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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index de7d761dc68169f3f0df446f42ca07cd9f3b16aa..6b2570c9808ab9083a06c4fc41439c6fd99b22e2 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -70,7 +70,7 @@ GetOTURepCommand::GetOTURepCommand(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;             }
                                }
@@ -78,7 +78,7 @@ GetOTURepCommand::GetOTURepCommand(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;            }
                                }
@@ -86,7 +86,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                it = parameters.find("phylip");
                                //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["phylip"] = inputDir + it->second;           }
                                }
@@ -94,7 +94,7 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                it = parameters.find("column");
                                //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["column"] = inputDir + it->second;           }
                                }
@@ -102,7 +102,7 @@ GetOTURepCommand::GetOTURepCommand(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;             }
                                }
@@ -110,7 +110,7 @@ GetOTURepCommand::GetOTURepCommand(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;            }
                                }
@@ -153,7 +153,7 @@ GetOTURepCommand::GetOTURepCommand(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;  }
                        }
                        
@@ -179,13 +179,13 @@ GetOTURepCommand::GetOTURepCommand(string option)  {
                                        m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine();
                                        abort = true;
                                }else { 
-                                       splitAtDash(groups, Groups);
+                                       m->splitAtDash(groups, Groups);
                                }
                        }
                        globaldata->Groups = Groups;
                        
                        string temp = validParameter.validFile(parameters, "large", false);             if (temp == "not found") {      temp = "F";     }
-                       large = isTrue(temp);
+                       large = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
                        convert(temp, precision); 
@@ -307,7 +307,7 @@ int GetOTURepCommand::execute(){
                        delete nameMap;
                        
                        //openfile for getMap to use
-                       openInputFile(distFile, inRow);
+                       m->openInputFile(distFile, inRow);
                        
                        if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); return 0; }
                }
@@ -322,7 +322,7 @@ int GetOTURepCommand::execute(){
                                names.clear();
                                binnames = globaldata->gListVector->get(i);
                                
-                               splitAtComma(binnames, names);
+                               m->splitAtComma(binnames, names);
                                
                                for (int j = 0; j < names.size(); j++) {
                                        nameToIndex[names[j]] = i;
@@ -386,7 +386,7 @@ int GetOTURepCommand::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;
@@ -489,7 +489,7 @@ int GetOTURepCommand::execute(){
 void GetOTURepCommand::readNamesFile() {
        try {
                vector<string> dupNames;
-               openInputFile(namefile, inNames);
+               m->openInputFile(namefile, inNames);
                
                string name, names, sequence;
        
@@ -500,7 +500,7 @@ void GetOTURepCommand::readNamesFile() {
                        dupNames.clear();
                        
                        //parse names into vector
-                       splitAtComma(names, dupNames);
+                       m->splitAtComma(names, dupNames);
                        
                        //store names in fasta map
                        sequence = fasta->getSequence(name);
@@ -508,7 +508,7 @@ void GetOTURepCommand::readNamesFile() {
                                fasta->push_back(dupNames[i], sequence);
                        }
                
-                       gobble(inNames);
+                       m->gobble(inNames);
                }
                inNames.close();
 
@@ -598,15 +598,15 @@ int GetOTURepCommand::process(ListVector* processList) {
                string nameRep;
 
                //create output file
-               if (outputDir == "") { outputDir += hasPath(listfile); }
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
                                
                ofstream newNamesOutput;
                string outputNamesFile;
                map<string, ofstream*> filehandles;
                
                if (Groups.size() == 0) { //you don't want to use groups
-                       outputNamesFile  = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
-                       openOutputFile(outputNamesFile, newNamesOutput);
+                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
+                       m->openOutputFile(outputNamesFile, newNamesOutput);
                        outputNames.push_back(outputNamesFile);
                        outputNameFiles[outputNamesFile] = processList->getLabel();
                }else{ //you want to use groups
@@ -614,9 +614,9 @@ int GetOTURepCommand::process(ListVector* processList) {
                        for (int i=0; i<Groups.size(); i++) {
                                temp = new ofstream;
                                filehandles[Groups[i]] = temp;
-                               outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
+                               outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
                                
-                               openOutputFile(outputNamesFile, *(temp));
+                               m->openOutputFile(outputNamesFile, *(temp));
                                outputNames.push_back(outputNamesFile);
                                outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i];
                        }
@@ -639,7 +639,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                        
                        string temp = processList->get(i);
                        vector<string> namesInBin;
-                       splitAtComma(temp, namesInBin);
+                       m->splitAtComma(temp, namesInBin);
                        
                        if (Groups.size() == 0) {
                                nameRep = findRep(namesInBin);
@@ -655,7 +655,7 @@ int GetOTURepCommand::process(ListVector* processList) {
                                        
                                        if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
                                        
-                                       if (inUsersGroups(thisgroup, Groups)) { //add this name to correct group
+                                       if (m->inUsersGroups(thisgroup, Groups)) { //add this name to correct group
                                                NamesInGroup[thisgroup].push_back(namesInBin[j]);
                                        }
                                }
@@ -701,27 +701,27 @@ int GetOTURepCommand::processNames(string filename, string label) {
        try{
 
                //create output file
-               if (outputDir == "") { outputDir += hasPath(listfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + label + ".rep.fasta";
-               openOutputFile(outputFileName, out);
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta";
+               m->openOutputFile(outputFileName, out);
                vector<repStruct> reps;
                outputNames.push_back(outputFileName);
                
                ofstream out2;
                string tempNameFile = filename + ".temp";
-               openOutputFile(tempNameFile, out2);
+               m->openOutputFile(tempNameFile, out2);
                
                ifstream in;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                
                int i = 0;
                while (!in.eof()) {
                        string rep, binnames;
-                       in >> i >> rep >> binnames; gobble(in);
+                       in >> i >> rep >> binnames; m->gobble(in);
                        out2 << rep << '\t' << binnames << endl;
                        
                        vector<string> names;
-                       splitAtComma(binnames, names);
+                       m->splitAtComma(binnames, names);
                        int binsize = names.size();
                        
                        //if you have a groupfile