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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 613f9b7d6f13b04dec679a162ba71faf25326c65..0f4c89a28ce7ca2b01eae1de815bebfb78ff6a77 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -68,7 +68,7 @@ AlignCommand::AlignCommand(string option)  {
 
                                //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;         }
                                }
@@ -86,12 +86,12 @@ AlignCommand::AlignCommand(string option)  {
                        candidateFileName = validParameter.validFile(parameters, "candidate", false);
                        if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(candidateFileName, candidateFileNames);
+                               m->splitAtDash(candidateFileName, candidateFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < candidateFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(candidateFileNames[i]);
+                                               string path = m->hasPath(candidateFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
                                        }
@@ -99,14 +99,14 @@ AlignCommand::AlignCommand(string option)  {
                                        int ableToOpen;
                                        ifstream in;
 
-                                       ableToOpen = openInputFile(candidateFileNames[i], in, "noerror");
+                                       ableToOpen = m->openInputFile(candidateFileNames[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(candidateFileNames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
                                                        m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        candidateFileNames[i] = tryPath;
                                                }
                                        }
@@ -147,7 +147,7 @@ AlignCommand::AlignCommand(string option)  {
                        convert(temp, processors); 
                        
                        temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
-                       flip = isTrue(temp); 
+                       flip = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
                        convert(temp, threshold); 
@@ -230,10 +230,10 @@ int AlignCommand::execute(){
                        
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
-                       if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
-                       string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
-                       string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
-                       string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
+                       if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
+                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
+                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
+                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";
                        bool hasAccnos = true;
                        
                        int numFastaSeqs = 0;
@@ -279,7 +279,7 @@ int AlignCommand::execute(){
                                
                                if (pid == 0) { //you are the root process 
                                        
-                                       MPIPos = setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
+                                       MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
                                        
                                        //send file positions to all processes
                                        for(int i = 1; i < processors; i++) { 
@@ -346,8 +346,9 @@ int AlignCommand::execute(){
                                }
                                
 #else
-               vector<unsigned long int> positions = divideFile(candidateFileNames[s], processors);
-                                                       
+
+               vector<unsigned long int> positions = m->divideFile(candidateFileNames[s], processors);
+                               
                for (int i = 0; i < (positions.size()-1); i++) {
                        lines.push_back(new linePair(positions[i], positions[(i+1)]));
                }       
@@ -358,7 +359,7 @@ int AlignCommand::execute(){
                                if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
                                
                                //delete accnos file if its blank else report to user
-                               if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
+                               if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                                else { 
                                        m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
                                        if (!flip) {
@@ -386,7 +387,7 @@ int AlignCommand::execute(){
                                vector<string> nonBlankAccnosFiles;
                                //delete blank accnos files generated with multiple processes
                                for(int i=0;i<processors;i++){  
-                                       if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
+                                       if (!(m->isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
                                                nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
                                        }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
                                }
@@ -414,7 +415,7 @@ int AlignCommand::execute(){
                        if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
                        
                        //delete accnos file if its blank else report to user
-                       if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
+                       if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                        else { 
                                m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
                                if (!flip) {
@@ -466,15 +467,15 @@ int AlignCommand::execute(){
 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
        try {
                ofstream alignmentFile;
-               openOutputFile(alignFName, alignmentFile);
+               m->openOutputFile(alignFName, alignmentFile);
                
                ofstream accnosFile;
-               openOutputFile(accnosFName, accnosFile);
+               m->openOutputFile(accnosFName, accnosFile);
                
                NastReport report(reportFName);
                
                ifstream inFASTA;
-               openInputFile(filename, inFASTA);
+               m->openInputFile(filename, inFASTA);
 
                inFASTA.seekg(filePos->start);
 
@@ -485,7 +486,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        
                        if (m->control_pressed) {  return 0; }
                        
-                       Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
+                       Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
        
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
@@ -769,7 +770,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                                //pass numSeqs to parent
                                ofstream out;
                                string tempFile = alignFileName + toString(getpid()) + ".num.temp";
-                               openOutputFile(tempFile, out);
+                               m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();
                                
@@ -786,7 +787,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                for (int i = 0; i < processIDS.size(); i++) {
                        ifstream in;
                        string tempFile =  alignFileName + 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());
                }
@@ -806,8 +807,8 @@ void AlignCommand::appendAlignFiles(string temp, string filename) {
                
                ofstream output;
                ifstream input;
-               openOutputFileAppend(filename, output);
-               openInputFile(temp, input);
+               m->openOutputFileAppend(filename, output);
+               m->openInputFile(temp, input);
                
                while(char c = input.get()){
                        if(input.eof())         {       break;                  }
@@ -829,8 +830,8 @@ void AlignCommand::appendReportFiles(string temp, string filename) {
                
                ofstream output;
                ifstream input;
-               openOutputFileAppend(filename, output);
-               openInputFile(temp, input);
+               m->openOutputFileAppend(filename, output);
+               m->openInputFile(temp, input);
 
                while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line