removed unused copy constructors and comments within comments that where causing...

[mothur.git] / trimoligos.cpp

diff --git a/trimoligos.cpp b/trimoligos.cpp
index f0b5a80880240e78674d6d97198ba7d47c8793ab..245cfdcac8819d076782b85795300c0dfb034462 100644 (file)
--- a/trimoligos.cpp
+++ b/trimoligos.cpp
@@ -12,6 +12,28 @@
 #include "needlemanoverlap.hpp"
 
 
+/********************************************************************/
+//strip, pdiffs, bdiffs, primers, barcodes, revPrimers
+TrimOligos::TrimOligos(int p, int b, int l, int s, map<string, int> pr, map<string, int> br, vector<string> r, vector<string> lk, vector<string> sp){
+       try {
+               m = MothurOut::getInstance();
+               
+               pdiffs = p;
+               bdiffs = b;
+        ldiffs = l;
+        sdiffs = s;
+               
+               barcodes = br;
+               primers = pr;
+               revPrimer = r;
+        linker = lk;
+        spacer = sp;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimOligos", "TrimOligos");
+               exit(1);
+       }
+}
 /********************************************************************/
 //strip, pdiffs, bdiffs, primers, barcodes, revPrimers
 TrimOligos::TrimOligos(int p, int b, map<string, int> pr, map<string, int> br, vector<string> r){
@@ -69,9 +91,9 @@ int TrimOligos::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
                        
                        Alignment* alignment;
                        if (barcodes.size() > 0) {
-                               map<string,int>::iterator it=barcodes.begin();
+                               map<string,int>::iterator it; 
                                
-                               for(it;it!=barcodes.end();it++){
+                               for(it=barcodes.begin();it!=barcodes.end();it++){
                                        if(it->first.length() > maxLength){
                                                maxLength = it->first.length();
                                        }
@@ -296,9 +318,9 @@ int TrimOligos::stripForward(Sequence& seq, int& group){
                        
                        Alignment* alignment;
                        if (primers.size() > 0) {
-                               map<string,int>::iterator it=primers.begin();
+                               map<string,int>::iterator it; 
                                
-                               for(it;it!=primers.end();it++){
+                               for(it=primers.begin();it!=primers.end();it++){
                                        if(it->first.length() > maxLength){
                                                maxLength = it->first.length();
                                        }
@@ -375,7 +397,7 @@ int TrimOligos::stripForward(Sequence& seq, int& group){
        }
 }
 //*******************************************************************/
-int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
+int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group, bool keepForward){
        try {
                string rawSequence = seq.getUnaligned();
                int success = pdiffs + 1;       //guilty until proven innocent
@@ -390,9 +412,9 @@ int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
                        
                        if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
                                group = it->second;
-                               seq.setUnaligned(rawSequence.substr(oligo.length()));
+                               if (!keepForward) { seq.setUnaligned(rawSequence.substr(oligo.length())); }
                                if(qual.getName() != ""){
-                                       qual.trimQScores(oligo.length(), -1);
+                                       if (!keepForward) {  qual.trimQScores(oligo.length(), -1); }
                                }
                                success = 0;
                                break;
@@ -408,9 +430,9 @@ int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
                        
                        Alignment* alignment;
                        if (primers.size() > 0) {
-                               map<string,int>::iterator it=primers.begin();
+                               map<string,int>::iterator it; 
                                
-                               for(it;it!=primers.end();it++){
+                               for(it=primers.begin();it!=primers.end();it++){
                                        if(it->first.length() > maxLength){
                                                maxLength = it->first.length();
                                        }
@@ -470,9 +492,9 @@ int TrimOligos::stripForward(Sequence& seq, QualityScores& qual, int& group){
                        else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
                        else{                                                                                                   //use the best match
                                group = minGroup;
-                               seq.setUnaligned(rawSequence.substr(minPos));
+                               if (!keepForward) { seq.setUnaligned(rawSequence.substr(minPos)); }
                                if(qual.getName() != ""){
-                                       qual.trimQScores(minPos, -1);
+                                       if (!keepForward) { qual.trimQScores(minPos, -1); }
                                }
                                success = minDiff;
                        }
@@ -550,6 +572,129 @@ bool TrimOligos::stripReverse(Sequence& seq){
                exit(1);
        }
 }
+//******************************************************************/
+bool TrimOligos::stripLinker(Sequence& seq, QualityScores& qual){
+       try {
+               string rawSequence = seq.getUnaligned();
+               bool success = 0;       //guilty until proven innocent
+               
+               for(int i=0;i<linker.size();i++){
+                       string oligo = linker[i];
+                       
+                       if(rawSequence.length() < oligo.length()){
+                               success = 0;
+                               break;
+                       }
+                       
+                       if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+                               seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+                               if(qual.getName() != ""){
+                                       qual.trimQScores(-1, rawSequence.length()-oligo.length());
+                               }
+                               success = 1;
+                               break;
+                       }
+               }       
+               return success;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimOligos", "stripLinker");
+               exit(1);
+       }
+}
+//******************************************************************/
+bool TrimOligos::stripLinker(Sequence& seq){
+       try {
+               
+               string rawSequence = seq.getUnaligned();
+               bool success = 0;       //guilty until proven innocent
+               
+               for(int i=0;i<linker.size();i++){
+                       string oligo = linker[i];
+                       
+                       if(rawSequence.length() < oligo.length()){
+                               success = 0;
+                               break;
+                       }
+                       
+                       if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+                               seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+                               success = 1;
+                               break;
+                       }
+               }       
+               
+               return success;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimOligos", "stripLinker");
+               exit(1);
+       }
+}
+
+//******************************************************************/
+bool TrimOligos::stripSpacer(Sequence& seq, QualityScores& qual){
+       try {
+               string rawSequence = seq.getUnaligned();
+               bool success = 0;       //guilty until proven innocent
+               
+               for(int i=0;i<spacer.size();i++){
+                       string oligo = spacer[i];
+                       
+                       if(rawSequence.length() < oligo.length()){
+                               success = 0;
+                               break;
+                       }
+                       
+                       if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+                               seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+                               if(qual.getName() != ""){
+                                       qual.trimQScores(-1, rawSequence.length()-oligo.length());
+                               }
+                               success = 1;
+                               break;
+                       }
+               }       
+               return success;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimOligos", "stripSpacer");
+               exit(1);
+       }
+}
+//******************************************************************/
+bool TrimOligos::stripSpacer(Sequence& seq){
+       try {
+               
+               string rawSequence = seq.getUnaligned();
+               bool success = 0;       //guilty until proven innocent
+               
+               for(int i=0;i<spacer.size();i++){
+                       string oligo = spacer[i];
+                       
+                       if(rawSequence.length() < oligo.length()){
+                               success = 0;
+                               break;
+                       }
+                       
+                       if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
+                               seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
+                               success = 1;
+                               break;
+                       }
+               }       
+               
+               return success;
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimOligos", "stripSpacer");
+               exit(1);
+       }
+}
 
 //******************************************************************/
 bool TrimOligos::compareDNASeq(string oligo, string seq){