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

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 4077619b4a515495cc00489b3b403d74180feba4..5dbcdec9cb90f2082912017064f876fd6210e464 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -43,7 +43,7 @@ SeqSummaryCommand::SeqSummaryCommand(string option)  {
                                it = parameters.find("fasta");
                                //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["fasta"] = inputDir + it->second;            }
                                }
@@ -57,7 +57,7 @@ SeqSummaryCommand::SeqSummaryCommand(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       
                        }
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = "1";                             }
@@ -98,7 +98,7 @@ int SeqSummaryCommand::execute(){
                
                if (abort == true) { return 0; }
                
-               string summaryFile = outputDir + getSimpleName(fastafile) + ".summary";
+               string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
                                
                int numSeqs = 0;
                
@@ -143,7 +143,7 @@ int SeqSummaryCommand::execute(){
                                                MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
                                                delete buf2;
                                                
-                                               MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+                                               MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
                                        
                                                for(int i = 1; i < processors; i++) { 
                                                        MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
@@ -224,7 +224,7 @@ int SeqSummaryCommand::execute(){
                                
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
-                       vector<unsigned long int> positions = divideFile(fastafile, processors);
+                       vector<unsigned long int> positions = m->divideFile(fastafile, processors);
                                
                        for (int i = 0; i < (positions.size()-1); i++) {
                                lines.push_back(new linePair(positions[i], positions[(i+1)]));
@@ -239,7 +239,7 @@ int SeqSummaryCommand::execute(){
                                        rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
                                        //append files
                                        for(int i=1;i<processors;i++){
-                                               appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
+                                               m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
                                                remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
                                        }
                                }
@@ -308,7 +308,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
        try {
                
                ofstream outSummary;
-               openOutputFile(sumFile, outSummary);
+               m->openOutputFile(sumFile, outSummary);
                
                //print header if you are process 0
                if (filePos->start == 0) {
@@ -316,7 +316,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                }
                                
                ifstream in;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                                
                in.seekg(filePos->start);
 
@@ -327,7 +327,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                
                        if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
                                        
-                       Sequence current(in); gobble(in);
+                       Sequence current(in); m->gobble(in);
        
                        if (current.getName() != "") {
                                startPosition.push_back(current.getStartPos());
@@ -437,7 +437,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                                //pass numSeqs to parent
                                ofstream out;
                                string tempFile = fastafile + toString(getpid()) + ".num.temp";
-                               openOutputFile(tempFile, out);
+                               m->openOutputFile(tempFile, out);
                                
                                out << num << endl;
                                for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
@@ -462,15 +462,15 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                for (int i = 0; i < processIDS.size(); i++) {
                        string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
                        ifstream in;
-                       openInputFile(tempFilename, in);
+                       m->openInputFile(tempFilename, in);
                        
                        int temp, tempNum;
-                       in >> tempNum; gobble(in); num += tempNum;
-                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               gobble(in);
-                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               gobble(in);
-                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               gobble(in);
-                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               gobble(in);
-                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               gobble(in);
+                       in >> tempNum; m->gobble(in); num += tempNum;
+                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
+                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
+                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
+                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
+                       for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
                                
                        in.close();
                        remove(tempFilename.c_str());