added modify names parameter to set.dir

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 5bfdc44128dd300cc22a33e8fa696d032dcab774..b9f2434d19d4cc842bfac1dce4f6de5a0d1b742d 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -74,7 +74,7 @@ int Pintail::doPrep() {
        #ifdef USE_MPI
                //do nothing
        #else
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        //find breakup of templatefile for quantiles
                        if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
                        else { 
@@ -92,7 +92,7 @@ int Pintail::doPrep() {
                m->mothurOut("Getting conservation... "); cout.flush();
                if (consfile == "") { 
                        m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
-                       probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName)); 
+                       probabilityProfile = decalc->calcFreq(templateSeqs, templateFileName); 
                        if (m->control_pressed) {  return 0;  }
                        m->mothurOut("Done."); m->mothurOutEndLine();
                }else                           {   probabilityProfile = readFreq();    m->mothurOut("Done.");            }
@@ -170,20 +170,20 @@ int Pintail::doPrep() {
                        string noOutliers, outliers;
                        
                        if ((!filter) && (seqMask == "")) {
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
+                               noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.quan";
                        }else if ((!filter) && (seqMask != "")) { 
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
+                               noOutliers =m->getRootName(m->getSimpleName(templateFileName)) + "pintail.masked.quan";
                        }else if ((filter) && (seqMask != "")) { 
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "masked.quan";
+                               noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "masked.quan";
                        }else if ((filter) && (seqMask == "")) { 
-                               noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
+                               noOutliers = m->getRootName(m->getSimpleName(templateFileName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastafile)) + "quan";
                        }
 
                        decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
                        
                        if (m->control_pressed) {  return 0;  }
                
-                       string outputString = "";
+                       string outputString = "#" + m->getVersion() + "\n";
                        
                        //adjust quantiles
                        for (int i = 0; i < quantilesMembers.size(); i++) {
@@ -249,8 +249,9 @@ int Pintail::doPrep() {
        }
 }
 //***************************************************************************************************************
-int Pintail::print(ostream& out, ostream& outAcc) {
+Sequence Pintail::print(ostream& out, ostream& outAcc) {
        try {
+               
                int index = ceil(deviation);
                
                //is your DE value higher than the 95%
@@ -279,7 +280,7 @@ int Pintail::print(ostream& out, ostream& outAcc) {
                for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
                out << endl;
                
-               return 0;
+               return *querySeq;
                
        }
        catch(exception& e) {
@@ -289,9 +290,9 @@ int Pintail::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Pintail::print(MPI_File& out, MPI_File& outAcc) {
+Sequence Pintail::print(MPI_File& out, MPI_File& outAcc) {
        try {
-               bool results = false;
+               
                string outputString = "";
                int index = ceil(deviation);
                
@@ -319,7 +320,7 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
                        MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
                        delete buf;
 
-                       results = true;
+                       return *querySeq;
                }
                outputString += "Observed\t";
                
@@ -339,7 +340,7 @@ int Pintail::print(MPI_File& out, MPI_File& outAcc) {
                MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
                delete buf2;
                
-               return results;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "Pintail", "print");
@@ -449,6 +450,9 @@ vector<float> Pintail::readFreq() {
                if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
                istringstream iss (tempBuf,istringstream::in);
                
+               //read version
+               string line = m->getline(iss); m->gobble(iss);
+               
                while(!iss.eof()) {
                        iss >> pos >> num;
        
@@ -463,7 +467,7 @@ vector<float> Pintail::readFreq() {
                                prob.push_back(Pi);  
                        }
                        
-                       gobble(iss);
+                       m->gobble(iss);
                }
        
                MPI_File_close(&inMPI);
@@ -471,7 +475,10 @@ vector<float> Pintail::readFreq() {
        #else   
 
                ifstream in;
-               openInputFile(consfile, in);
+               m->openInputFile(consfile, in);
+               
+               //read version
+               string line = m->getline(in); m->gobble(in);
                                
                while(!in.eof()){
                        
@@ -488,7 +495,7 @@ vector<float> Pintail::readFreq() {
                                prob.push_back(Pi);  
                        }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                
@@ -522,8 +529,8 @@ Sequence* Pintail::findPairs(Sequence* q) {
 //**************************************************************************************************
 void Pintail::createProcessesQuan() {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+               int process = 1;
                vector<int> processIDS;
                                
                //loop through and create all the processes you want
@@ -540,8 +547,7 @@ void Pintail::createProcessesQuan() {
                                //write out data to file so parent can read it
                                ofstream out;
                                string s = toString(getpid()) + ".temp";
-                               openOutputFile(s, out);
-                               
+                               m->openOutputFile(s, out);
                                                                
                                //output observed distances
                                for (int i = 0; i < quantilesMembers.size(); i++) {
@@ -555,20 +561,27 @@ void Pintail::createProcessesQuan() {
                                out.close();
                                
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
+               //parent does its part
+               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[0]->start, templateLines[0]->end);
+               
                //force parent to wait until all the processes are done
-               for (int i=0;i<processors;i++) { 
+               for (int i=0;i<(processors-1);i++) { 
                        int temp = processIDS[i];
                        wait(&temp);
                }
 
                //get data created by processes
-               for (int i=0;i<processors;i++) { 
+               for (int i=0;i<(processors-1);i++) { 
                        ifstream in;
                        string s = toString(processIDS[i]) + ".temp";
-                       openInputFile(s, in);
+                       m->openInputFile(s, in);
                        
                        vector< vector<float> > quan; 
                        quan.resize(100);
@@ -578,7 +591,7 @@ void Pintail::createProcessesQuan() {
                                int num;
                                in >> num; 
                                
-                               gobble(in);
+                               m->gobble(in);
 
                                vector<float> q;  float w; 
                                for (int j = 0; j < num; j++) {
@@ -587,7 +600,7 @@ void Pintail::createProcessesQuan() {
                                }
 
                                quan[h] = q;
-                               gobble(in);
+                               m->gobble(in);
                        }
                        
        
@@ -599,9 +612,9 @@ void Pintail::createProcessesQuan() {
                        }
                                        
                        in.close();
-                       remove(s.c_str());
+                       m->mothurRemove(s);
                }
-               
+
 #else
                quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 #endif         
@@ -648,6 +661,9 @@ vector< vector<float> > Pintail::readQuantiles() {
                istringstream iss (tempBuf,istringstream::in);
                delete buffer;
                
+               //read version
+               string line = m->getline(iss); m->gobble(iss);
+               
                while(!iss.eof()) {
                        iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine; 
                        
@@ -662,7 +678,7 @@ vector< vector<float> > Pintail::readQuantiles() {
                        
                        quan.push_back(temp);  
                        
-                       gobble(iss);
+                       m->gobble(iss);
                }
        
                MPI_File_close(&inMPI);
@@ -670,7 +686,10 @@ vector< vector<float> > Pintail::readQuantiles() {
        #else   
 
                ifstream in;
-               openInputFile(quanfile, in);
+               m->openInputFile(quanfile, in);
+               
+               //read version
+               string line = m->getline(in); m->gobble(in);
                        
                while(!in.eof()){
                        
@@ -687,7 +706,7 @@ vector< vector<float> > Pintail::readQuantiles() {
                        
                        quan.push_back(temp);  
        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
        #endif
@@ -737,7 +756,7 @@ void Pintail::printQuanFile(string file, string outputString) {
                        //delete FileName;
                #else
                        ofstream outQuan;
-                       openOutputFile(file, outQuan);
+                       m->openOutputFile(file, outQuan);
                        
                        outQuan << outputString;