#include "mothur.h"
+
/***********************************************/
class MothurOut {
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; }
+ vector<string> Groups;
+ vector<string> Treenames;
+ map<string, string> names;
+ vector<string> namesOfGroups;
+ string saveNextLabel, argv;
+
+ //functions from mothur.h
+ //file operations
+ vector<unsigned long int> divideFile(string, int&);
+ vector<unsigned long int> setFilePosEachLine(string, int&);
+ vector<unsigned long int> setFilePosFasta(string, int&);
+ string sortFile(string, string);
+ void 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);
+
+ //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);
+ bool isTrue(string);
+ bool isContainingOnlyDigits(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);
+
+ //math operation
+ int factorial(int num);
+ vector<vector<double> > binomial(int);
+ float ceilDist(float, int);
+ float roundDist(float, int);
+ unsigned int fromBase36(string);
int control_pressed;
- bool executing;
-
+ 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 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 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; };
+ 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";
+ gui = false;
+ };
~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;
+
+
ofstream out;
int mem_usage(double&, double&);
projects / mothur.git / blobdiff