#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 {
static MothurOut* getInstance();
void setFileName(string);
- void mothurOut(string);
- void mothurOutEndLine();
+ 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();
void setReleaseDate(string r) { releaseDate = r; }
string getVersion() { return version; }
void setVersion(string r) { version = r; }
- vector<string> Groups;
+
+ 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> namesOfGroups;
- string saveNextLabel, argv;
+ //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 int> divideFile(string, int&);
- vector<unsigned long int> setFilePosEachLine(string, int&);
- vector<unsigned long int> setFilePosFasta(string, int&);
+ bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
+ 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);
- void appendFiles(string, string);
+ int appendFiles(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
string hasPath(string);
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);
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 splitAtDash(string&, set<string>&);
void splitAtDash(string&, vector<string>&);
void splitAtChar(string&, vector<string>&, char);
+ void splitAtChar(string&, string&, char);
+ int removeConfidences(string&);
+ string makeList(vector<string>&);
//math operation
int factorial(int num);
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
+ int getRandomIndex(int); //highest
int control_pressed;
- bool executing, runParse, jumble;
+ 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.
string getPhylipFile() { return phylipfile; }
string getOligosFile() { return oligosfile; }
string getAccnosFile() { return accnosfile; }
string getTaxonomyFile() { return taxonomyfile; }
+ string getFlowFile() { return flowfile; }
+ string getBiomFile() { return biomfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = 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 setBiomFile(string f) { biomfile = getFullPathName(f); }
void setProcessors(string p) { processors = p; }
void printCurrentFiles();
+ bool hasCurrentFiles();
void clearCurrentFiles();
private:
accnosfile = "";
taxonomyfile = "";
processors = "1";
- };
+ flowfile = "";
+ biomfile = "";
+ gui = false;
+ printedHeaders = false;
+ commandInputsConvertError = false;
+ mothurCalling = false;
+ debug = 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;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
+ 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&);