligner::minCoverageFilter(vector ref){ try { - vector newRefs; + vector newRefs; - string queryAligned = query->getAligned(); + string queryAligned = query.getAligned(); for (int i = 0; i < ref.size(); i++) { - string refAligned = ref[i]->getAligned(); + string refAligned = ref[i].getAligned(); int numBases = 0; int numCovered = 0; @@ -205,9 +201,9 @@ vector Maligner::minCoverageFilter(vector ref){ //if coverage above minimum if (coverage > minCoverage) { newRefs.push_back(ref[i]); - }else { - delete ref[i]; - } + }//else { + //delete ref[i]; + //} } return newRefs; @@ -222,7 +218,7 @@ vector Maligner::minCoverageFilter(vector ref){ int Maligner::computeChimeraPenalty() { try { - int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases()); + int numAllowable = ((1.0 - (1.0/minDivR)) * query.getNumBases()); // if(numAllowable < 1){ numAllowable = 1; } @@ -238,16 +234,16 @@ int Maligner::computeChimeraPenalty() { } /***********************************************************************/ //this is a vertical filter -void Maligner::verticalFilter(vector seqs) { +vector Maligner::verticalFilter(vector seqs) { try { - vector gaps; gaps.resize(query->getAligned().length(), 0); + vector gaps; gaps.resize(query.getAligned().length(), 0); - string filterString = (string(query->getAligned().length(), '1')); + string filterString = (string(query.getAligned().length(), '1')); //for each sequence for (int i = 0; i < seqs.size(); i++) { - string seqAligned = seqs[i]->getAligned(); + string seqAligned = seqs[i].getAligned(); for (int j = 0; j < seqAligned.length(); j++) { //if this spot is a gap @@ -257,7 +253,7 @@ void Maligner::verticalFilter(vector seqs) { //zero out spot where all sequences have blanks int numColRemoved = 0; - for(int i = 0; i < seqs[0]->getAligned().length(); i++){ + for(int i = 0; i < seqs[0].getAligned().length(); i++){ if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; } } @@ -265,7 +261,7 @@ void Maligner::verticalFilter(vector seqs) { //for each sequence for (int i = 0; i < seqs.size(); i++) { - string seqAligned = seqs[i]->getAligned(); + string seqAligned = seqs[i].getAligned(); string newAligned = ""; int count = 0; @@ -278,10 +274,10 @@ void Maligner::verticalFilter(vector seqs) { } } - seqs[i]->setAligned(newAligned); + seqs[i].setAligned(newAligned); } - string query = seqs[seqs.size()-1]->getAligned(); + string query = seqs[seqs.size()-1].getAligned(); int queryLength = query.length(); unalignedMap.resize(queryLength, 0); @@ -297,6 +293,8 @@ void Maligner::verticalFilter(vector seqs) { } spotMap = newMap; + + return seqs; } catch(exception& e) { m->errorOut(e, "Maligner", "verticalFilter"); @@ -333,19 +331,19 @@ vector< vector > Maligner::buildScoreMatrix(int cols, int rows) { //*************************************************************************************************************** -void Maligner::fillScoreMatrix(vector >& ms, vector seqs, int penalty) { +void Maligner::fillScoreMatrix(vector >& ms, vector seqs, int penalty) { try{ //get matrix dimensions - int numCols = query->getAligned().length(); + int numCols = query.getAligned().length(); int numRows = seqs.size(); // cout << numRows << endl; //initialize first col - string queryAligned = query->getAligned(); + string queryAligned = query.getAligned(); for (int i = 0; i < numRows; i++) { - string subjectAligned = seqs[i]->getAligned(); + string subjectAligned = seqs[i].getAligned(); //are you both gaps? if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) { @@ -366,7 +364,7 @@ void Maligner::fillScoreMatrix(vector >& ms, vectorgetAligned(); + string subjectAligned = seqs[i].getAligned(); int matchMisMatchScore = 0; //are you both gaps? @@ -434,7 +432,7 @@ vector Maligner::extractHighestPath(vector > try { //get matrix dimensions - int numCols = query->getAligned().length(); + int numCols = query.getAligned().length(); int numRows = ms.size(); @@ -480,7 +478,7 @@ vector Maligner::extractHighestPath(vector > } } //*************************************************************************************************************** -vector Maligner::mapTraceRegionsToAlignment(vector path, vector seqs) { +vector Maligner::mapTraceRegionsToAlignment(vector path) { try { vector trace; @@ -614,7 +612,7 @@ vector Maligner::extractHighestPath(vector > } } -//*************************************************************************************************************** +*************************************************************************************************************** vector Maligner::mapTraceRegionsToAlignment(vector path, vector seqs) { try { @@ -668,14 +666,14 @@ vector Maligner::mapTraceRegionsToAlignment(vector p */ //*************************************************************************************************************** -string Maligner::constructChimericSeq(vector trace, vector seqs) { +string Maligner::constructChimericSeq(vector trace, vector seqs) { try { string chimera = ""; for (int i = 0; i < trace.size(); i++) { // cout << i << '\t' << trace[i].row << '\t' << trace[i].col << '\t' << trace[i].oldCol << endl; - string seqAlign = seqs[trace[i].row]->getAligned(); + string seqAlign = seqs[trace[i].row].getAligned(); seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1)); chimera += seqAlign; } @@ -692,7 +690,7 @@ string Maligner::constructChimericSeq(vector trace, vector trace, vector seqs) { +string Maligner::constructAntiChimericSeq(vector trace, vector seqs) { try { string antiChimera = ""; @@ -701,7 +699,7 @@ string Maligner::constructAntiChimericSeq(vector trace, vectorgetAligned(); + string seqAlign = seqs[trace[oppositeIndex].row].getAligned(); seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1)); antiChimera += seqAlign; }