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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index de6f438d81f7fcd62e111d97a02e87d63aad1e66..4d99aa4d32a19b3f8db893c9f30186ad878a50d5 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -41,7 +41,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                it = parameters.find("template");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       string path = hasPath(it->second);
+                                       string 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;         }
                                }
@@ -51,12 +51,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", false);
                        if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check 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];               }
                                        }
@@ -64,14 +64,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(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;
                                                }
                                        }
@@ -99,12 +99,12 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", false);
                        if (namefile == "not found") { namefile = ""; }
                        else { 
-                               splitAtDash(namefile, nameFileNames);
+                               m->splitAtDash(namefile, nameFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < nameFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(nameFileNames[i]);
+                                               string path = m->hasPath(nameFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
                                        }
@@ -112,14 +112,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                        int ableToOpen;
                                        ifstream in;
                                        
-                                       ableToOpen = openInputFile(nameFileNames[i], in, "noerror");
+                                       ableToOpen = m->openInputFile(nameFileNames[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(nameFileNames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
                                                        m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        nameFileNames[i] = tryPath;
                                                }
                                        }
@@ -150,7 +150,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        convert(temp, ksize);
                        
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
-                       svg = isTrue(temp);
+                       svg = m->isTrue(temp);
                        if (nameFileNames.size() != 0) { svg = true; }
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
@@ -217,7 +217,7 @@ int ChimeraCheckCommand::execute(){
 
                        if (m->control_pressed) { delete chimera;       return 0;       }
                        
-                       string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
+                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
                        outputNames.push_back(outputFileName);
                        
                #ifdef USE_MPI
@@ -248,7 +248,7 @@ int ChimeraCheckCommand::execute(){
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } delete chimera; return 0;  }
                                
                                if (pid == 0) { //you are the root process 
-                                       MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
+                                       MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
                                        
                                        //send file positions to all processes
                                        for(int j = 1; j < processors; j++) { 
@@ -299,7 +299,7 @@ int ChimeraCheckCommand::execute(){
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
                        
-                       vector<unsigned long int> positions = divideFile(fastaFileNames[i], processors);
+                       vector<unsigned long int> positions = m->divideFile(fastaFileNames[i], processors);
                                
                        for (int s = 0; s < (positions.size()-1); s++) {
                                lines.push_back(new linePair(positions[s], positions[(s+1)]));
@@ -321,7 +321,7 @@ int ChimeraCheckCommand::execute(){
                                                
                                        //append output files
                                        for(int j=1;j<processors;j++){
-                                               appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
+                                               m->appendFiles((outputFileName + toString(processIDS[j]) + ".temp"), outputFileName);
                                                remove((outputFileName + toString(processIDS[j]) + ".temp").c_str());
                                        }
                                        
@@ -365,12 +365,12 @@ int ChimeraCheckCommand::execute(){
 int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string filename){
        try {
                ofstream out;
-               openOutputFile(outputFName, out);
+               m->openOutputFile(outputFName, out);
                
                ofstream out2;
                
                ifstream inFASTA;
-               openInputFile(filename, inFASTA);
+               m->openInputFile(filename, inFASTA);
 
                inFASTA.seekg(filePos->start);
 
@@ -381,7 +381,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 
                        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
                                //find chimeras
@@ -437,7 +437,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                        istringstream iss (tempBuf,istringstream::in);
                        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
                                //find chimeras
@@ -484,7 +484,7 @@ int ChimeraCheckCommand::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();
                                
@@ -501,7 +501,7 @@ int ChimeraCheckCommand::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());
                }