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

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index ced5a6384c792188d34068f4d899ff5ef306adeb..fb1a7029636d3ee2e28045c8d1b233bec7c8a889 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -57,7 +57,7 @@ ClusterSplitCommand::ClusterSplitCommand(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;           }
                                }
@@ -65,7 +65,7 @@ ClusterSplitCommand::ClusterSplitCommand(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;           }
                                }
@@ -73,7 +73,7 @@ ClusterSplitCommand::ClusterSplitCommand(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;             }
                                }
@@ -81,7 +81,7 @@ ClusterSplitCommand::ClusterSplitCommand(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 @@ ClusterSplitCommand::ClusterSplitCommand(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;            }
                                }
@@ -142,10 +142,10 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        convert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
-                       hard = isTrue(temp);
+                       hard = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "large", false);                    if (temp == "not found") { temp = "F"; }
-                       large = isTrue(temp);
+                       large = m->isTrue(temp);
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
                        convert(temp, processors); 
@@ -271,7 +271,7 @@ int ClusterSplitCommand::execute(){
                        if (namefile == "") {  //you need to make a namefile for split matrix
                                ofstream out;
                                namefile = phylipfile + ".names";
-                               openOutputFile(namefile, out);
+                               m->openOutputFile(namefile, out);
                                for (int i = 0; i < listToMakeNameFile->getNumBins(); i++) {
                                        string bin = listToMakeNameFile->get(i);
                                        out << bin << '\t' << bin << endl;
@@ -497,13 +497,13 @@ int ClusterSplitCommand::execute(){
                                        for(int i=0;i<processors;i++){
                                                string filename = toString(processIDS[i]) + ".temp";
                                                ifstream in;
-                                               openInputFile(filename, in);
+                                               m->openInputFile(filename, in);
                                                
-                                               in >> tag; gobble(in);
+                                               in >> tag; m->gobble(in);
                                                
                                                while(!in.eof()) {
                                                        string tempName;
-                                                       in >> tempName; gobble(in);
+                                                       in >> tempName; m->gobble(in);
                                                        listFileNames.push_back(tempName);
                                                }
                                                in.close();
@@ -512,15 +512,15 @@ int ClusterSplitCommand::execute(){
                                                //get labels
                                                filename = toString(processIDS[i]) + ".temp.labels";
                                                ifstream in2;
-                                               openInputFile(filename, in2);
+                                               m->openInputFile(filename, in2);
                                                
                                                float tempCutoff;
-                                               in2 >> tempCutoff; gobble(in2);
+                                               in2 >> tempCutoff; m->gobble(in2);
                                                if (tempCutoff < cutoff) { cutoff = tempCutoff; }
                                                
                                                while(!in2.eof()) {
                                                        string tempName;
-                                                       in2 >> tempName; gobble(in2);
+                                                       in2 >> tempName; m->gobble(in2);
                                                        if (labels.count(tempName) == 0) { labels.insert(tempName); }
                                                }
                                                in2.close();
@@ -586,12 +586,12 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
                //read in singletons
                if (singleton != "none") {
                        ifstream in;
-                       openInputFile(singleton, in);
+                       m->openInputFile(singleton, in);
                                
                        string firstCol, secondCol;
                        listSingle = new ListVector();
                        while (!in.eof()) {
-                               in >> firstCol >> secondCol; gobble(in);
+                               in >> firstCol >> secondCol; m->gobble(in);
                                listSingle->push_back(secondCol);
                        }
                        in.close();
@@ -632,7 +632,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
                        
                        string filledInList = listNames[k] + "filledInTemp";
                        ofstream outFilled;
-                       openOutputFile(filledInList, outFilled);
+                       m->openOutputFile(filledInList, outFilled);
        
                        //for each label needed
                        for(int l = 0; l < orderFloat.size(); l++){
@@ -689,12 +689,12 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
 //**********************************************************************************************************************
 int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> userLabels, ListVector* listSingle){
        try {
-               if (outputDir == "") { outputDir += hasPath(distfile); }
-               fileroot = outputDir + getRootName(getSimpleName(distfile));
+               if (outputDir == "") { outputDir += m->hasPath(distfile); }
+               fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
                
