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#ifndef MOTHUROUT_H
#define MOTHUROUT_H
/*
* mothurOut.h
* Mothur
*
* Created by westcott on 2/25/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
/***********************************************/
struct logger {
logger() {}
~logger() {}
template< class T >
logger& operator <<( const T& o ) {
cout << o; return *this;
}
logger& operator<<(ostream& (*m)(ostream&) ) {
cout << m; return *this;
}
};
/***********************************************/
class MothurOut {
public:
static MothurOut* getInstance();
void setFileName(string);
void mothurOut(string); //writes to cout and the logfile
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 mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
string getDefaultPath() { return defaultPath; }
void setDefaultPath(string);
string getOutputDir() { return outputDir; }
void setOutputDir(string);
string getReleaseDate() { return releaseDate; }
void setReleaseDate(string r) { releaseDate = r; }
string getVersion() { return version; }
void setVersion(string r) { version = r; }
void addGroup(string g) { Groups.push_back(g); }
void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
void clearGroups() { Groups.clear(); }
int getNumGroups() { return Groups.size(); }
vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
void addAllGroup(string g) { namesOfGroups.push_back(g); }
void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
void clearAllGroups() { namesOfGroups.clear(); }
int getNumAllGroups() { return namesOfGroups.size(); }
vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
map<string, string> names;
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode;
bool printedHeaders, commandInputsConvertError;
//functions from mothur.h
//file operations
vector<unsigned long long> divideFile(string, int&);
int divideFile(string, int&, vector<string>&);
vector<unsigned long long> setFilePosEachLine(string, int&);
vector<unsigned long long> setFilePosFasta(string, int&);
string sortFile(string, string);
int appendFiles(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
string hasPath(string);
string getExtension(string);
string getPathName(string);
string getSimpleName(string);
string getRootName(string);
bool isBlank(string);
int openOutputFile(string, ofstream&);
int openOutputFileAppend(string, ofstream&);
int openInputFile(string, ifstream&);
int openInputFile(string, ifstream&, string); //no error given
string getline(ifstream&);
string getline(istringstream&);
void gobble(istream&);
void gobble(istringstream&);
map<string, int> readNames(string);
int readNames(string, map<string, string>&);
int readNames(string, map<string, vector<string> >&);
int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
int mothurRemove(string);
bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
//searchs and checks
bool checkReleaseVersion(ifstream&, string);
bool anyLabelsToProcess(string, set<string>&, string);
bool inUsersGroups(vector<string>, vector<string>);
bool inUsersGroups(string, vector<string>);
void getNumSeqs(ifstream&, int&);
int getNumSeqs(ifstream&);
int getNumNames(string);
int getNumChar(string, char);
bool isTrue(string);
bool isContainingOnlyDigits(string);
bool isNumeric1(string);
//string manipulation
void splitAtEquals(string&, string&);
void splitAtComma(string&, string&);
void splitAtComma(string&, vector<string>&);
void splitAtDash(string&, set<int>&);
void splitAtDash(string&, set<string>&);
void splitAtDash(string&, vector<string>&);
void splitAtChar(string&, vector<string>&, char);
int removeConfidences(string&);
//math operation
int factorial(int num);
vector<vector<double> > binomial(int);
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
int getRandomIndex(int); //highest
int control_pressed;
bool executing, runParse, jumble, gui;
//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
string getPhylipFile() { return phylipfile; }
string getColumnFile() { return columnfile; }
string getListFile() { return listfile; }
string getRabundFile() { return rabundfile; }
string getSabundFile() { return sabundfile; }
string getNameFile() { return namefile; }
string getGroupFile() { return groupfile; }
string getOrderFile() { return orderfile; }
string getOrderGroupFile() { return ordergroupfile; }
string getTreeFile() { return treefile; }
string getSharedFile() { return sharedfile; }
string getRelAbundFile() { return relabundfile; }
string getDesignFile() { return designfile; }
string getFastaFile() { return fastafile; }
string getSFFFile() { return sfffile; }
string getQualFile() { return qualfile; }
string getOligosFile() { return oligosfile; }
string getAccnosFile() { return accnosfile; }
string getTaxonomyFile() { return taxonomyfile; }
string getFlowFile() { return flowfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setTreeFile(string f) { treefile = getFullPathName(f); }
void setGroupFile(string f) { groupfile = getFullPathName(f); }
void setPhylipFile(string f) { phylipfile = getFullPathName(f); }
void setColumnFile(string f) { columnfile = getFullPathName(f); }
void setNameFile(string f) { namefile = getFullPathName(f); }
void setRabundFile(string f) { rabundfile = getFullPathName(f); }
void setSabundFile(string f) { sabundfile = getFullPathName(f); }
void setSharedFile(string f) { sharedfile = getFullPathName(f); }
void setRelAbundFile(string f) { relabundfile = getFullPathName(f); }
void setOrderFile(string f) { orderfile = getFullPathName(f); }
void setOrderGroupFile(string f) { ordergroupfile = getFullPathName(f); }
void setDesignFile(string f) { designfile = getFullPathName(f); }
void setFastaFile(string f) { fastafile = getFullPathName(f); }
void setSFFFile(string f) { sfffile = getFullPathName(f); }
void setQualFile(string f) { qualfile = getFullPathName(f); }
void setOligosFile(string f) { oligosfile = getFullPathName(f); }
void setAccnosFile(string f) { accnosfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setProcessors(string p) { processors = p; }
void printCurrentFiles();
bool hasCurrentFiles();
void clearCurrentFiles();
private:
static MothurOut* _uniqueInstance;
MothurOut( const MothurOut& ); // Disable copy constructor
void operator=( const MothurOut& ); // Disable assignment operator
MothurOut() {
control_pressed = false; defaultPath="";
phylipfile = "";
columnfile = "";
listfile = "";
rabundfile = "";
sabundfile = "";
namefile = "";
groupfile = "";
designfile = "";
orderfile = "";
treefile = "";
sharedfile = "";
ordergroupfile = "";
relabundfile = "";
fastafile = "";
qualfile = "";
sfffile = "";
oligosfile = "";
accnosfile = "";
taxonomyfile = "";
processors = "1";
flowfile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
sharedHeaderMode = "";
}
~MothurOut();
string logFileName;
string defaultPath, outputDir;
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
vector<string> Groups;
vector<string> namesOfGroups;
ofstream out;
int mem_usage(double&, double&);
};
/***********************************************/
#endif
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