+/*
+ * qualityscores.cpp
+ * Mothur
+ *
+ * Created by Pat Schloss on 7/12/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "qualityscores.h"
+
+/**************************************************************************************************/
+
+QualityScores::QualityScores(){
+ try {
+ m = MothurOut::getInstance();
+ seqName = "";
+ seqLength = -1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "QualityScores");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+QualityScores::QualityScores(ifstream& qFile){
+ try {
+
+ m = MothurOut::getInstance();
+
+ seqName = "";
+ seqLength = -1;
+ int score;
+
+ string line;
+ getline(qFile, line);
+ istringstream nameStream(line);
+
+ nameStream >> seqName;
+ seqName = seqName.substr(1);
+
+ getline(qFile, line);
+ istringstream qualStream(line);
+
+ while(qualStream){
+ qualStream >> score;
+ qScores.push_back(score);
+ }
+ qScores.pop_back();
+
+ seqLength = qScores.size();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "QualityScores");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
+string QualityScores::getName(){
+
+ try {
+ return seqName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "getName");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::printQScores(ofstream& qFile){
+ try {
+
+ double aveQScore = calculateAverage();
+
+ qFile << '>' << seqName << '\t' << aveQScore << endl;
+
+ for(int i=0;i<seqLength;i++){
+ qFile << qScores[i] << ' ';
+ }
+ qFile << endl;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "printQScores");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::trimQScores(int start, int end){
+ try {
+ vector<int> hold;
+
+ if(end == -1){
+ hold = vector<int>(qScores.begin()+start, qScores.end());
+ qScores = hold;
+ }
+ if(start == -1){
+ hold = vector<int>(qScores.begin(), qScores.begin()+end); //not sure if indexing is correct
+ qScores = hold;
+ }
+
+ seqLength = qScores.size();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "trimQScores");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void QualityScores::flipQScores(){
+ try {
+
+ vector<int> temp = qScores;
+ for(int i=0;i<seqLength;i++){
+ qScores[seqLength - i - 1] = temp[i];
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "flipQScores");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+bool QualityScores::stripQualThreshold(Sequence& sequence, double qThreshold){
+ try {
+ string rawSequence = sequence.getUnaligned();
+ int seqLength = sequence.getNumBases();
+
+ if(seqName != sequence.getName()){
+ m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
+ m->mothurOutEndLine();
+ }
+
+ int end;
+ for(int i=0;i<seqLength;i++){
+ end = i;
+ if(qScores[i] < qThreshold){
+ break;
+ }
+ }
+
+ sequence.setUnaligned(rawSequence.substr(0,end));
+ trimQScores(-1, end);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "flipQScores");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
+bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshold){
+ try {
+ string rawSequence = sequence.getUnaligned();
+ int seqLength = sequence.getNumBases();
+
+ if(seqName != sequence.getName()){
+ m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
+ m->mothurOutEndLine();
+ }
+
+ int end = -1;
+ double rollingSum = 0.0000;
+
+ for(int i=0;i<seqLength;i++){
+
+ rollingSum += (double)qScores[i];
+
+ if(rollingSum / (double)(i+1) < qThreshold){
+ end = i;
+// cout << i+1 << '\t' << seqName << '\t' << rollingSum / (double)(i+1) << endl;
+ break;
+ }
+ }
+
+ if(end == -1){ end = seqLength; }
+
+ sequence.setUnaligned(rawSequence.substr(0,end));
+ trimQScores(-1, end);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "flipQScores");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
+bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int windowSize, double qThreshold){
+ try {
+ string rawSequence = sequence.getUnaligned();
+ int seqLength = sequence.getNumBases();
+
+ if(seqName != sequence.getName()){
+ m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
+ m->mothurOutEndLine();
+ }
+
+ int end = windowSize;
+ int start = 0;
+
+
+ while(start < seqLength){
+ double windowSum = 0.0000;
+
+ for(int i=start;i<end;i++){
+ windowSum += qScores[i];
+ }
+ double windowAverage = windowSum / (double)(end-start);
+
+ if(windowAverage < qThreshold){
+ end = start;
+ break;
+ }
+ start += stepSize;
+ end = start + windowSize;
+ if(end >= seqLength){ end = seqLength - 1; }
+ }
+
+
+ if(end == -1){ end = seqLength; }
+
+ sequence.setUnaligned(rawSequence.substr(0,end));
+ trimQScores(-1, end);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "QualityScores", "flipQScores");
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
+double QualityScores::calculateAverage(){
+
+ double aveQScore = 0.0000;
+
+ for(int i=0;i<seqLength;i++){
+ aveQScore += (double) qScores[i];
+ }
+ aveQScore /= (double) seqLength;
+
+ return aveQScore;
+}
+
+/**************************************************************************************************/
+
+bool QualityScores::cullQualAverage(Sequence& sequence, double qAverage){
+ try {
+ string rawSequence = sequence.getUnaligned();
+ bool success = 0; //guilty until proven innocent
+
+ if(seqName != sequence.getName()) {
+ m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
+ m->mothurOutEndLine();
+ }
+
+ double aveQScore = calculateAverage();
+
+ if(aveQScore >= qAverage) { success = 1; }
+ else { success = 0; }
+
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/