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

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index e647bf2430c629af70613b79abcaafc78ab325fa..8489bfefc841f6dd34fea17ef15b416e08c4c6c8 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -46,7 +46,7 @@ SensSpecCommand::SensSpecCommand(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;             }
                                }
@@ -54,7 +54,7 @@ SensSpecCommand::SensSpecCommand(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;           }
                                }
@@ -62,7 +62,7 @@ SensSpecCommand::SensSpecCommand(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;           }
                                }
@@ -70,7 +70,7 @@ SensSpecCommand::SensSpecCommand(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;             }
                                }
@@ -94,15 +94,15 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        outputDir = validParameter.validFile(parameters, "outputdir", false);
                        if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(listFile); //if user entered a file with a path then preserve it   
+                               outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it        
                        }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "hard", false);
                        if (temp == "not found"){       hard = 0;       }
-                       else if(!isTrue(temp))  {       hard = 0;       }
-                       else if(isTrue(temp))   {       hard = 1;       }
+                       else if(!m->isTrue(temp))       {       hard = 0;       }
+                       else if(m->isTrue(temp))        {       hard = 1;       }
                        
 //                     temp = validParameter.validFile(parameters, "name", true);
 //                     if (temp == "not found")        {       nameFile = "";          }
@@ -178,7 +178,7 @@ void SensSpecCommand::processPhylip(){
                //probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
                
                ifstream inputListFile;
-               openInputFile(listFile, inputListFile);
+               m->openInputFile(listFile, inputListFile);
                
                string origCutoff = "";
                bool getCutoff = 0;
@@ -210,13 +210,13 @@ void SensSpecCommand::processPhylip(){
                                }
                                seqMap[seqName] = i;
                        }
-                       gobble(inputListFile);
+                       m->gobble(inputListFile);
                
                        int lNumSeqs = seqMap.size();
                        int pNumSeqs = 0;
 
                        ifstream phylipFile;
-                       openInputFile(distFile, phylipFile);
+                       m->openInputFile(distFile, phylipFile);
                        phylipFile >> pNumSeqs;
                        if(pNumSeqs != lNumSeqs){       cout << "numSeq mismatch!" << endl;     }
                        
@@ -278,7 +278,7 @@ void SensSpecCommand::processPhylip(){
 void SensSpecCommand::processColumn(){
        try{            
                ifstream inputListFile;
-               openInputFile(listFile, inputListFile);
+               m->openInputFile(listFile, inputListFile);
                
                string origCutoff = "";
                bool getCutoff = 0;
@@ -326,12 +326,12 @@ void SensSpecCommand::processColumn(){
                                        }
                                }
                        }
-                       gobble(inputListFile);
+                       m->gobble(inputListFile);
                        
                        int numDists = (numSeqs * (numSeqs-1) / 2);
 
                        ifstream columnFile;
-                       openInputFile(distFile, columnFile);
+                       m->openInputFile(distFile, columnFile);
                        string seqNameA, seqNameB, seqPairString;
                        double distance;
                        
@@ -377,7 +377,7 @@ void SensSpecCommand::processColumn(){
                                        seqPairSet.erase(it);   
                                }
                                
-                               gobble(columnFile);
+                               m->gobble(columnFile);
                        }
                        falsePositives += seqPairSet.size();
                        
@@ -395,7 +395,7 @@ void SensSpecCommand::processColumn(){
 void SensSpecCommand::setUpOutput(){
        try{            
                ofstream sensSpecFile;
-               openOutputFile(sensSpecFileName, sensSpecFile);
+               m->openOutputFile(sensSpecFileName, sensSpecFile);
                
                sensSpecFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
 
@@ -440,7 +440,7 @@ void SensSpecCommand::outputStatistics(string label, string cutoff){
                if(nPrime == 0)         {       negativePredictiveValue = 0;    matthewsCorrCoef = 0;                                                   }
                
                ofstream sensSpecFile;
-               openOutputFileAppend(sensSpecFileName, sensSpecFile);
+               m->openOutputFileAppend(sensSpecFileName, sensSpecFile);
                
                sensSpecFile << label << '\t' << cutoff << '\t';
                sensSpecFile << truePositives << '\t' << trueNegatives << '\t' << falsePositives << '\t' << falseNegatives << '\t';