void mothurOutEndLine(); //writes to cout and the logfile
void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
+ void mothurOutJustToScreen(string); //writes to cout
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
int control_pressed;
bool executing, runParse, jumble, gui, mothurCalling, debug;
- //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
+ //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
string getPhylipFile() { return phylipfile; }
string getColumnFile() { return columnfile; }
string getListFile() { return listfile; }
string getFlowFile() { return flowfile; }
string getBiomFile() { return biomfile; }
string getCountTableFile() { return counttablefile; }
+ string getSummaryFile() { return summaryfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setSummaryFile(string f) { summaryfile = getFullPathName(f); }
void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
flowfile = "";
biomfile = "";
counttablefile = "";
+ summaryfile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
vector<string> Groups;
vector<string> namesOfGroups;