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

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 087e63f58b983b092fffd09ba191665b3826a7d0..70470b015684b386947056686789da5077000565 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -68,7 +68,7 @@ SummaryCommand::SummaryCommand(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->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
 
                        //check for optional parameter and set defaults
@@ -76,7 +76,7 @@ SummaryCommand::SummaryCommand(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;  }
                        }
                        
@@ -91,7 +91,7 @@ SummaryCommand::SummaryCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
@@ -101,7 +101,7 @@ SummaryCommand::SummaryCommand(string option)  {
                        convert(temp, size); 
                        
                        temp = validParameter.validFile(parameters, "groupmode", false);                if (temp == "not found") { temp = "F"; }
-                       groupMode = isTrue(temp);
+                       groupMode = m->isTrue(temp);
                        
        
                }
@@ -160,7 +160,7 @@ int SummaryCommand::execute(){
                        numLines = 0;
                        numCols = 0;
                        
-                       string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
+                       string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
                        globaldata->inputFileName = inputFileNames[p];
                        outputNames.push_back(fileNameRoot);
                        
@@ -234,7 +234,7 @@ int SummaryCommand::execute(){
                        if (sumCalculators.size() == 0) { if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
                        
                        ofstream outputFileHandle;
-                       openOutputFile(fileNameRoot, outputFileHandle);
+                       m->openOutputFile(fileNameRoot, outputFileHandle);
                        outputFileHandle << "label";
                        
                        read = new ReadOTUFile(globaldata->inputFileName);      
@@ -285,7 +285,7 @@ int SummaryCommand::execute(){
                                        numLines++;
                                }
                                
-                               if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = sabund->getLabel();
                                        
                                        delete sabund;
@@ -401,7 +401,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
                input = globaldata->ginput;
                vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
                
-               string sharedFileRoot = getRootName(filename);
+               string sharedFileRoot = m->getRootName(filename);
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
@@ -420,7 +420,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
                
                        for (int i = 0; i < lookup.size(); i++) {
                                RAbundVector rav = lookup[i]->getRAbundVector();
-                               openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+                               m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
                                rav.print(*(filehandles[lookup[i]->getGroup()]));
                                (*(filehandles[lookup[i]->getGroup()])).close();
                        }
@@ -449,10 +449,10 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
        try {
                
                ofstream out;
-               string combineFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "groups.summary";
+               string combineFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "groups.summary";
                
                //open combined file
-               openOutputFile(combineFileName, out);
+               m->openOutputFile(combineFileName, out);
                
                //open each groups summary file
                string newLabel = "";
@@ -461,7 +461,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                for (int i=0; i<outputNames.size(); i++) {
                        temp = new ifstream;
                        filehandles[outputNames[i]] = temp;
-                       openInputFile(outputNames[i], *(temp));
+                       m->openInputFile(outputNames[i], *(temp));
                        
                        //read through first line - labels
                        string tempLabel;
@@ -474,7 +474,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                                }
                        }else{  for (int j = 0; j < numCols+1; j++) {  *(temp) >> tempLabel;  }  }
                        
-                       gobble(*(temp));
+                       m->gobble(*(temp));
                }
                
                //output label line to new file
@@ -496,7 +496,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                                }
                                
                                out << endl;
-                               gobble(*(filehandles[outputNames[i]]));
+                               m->gobble(*(filehandles[outputNames[i]]));
                        }
                }