#include "maligner.h"
/***********************************************************************/ //int num, int match, int misMatch, , string mode, Database* dataLeft, Database* dataRight
-Maligner::Maligner(vector<Sequence*> 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<Sequence> 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";
}
int chimeraPenalty = computeChimeraPenalty();
-
+
//fills outputResults
chimera = chimeraMaligner(chimeraPenalty, 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;
}
}
}
/***********************************************************************/
-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<Sequence*> temp = refSeqs;
+ vector<Sequence> 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; }
+ //for (int i = 0; i < refSeqs.size(); i++) { cout << refSeqs[i]->getName() << endl ; }//<< refSeqs[i]->getAligned() << endl
- vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
+ vector< vector<score_struct> > matrix = buildScoreMatrix(query.getAligned().length(), refSeqs.size()); //builds and initializes
if (m->control_pressed) { return chimera; }
fillScoreMatrix(matrix, refSeqs, chimeraPenalty);
-
+
+ vector<score_struct> path = extractHighestPath(matrix);
+
+ if (m->control_pressed) { return chimera; }
+
+ vector<trace_struct> 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();
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+// cout << queryInRange << endl;
+ string chimeraSeq = constructChimericSeq(trace, refSeqs);
+// cout << chimeraSeq << endl;
+
+// cout << queryInRange.length() << endl;
+// cout << chimeraSeq.length() << endl;
+
+ percentIdenticalQueryChimera = computePercentID(queryInRange, chimeraSeq);
+
+// cout << percentIdenticalQueryChimera << endl;
+ /*
vector<trace_struct> trace = extractHighestPath(matrix);
//cout << "traces\n";
int traceStart = trace[0].col;
int traceEnd = trace[trace.size()-1].oldCol;
string queryInRange = query->getAligned();
- queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart+1));
+ queryInRange = queryInRange.substr(traceStart, (traceEnd-traceStart));*/
if (m->control_pressed) { return chimera; }
int regionEnd = trace[i].oldCol;
int seqIndex = trace[i].row;
+// 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 = regionStart;
- temp.regionEnd = 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);
- //cout << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << endl;
+ //cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " << temp.divR << endl;
+
outputResults.push_back(temp);
}
}
/***********************************************************************/
//removes top matches that do not have minimum coverage with query.
-vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
+vector<Sequence> Maligner::minCoverageFilter(vector<Sequence> ref){
try {
- vector<Sequence*> newRefs;
+ vector<Sequence> 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;
//if coverage above minimum
if (coverage > minCoverage) {
newRefs.push_back(ref[i]);
- }else {
- delete ref[i];
- }
+ }//else {
+ //delete ref[i];
+ //}
}
return newRefs;
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; }
}
/***********************************************************************/
//this is a vertical filter
-void Maligner::verticalFilter(vector<Sequence*> seqs) {
+vector<Sequence> Maligner::verticalFilter(vector<Sequence> seqs) {
try {
- vector<int> gaps; gaps.resize(query->getAligned().length(), 0);
+ vector<int> 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
//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++; }
}
//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;
}
}
- seqs[i]->setAligned(newAligned);
+ seqs[i].setAligned(newAligned);
}
-
+
+ string query = seqs[seqs.size()-1].getAligned();
+ int queryLength = query.length();
+
+ unalignedMap.resize(queryLength, 0);
+
+
+ for(int i=1;i<queryLength;i++){
+ if(query[i] != '.' && query[i] != '-'){
+ unalignedMap[i] = unalignedMap[i-1] + 1;
+ }
+ else{
+ unalignedMap[i] = unalignedMap[i-1];
+ }
+ }
+
spotMap = newMap;
+
+ return seqs;
}
catch(exception& e) {
m->errorOut(e, "Maligner", "verticalFilter");
//***************************************************************************************************************
-void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence*> seqs, int penalty) {
+void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequence> 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]))) {
//fill rest of matrix
for (int j = 1; j < numCols; j++) { //iterate through matrix columns
+// for (int i = 0; i < 1; i++) { //iterate through matrix rows
for (int i = 0; i < numRows; i++) { //iterate through matrix rows
- string subjectAligned = seqs[i]->getAligned();
+ string subjectAligned = seqs[i].getAligned();
int matchMisMatchScore = 0;
//are you both gaps?
