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

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 35f3b988f86ec2e868d8eb5a825efc853e1662e7..8a80d4dc2517309b3778186ed6ac4e5c937a73f1 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -45,7 +45,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                it = parameters.find("template");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["template"] = inputDir + it->second;         }
                                }
@@ -56,12 +56,12 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", false);
                        if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(fastafile, fastaFileNames);
+                               m->splitAtDash(fastafile, fastaFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < fastaFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(fastaFileNames[i]);
+                                               string path = m->hasPath(fastaFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
                                        }
@@ -69,14 +69,14 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                        int ableToOpen;
                                        ifstream in;
                                        
-                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                                       ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
                                
                                        //if you can't open it, try default location
                                        if (ableToOpen == 1) {
                                                if (m->getDefaultPath() != "") { //default path is set
-                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
                                                        m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
@@ -97,7 +97,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
 
                        templatefile = validParameter.validFile(parameters, "template", true);
@@ -138,7 +138,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        convert(temp, parents); 
                        
                        temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
-                       realign = isTrue(temp); 
+                       realign = m->isTrue(temp); 
                        
                        search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
                        
@@ -219,8 +219,8 @@ int ChimeraSlayerCommand::execute(){
                        
                        chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);   
                                                        
-                       string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
-                       string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
                        
                        if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
                        
@@ -277,7 +277,7 @@ int ChimeraSlayerCommand::execute(){
                                        MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
                                        delete buf2;
 
-                                       MPIPos = setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
+                                       MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
                                        
                                        //send file positions to all processes
                                        for(int i = 1; i < processors; i++) { 
@@ -319,13 +319,13 @@ int ChimeraSlayerCommand::execute(){
                                
                #else
                        ofstream outHeader;
-                       string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
-                       openOutputFile(tempHeader, outHeader);
+                       string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
+                       m->openOutputFile(tempHeader, outHeader);
                        
                        chimera->printHeader(outHeader);
                        outHeader.close();
                        
-                       vector<unsigned long int> positions = divideFile(fastaFileNames[s], processors);
+                       vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
                                
                        for (int i = 0; i < (positions.size()-1); i++) {
                                lines.push_back(new linePair(positions[i], positions[(i+1)]));
@@ -348,13 +348,13 @@ int ChimeraSlayerCommand::execute(){
                                                
                                        //append output files
                                        for(int i=1;i<processors;i++){
-                                               appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
+                                               m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
                                                remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
                                        }
                                        
                                        //append output files
                                        for(int i=1;i<processors;i++){
-                                               appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+                                               m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
                                                remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
                                        }
                                        
@@ -368,7 +368,7 @@ int ChimeraSlayerCommand::execute(){
                                
                        #endif
                        
-                       appendFiles(outputFileName, tempHeader);
+                       m->appendFiles(outputFileName, tempHeader);
                
                        remove(outputFileName.c_str());
                        rename(tempHeader.c_str(), outputFileName.c_str());
@@ -403,13 +403,13 @@ int ChimeraSlayerCommand::execute(){
 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){
        try {
                ofstream out;
-               openOutputFile(outputFName, out);
+               m->openOutputFile(outputFName, out);
                
                ofstream out2;
-               openOutputFile(accnos, out2);
+               m->openOutputFile(accnos, out2);
                
                ifstream inFASTA;
-               openInputFile(filename, inFASTA);
+               m->openInputFile(filename, inFASTA);
 
                inFASTA.seekg(filePos->start);
 
@@ -420,7 +420,7 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f
                
                        if (m->control_pressed) {       return 1;       }
                
-                       Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
+                       Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
                                
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
                                
@@ -483,7 +483,7 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
 
                        delete buf4;
 
-                       Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
+                       Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
                
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
                                
@@ -539,7 +539,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                                //pass numSeqs to parent
                                ofstream out;
                                string tempFile = outputFileName + toString(getpid()) + ".num.temp";
-                               openOutputFile(tempFile, out);
+                               m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();
                                
@@ -556,7 +556,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                for (int i = 0; i < processIDS.size(); i++) {
                        ifstream in;
                        string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
-                       openInputFile(tempFile, in);
+                       m->openInputFile(tempFile, in);
                        if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
                        in.close(); remove(tempFile.c_str());
                }