-               openOutputFile(fileroot+ tag + ".sabund",       outSabund);
-               openOutputFile(fileroot+ tag + ".rabund",       outRabund);
-               openOutputFile(fileroot+ tag + ".list",         outList);
+               m->openOutputFile(fileroot+ tag + ".sabund",    outSabund);
+               m->openOutputFile(fileroot+ tag + ".rabund",    outRabund);
+               m->openOutputFile(fileroot+ tag + ".list",              outList);
                                
                outputNames.push_back(fileroot+ tag + ".sabund");
                outputNames.push_back(fileroot+ tag + ".rabund");
@@ -718,7 +718,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                        if (listSingle != NULL) {
                                for (int j = 0; j < listSingle->getNumBins(); j++) {
                                        outList << listSingle->get(j) << '\t';
-                                       rabund->push_back(getNumNames(listSingle->get(j)));
+                                       rabund->push_back(m->getNumNames(listSingle->get(j)));
                                }
                        }
                        
@@ -735,7 +735,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
                                else {          
                                        for (int j = 0; j < list->getNumBins(); j++) {
                                                outList << list->get(j) << '\t';
-                                               rabund->push_back(getNumNames(list->get(j)));
+                                               rabund->push_back(m->getNumNames(list->get(j)));
                                        }
                                        delete list;
                                }
@@ -775,7 +775,7 @@ void ClusterSplitCommand::printData(ListVector* oldList){
                RAbundVector oldRAbund = oldList->getRAbundVector();
                
                oldRAbund.setLabel(label);
-               if (isTrue(showabund)) {
+               if (m->isTrue(showabund)) {
                        oldRAbund.getSAbundVector().print(cout);
                }
                oldRAbund.print(outRabund);
@@ -811,7 +811,7 @@ int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> >
                                //write out names to file
                                string filename = toString(getpid()) + ".temp";
                                ofstream out;
-                               openOutputFile(filename, out);
+                               m->openOutputFile(filename, out);
                                out << tag << endl;
                                for (int j = 0; j < listFileNames.size(); j++) { out << listFileNames[j] << endl;  }
                                out.close();
@@ -819,7 +819,7 @@ int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> >
                                //print out labels
                                ofstream outLabels;
                                filename = toString(getpid()) + ".temp.labels";
-                               openOutputFile(filename, outLabels);
+                               m->openOutputFile(filename, outLabels);
                                
                                outLabels << cutoff << endl;
                                for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {
@@ -917,11 +917,11 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                        else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);     }
                        tag = cluster->getTag();
                
-                       if (outputDir == "") { outputDir += hasPath(thisDistFile); }
-                       fileroot = outputDir + getRootName(getSimpleName(thisDistFile));
+                       if (outputDir == "") { outputDir += m->hasPath(thisDistFile); }
+                       fileroot = outputDir + m->getRootName(m->getSimpleName(thisDistFile));
                        
                        ofstream listFile;
-                       openOutputFile(fileroot+ tag + ".list", listFile);
+                       m->openOutputFile(fileroot+ tag + ".list",      listFile);
                
                        listFileNames.push_back(fileroot+ tag + ".list");
                
@@ -950,9 +950,9 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                                float dist = matrix->getSmallDist();
                                float rndDist;
                                if (hard) {
-                                       rndDist = ceilDist(dist, precision); 
+                                       rndDist = m->ceilDist(dist, precision); 
                                }else{
-                                       rndDist = roundDist(dist, precision); 
+                                       rndDist = m->roundDist(dist, precision); 
                                }
 
                                if(previousDist <= 0.0000 && dist != previousDist){
@@ -995,8 +995,8 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                        remove(thisNamefile.c_str());
                        
                        if (saveCutoff != cutoff) { 
-                               if (hard)       {  saveCutoff = ceilDist(saveCutoff, precision);        }
-                               else            {       saveCutoff = roundDist(saveCutoff, precision);  }
+                               if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
+                               else            {       saveCutoff = m->roundDist(saveCutoff, precision);  }
                        
                                m->mothurOut("Cutoff was " + toString(cutoff) + " changed cutoff to " + toString(saveCutoff)); m->mothurOutEndLine();  
                        }