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

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index e596f672ed45f8f9f977e5264417e6781b959c38..531abc52561db977aa58fc274c7d7e91ee1d4a8d 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -18,7 +18,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                        
                /************calculate the probablity that each word will be in a specific taxonomy*************/
                string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
-               string tempfileroot = getRootName(getSimpleName(tempFile));
+               string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
                string phyloTreeName = tfileroot + "tree.train";
                string phyloTreeSumName = tfileroot + "tree.sum";
                string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
@@ -90,14 +90,14 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                #endif
 
                                
-                               openOutputFile(probFileName, out);
+                               m->openOutputFile(probFileName, out);
                                
                                //output mothur version
                                out << "#" << m->getVersion() << endl;
                                
                                out << numKmers << endl;
                                
-                               openOutputFile(probFileName2, out2);
+                               m->openOutputFile(probFileName2, out2);
                                
                                //output mothur version
                                out2 << "#" << m->getVersion() << endl;
@@ -408,8 +408,8 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        MPI_File_open(MPI_COMM_WORLD, inFileName2, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI2);  //comm, filename, mode, info, filepointer
 
                        if (pid == 0) {
-                               positions = setFilePosEachLine(inNumName, num);
-                               positions2 = setFilePosEachLine(inName, num2);
+                               positions = m->setFilePosEachLine(inNumName, num);
+                               positions2 = m->setFilePosEachLine(inName, num2);
                                
                                for(int i = 1; i < processors; i++) { 
                                        MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
@@ -515,9 +515,9 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
                        //read version
-                       string line = getline(in); gobble(in);
+                       string line = m->getline(in); m->gobble(in);
                        
-                       in >> numKmers; gobble(in);
+                       in >> numKmers; m->gobble(in);
                        
                        //initialze probabilities
                        wordGenusProb.resize(numKmers);
@@ -530,12 +530,12 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        vector<float> zeroCountProb; zeroCountProb.resize(numKmers);            
                        
                        //read version
-                       string line2 = getline(inNum); gobble(inNum);
+                       string line2 = m->getline(inNum); m->gobble(inNum);
                        
                        while (inNum) {
                                inNum >> zeroCountProb[count] >> num[count];  
                                count++;
-                               gobble(inNum);
+                               m->gobble(inNum);
                        }
                        inNum.close();
                
@@ -553,7 +553,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                                        wordGenusProb[kmer][name] = prob;
                                }
                                
-                               gobble(in);
+                               m->gobble(in);
                        }
                        in.close();
                        
@@ -571,10 +571,10 @@ bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file
                bool good = true;
                
                vector<string> lines;
-               lines.push_back(getline(file1));  
-               lines.push_back(getline(file2)); 
-               lines.push_back(getline(file3)); 
-               lines.push_back(getline(file4)); 
+               lines.push_back(m->getline(file1));  
+               lines.push_back(m->getline(file2)); 
+               lines.push_back(m->getline(file3)); 
+               lines.push_back(m->getline(file4)); 
 
                //before we added this check
                if ((lines[0][0] != '#') || (lines[1][0] != '#') || (lines[2][0] != '#') || (lines[3][0] != '#')) {  good = false;  }
@@ -586,12 +586,12 @@ bool Bayesian::checkReleaseDate(ifstream& file1, ifstream& file2, ifstream& file
                        string version = m->getVersion();
                        
                        vector<string> versionVector;
-                       splitAtChar(version, versionVector, '.');
+                       m->splitAtChar(version, versionVector, '.');
                        
                        //check each files version
                        for (int i = 0; i < lines.size(); i++) { 
                                vector<string> linesVector;
-                               splitAtChar(lines[i], linesVector, '.');
+                               m->splitAtChar(lines[i], linesVector, '.');
                        
                                if (versionVector.size() != linesVector.size()) { good = false; break; }
                                else {