if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
//leave the same
}else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
- //matchMisMatchScore = matchScore;
//leave the same
}else if (queryAligned[j] == subjectAligned[j]) {
matchMisMatchScore = matchScore;
-// ms[i][j].mismatches = ms[i][j-1].mismatches;
}else if (queryAligned[j] != subjectAligned[j]) {
matchMisMatchScore = misMatchPenalty;
-// ms[i][j].mismatches = ms[i][j-1].mismatches + 1;
}
-
+
//compute score based on previous columns scores
for (int prevIndex = 0; prevIndex < numRows; prevIndex++) { //iterate through rows
ms[i][j].prev = prevIndex;
}
}
+// cout << i << '\t' << j << '\t' << queryAligned[j] << '\t' << subjectAligned[j] << '\t' << matchMisMatchScore << '\t' << ms[i][j].score << endl;
+
}
+
}
- /* for(int i=0;i<numRows;i++){
- cout << seqs[i]->getName();
- for(int j=0;j<numCols;j++){
- cout << '\t' << ms[i][j].mismatches;
+
+
+
+
+// cout << numRows << '\t' << numCols << endl;
+// for(int i=0;i<numRows;i++){
+// cout << seqs[i]->getName();
+// for(int j=0;j<numCols;j++){
+// cout << '\t' << ms[i][j].score;
+// }
+// cout << endl;
+// }
+// cout << endl;
+//
+// for(int i=0;i<numRows;i++){
+// cout << seqs[i]->getName();
+// for(int j=0;j<numCols;j++){
+// cout << '\t' << ms[i][j].prev;
+// }
+// cout << endl;
+// }
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "fillScoreMatrix");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<score_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
+ try {
+
+ //get matrix dimensions
+ int numCols = query.getAligned().length();
+ int numRows = ms.size();
+
+
+ //find highest score scoring matrix
+ score_struct highestStruct;
+ int highestScore = 0;
+
+ for (int i = 0; i < numRows; i++) {
+ for (int j = 0; j < numCols; j++) {
+ if (ms[i][j].score > highestScore) {
+ highestScore = ms[i][j].score;
+ highestStruct = ms[i][j];
+ }
}
- cout << endl;
}
- cout << endl;*/
- /*cout << numRows << '\t' << numCols << endl;
- for(int i=0;i<numRows;i++){
- cout << seqs[i]->getName() << endl << seqs[i]->getAligned() << endl << endl;
- if ((seqs[i]->getName() == "S000003470") || (seqs[i]->getName() == "S000383265") || (seqs[i]->getName() == "7000004128191054")) {
- for(int j=0;j<numCols;j++){
- cout << '\t' << ms[i][j].score;
- }
- cout << endl;
- }
+
+ vector<score_struct> path;
+
+ int rowIndex = highestStruct.row;
+ int pos = highestStruct.col;
+ int score = highestStruct.score;
+
+// cout << rowIndex << '\t' << pos << '\t' << score << endl;
+
+ while (pos >= 0 && score > 0) {
+ score_struct temp = ms[rowIndex][pos];
+ score = temp.score;
+
+ if (score > 0) { path.push_back(temp); }
+
+ rowIndex = temp.prev;
+ pos--;
}
- cout << endl;*/
- /*for(int i=0;i<numRows;i++){
- cout << seqs[i]->getName();
- for(int j=0;j<numCols;j++){
- cout << '\t' << ms[i][j].prev;
+
+ reverse(path.begin(), path.end());
+
+ return path;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Maligner", "extractHighestPath");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path) {
+ try {
+ vector<trace_struct> trace;
+
+ int region_index = path[0].row;
+ int region_start = path[0].col;
+
+ for (int i = 1; i < path.size(); i++) {
+
+ int next_region_index = path[i].row;
+ //cout << i << '\t' << next_region_index << endl;
+
+ if (next_region_index != region_index) {
+
+ // add trace region
+ int col_index = path[i].col;
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = col_index-1;
+ temp.row = region_index;
+
+ trace.push_back(temp);
+
+ region_index = path[i].row;
+ region_start = col_index;
}
- cout << endl;
- }*/
+ }
+
+ // get last one
