moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 5295eace3546e14db6488ceb41e144915531c830..1bfdafeaa5f6540e4e8254572b0202c81c1a0325 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -102,8 +102,14 @@ int ChimeraSlayer::doPrep() {
                        //leftside
                        kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
                        ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
+                       bool needToGenerateLeft = true;
                        
-                       if(!kmerFileTestLeft){  
+                       if(kmerFileTestLeft){   
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+                               if (GoodFile) {  needToGenerateLeft = false;    }
+                       }
+                       
+                       if(needToGenerateLeft){ 
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
                                        
@@ -127,8 +133,14 @@ int ChimeraSlayer::doPrep() {
                        //rightside
                        kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
                        ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+                       bool needToGenerateRight = true;
+                       
+                       if(kmerFileTestRight){  
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+                               if (GoodFile) {  needToGenerateRight = false;   }
+                       }
                        
-                       if(!kmerFileTestRight){ 
+                       if(needToGenerateRight){        
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
                                        if (m->control_pressed) { return 0; } 
@@ -196,7 +208,7 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                                }
                        }
                        
-                       printBlock(chimeraResults[0], out);
+                       printBlock(chimeraResults[0], chimeraFlag, out);
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
@@ -240,7 +252,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                }
                        }
                        
-                       outputString = getBlock(chimeraResults[0]);
+                       outputString = getBlock(chimeraResults[0], chimeraFlag);
                        outputString += "\n";
        //cout << outputString << endl;         
                        //write to output file
@@ -387,7 +399,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
        }
 }
 //***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
        try {
        //out << ":)\n";
                
@@ -399,7 +411,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
                out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
                out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
                
-               out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+               out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
                
                //out << "Similarity of parents: " << data.ab << endl;
                //out << "Similarity of query to parentA: " << data.qa << endl;
@@ -422,7 +434,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
        }
 }
 //***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
        try {
                
                string outputString = "";
@@ -433,7 +445,7 @@ string ChimeraSlayer::getBlock(data_struct data){
                outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
                outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
                
-               outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+               outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
                
                return outputString;
        }