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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 195996e50d41ff81953f5715704964398b9715e9..2c1b6af3004e7351085e4538f7023e342bc181f9 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -21,12 +21,12 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
                
                //getting output filename
                filename = globaldata->inputFileName;
-               if (outputDir == "") { outputDir += hasPath(filename); }
+               if (outputDir == "") { outputDir += m->hasPath(filename); }
                
-               filename = outputDir + getRootName(getSimpleName(filename));
+               filename = outputDir + m->getRootName(m->getSimpleName(filename));
                filename = filename + "shared";
                
-               openOutputFile(filename, out);
+               m->openOutputFile(filename, out);
                pickedGroups = false;
                
                groupMap = globaldata->gGroupmap;
@@ -48,7 +48,7 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
                }
                
                //set fileroot
-               fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
+               fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile()));
                
                //clears file before we start to write to it below
                for (int i=0; i<groups.size(); i++) {
@@ -119,9 +119,9 @@ int SharedCommand::execute(){
                                groups += globaldata->Groups[i] + ".";
                        }
                
-                       string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
+                       string newGroupFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + groups + "groups";
                        ofstream outGroups;
-                       openOutputFile(newGroupFile, outGroups);
+                       m->openOutputFile(newGroupFile, outGroups);
                
                        vector<string> names = groupMap->getNamesSeqs();
                        string groupName;
@@ -172,7 +172,7 @@ int SharedCommand::execute(){
                                        userLabels.erase(SharedList->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = SharedList->getLabel();
                                        
                                        delete SharedList;
@@ -292,7 +292,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                                thislookup[i]->print(out);
                                
                                RAbundVector rav = thislookup[i]->getRAbundVector();
-                               openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+                               m->openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
                                rav.print(*(filehandles[thislookup[i]->getGroup()]));
                                (*(filehandles[thislookup[i]->getGroup()])).close();
                        }
@@ -315,7 +315,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
                                        (myIt->second)->print(out);
                                
                                        RAbundVector rav = (myIt->second)->getRAbundVector();
-                                       openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+                                       m->openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
                                        rav.print(*(filehandles[(myIt->second)->getGroup()]));
                                        (*(filehandles[(myIt->second)->getGroup()])).close();
                                }else{
@@ -377,14 +377,14 @@ int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 int SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;
-               string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+               string outputMisMatchName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
                
                //you have sequences in your list file that are not in your group file
                if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
                        outputMisMatchName += "missing.group";
                        m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
                        
-                       openOutputFile(outputMisMatchName, outMisMatch);
+                       m->openOutputFile(outputMisMatchName, outMisMatch);
                        
                        map<string, string> listNames;
                        map<string, string>::iterator itList;
@@ -458,7 +458,7 @@ int SharedCommand::createMisMatchFile() {
                
                        map<string, string>::iterator itMatch;
                        
-                       openOutputFile(outputMisMatchName, outMisMatch);
+                       m->openOutputFile(outputMisMatchName, outMisMatch);
                        
                        //loop through names in seqNames and if they aren't in namesIn list output them
                        for (int i = 0; i < seqNames.size(); i++) {
@@ -496,11 +496,11 @@ int SharedCommand::readOrderFile() {
                order.clear();
                
                ifstream in;
-               openInputFile(globaldata->getOrderGroupFile(), in);
+               m->openInputFile(globaldata->getOrderGroupFile(), in);
                string thisGroup;
                
                while(!in.eof()){
-                       in >> thisGroup; gobble(in);
+                       in >> thisGroup; m->gobble(in);
                                                
                        order.push_back(thisGroup);