+ trace_struct temp;
+ temp.col = region_start;
+ temp.oldCol = path[path.size()-1].col;
+ temp.row = region_index;
+ trace.push_back(temp);
+ return trace;
}
catch(exception& e) {
- m->errorOut(e, "Maligner", "fillScoreMatrix");
+ m->errorOut(e, "Maligner", "mapTraceRegionsToAlignment");
exit(1);
}
}
-//***************************************************************************************************************
+/***************************************************************************************************************
vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> > ms) {
try {
}
}
-//***************************************************************************************************************
+***************************************************************************************************************
vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> path, vector<Sequence*> seqs) {
try {
exit(1);
}
}
-
+*/
//***************************************************************************************************************
-string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
+string Maligner::constructChimericSeq(vector<trace_struct> trace, vector<Sequence> 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;
}
-
+// cout << chimera << endl;
+// if (chimera != "") { chimera = chimera.substr(0, (chimera.length()-1)); } //this was introducing a fence post error
+// cout << chimera << endl;
return chimera;
}
catch(exception& e) {
//***************************************************************************************************************
-string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence*> seqs) {
+string Maligner::constructAntiChimericSeq(vector<trace_struct> trace, vector<Sequence> seqs) {
try {
string antiChimera = "";
int oppositeIndex = trace.size() - i - 1;
- string seqAlign = seqs[trace[oppositeIndex].row]->getAligned();
+ string seqAlign = seqs[trace[oppositeIndex].row].getAligned();
seqAlign = seqAlign.substr(trace[i].col, (trace[i].oldCol-trace[i].col+1));
antiChimera += seqAlign;
}
if (queryAlign.length() != chimera.length()) {
m->mothurOut("Error, alignment strings are of different lengths: "); m->mothurOutEndLine();
- m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOutEndLine();
+ m->mothurOut(toString(queryAlign.length())); m->mothurOutEndLine();
m->mothurOut(toString(chimera.length())); m->mothurOutEndLine();
return -1.0;
}
-
- int numBases = 0;
+// cout << queryAlign.length() << endl;
int numIdentical = 0;
-
+ int countA = 0;
+ int countB = 0;
for (int i = 0; i < queryAlign.length(); i++) {
- if ((isalpha(queryAlign[i])) || (isalpha(chimera[i]))) {
- numBases++;
- if (queryAlign[i] == chimera[i]) {
- numIdentical++;
+ if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
+ ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
+ else {
+
+ bool charA = false; bool charB = false;
+ if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
+ if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
+
+
+ if (charA || charB) {
+
+ if (charA) { countA++; }
+ if (charB) { countB++; }
+
+ if (queryAlign[i] == chimera[i]) {
+ numIdentical++;
+ }
}
+// cout << queryAlign[i] << '\t' << chimera[i] << '\t' << countA << '\t' << countB << endl;
+
}
}
-
+
+// cout << "pat\t" << countA << '\t' << countB << '\t' << numIdentical << endl;
+
+
+ float numBases = (countA + countB) /(float) 2;
+
if (numBases == 0) { return 0; }
+// cout << numIdentical << '\t' << numBases << endl;
+
float percentIdentical = (numIdentical/(float)numBases) * 100;
-
+
+// cout << percentIdentical << endl;
+
return percentIdentical;
}