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

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 00f04b08d6a6d42437faced7e76c736e6075d5cb..0e23461c39803cd49cac67023d6c99255284f851 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -45,7 +45,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                it = parameters.find("list");
                                //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["list"] = inputDir + it->second;             }
                                }
@@ -53,7 +53,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(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;             }
                                }
@@ -61,7 +61,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                it = parameters.find("taxonomy");
                                //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["taxonomy"] = inputDir + it->second;         }
                                }
@@ -89,7 +89,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; allLines = 1;  }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -97,7 +97,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        convert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "probs", false);                                    if (temp == "not found"){       temp = "true";                  }
-                       probs = isTrue(temp);
+                       probs = m->isTrue(temp);
                        
                        
                        if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true;  }
@@ -171,7 +171,7 @@ int ClassifyOtuCommand::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;
@@ -241,18 +241,18 @@ int ClassifyOtuCommand::readNamesFile() {
        try {
                
                ifstream inNames;
-               openInputFile(namefile, inNames);
+               m->openInputFile(namefile, inNames);
                
                string name, names;
        
                while(inNames){
                        inNames >> name;                        //read from first column  A
                        inNames >> names;               //read from second column  A,B,C,D
-                       gobble(inNames);
+                       m->gobble(inNames);
                        
                        //parse names into vector
                        vector<string> theseNames;
-                       splitAtComma(names, theseNames);
+                       m->splitAtComma(names, theseNames);
 
                        for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = name;  }
                        
@@ -272,13 +272,13 @@ int ClassifyOtuCommand::readTaxonomyFile() {
        try {
                
                ifstream in;
-               openInputFile(taxfile, in);
+               m->openInputFile(taxfile, in);
                
                string name, tax;
        
                while(!in.eof()){
                        in >> name >> tax;              
-                       gobble(in);
+                       m->gobble(in);
                        
                        //are there confidence scores, if so remove them
                        if (tax.find_first_of('(') != -1) {  removeConfidences(tax);    }
@@ -306,7 +306,7 @@ string ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList,
 
                //parse names into vector
                string binnames = thisList->get(bin);
-               splitAtComma(binnames, names);
+               m->splitAtComma(binnames, names);
 
                //create a tree containing sequences from this bin
                PhyloTree* phylo = new PhyloTree();
@@ -417,11 +417,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                int size;
                
                //create output file
-               if (outputDir == "") { outputDir += hasPath(listfile); }
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
                                
                ofstream out;
-               string outputFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
-               openOutputFile(outputFile, out);
+               string outputFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".cons.taxonomy";
+               m->openOutputFile(outputFile, out);
                outputNames.push_back(outputFile);
                
                //for each bin in the list vector