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

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index 1d4f8c6694c570bbb7075c4150ae5125d29cc18e..a761d5a6eed759f3fd4f93d0d3500c20a4e87676 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -39,7 +39,7 @@ BinSeqCommand::BinSeqCommand(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(globaldata->getListFile()); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it       
                        }
 
                        
@@ -58,7 +58,7 @@ BinSeqCommand::BinSeqCommand(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;            }
                                }
@@ -66,7 +66,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                it = parameters.find("name");
                                //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["name"] = inputDir + it->second;             }
                                }
@@ -74,7 +74,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                                it = parameters.find("group");
                                //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["group"] = inputDir + it->second;            }
                                }
@@ -92,7 +92,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -111,7 +111,7 @@ BinSeqCommand::BinSeqCommand(string option) {
                        else if (groupfile == "not found") { groupfile = ""; }
                        
                        if (abort == false) { 
-//                             openInputFile(fastafile, in);
+//                             m->openInputFile(fastafile, in);
                                fasta = new FastaMap();
                                if (groupfile != "") {
                                        groupMap = new GroupMap(groupfile);
@@ -209,7 +209,7 @@ int BinSeqCommand::execute(){
                                userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = list->getLabel();
                                
                                delete list;
@@ -277,7 +277,7 @@ int BinSeqCommand::execute(){
 void BinSeqCommand::readNamesFile() {
        try {
                vector<string> dupNames;
-               openInputFile(namesfile, inNames);
+               m->openInputFile(namesfile, inNames);
                
                string name, names, sequence;
        
@@ -288,7 +288,7 @@ void BinSeqCommand::readNamesFile() {
                        dupNames.clear();
                        
                        //parse names into vector
-                       splitAtComma(names, dupNames);
+                       m->splitAtComma(names, dupNames);
                        
                        //store names in fasta map
                        sequence = fasta->getSequence(name);
@@ -296,7 +296,7 @@ void BinSeqCommand::readNamesFile() {
                                fasta->push_back(dupNames[i], sequence);
                        }
                
-                       gobble(inNames);
+                       m->gobble(inNames);
                }
                inNames.close();
 
@@ -312,8 +312,8 @@ int BinSeqCommand::process(ListVector* list) {
        try {
                                string binnames, name, sequence;
                                
-                               string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
-                               openOutputFile(outputFileName, out);
+                               string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
+                               m->openOutputFile(outputFileName, out);
                                
                                //save to output list of output file names
                                outputNames.push_back(outputFileName);