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#ifndef CURRENTFILE_H
#define CURRENTFILE_H
/*
* currentfile.h
* Mothur
*
* Created by westcott on 3/15/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
//NOT ThreadSafe - but designed to be read only from threads and read write from main thread.
#include "mothurout.h"
#include "utils.hpp"
/***********************************************/
class CurrentFile {
public:
static CurrentFile* getInstance() {
if(instance == 0) { instance = new CurrentFile(); }
return instance;
}
unsigned long long getRAMUsed();
unsigned long long getTotalRAM();
string getPhylipFile() { lock_guard<std::mutex> guard(currentProtector); return phylipfile; }
string getColumnFile() { lock_guard<std::mutex> guard(currentProtector); return columnfile; }
string getListFile() { lock_guard<std::mutex> guard(currentProtector); return listfile; }
string getRabundFile() { lock_guard<std::mutex> guard(currentProtector); return rabundfile; }
string getSabundFile() { lock_guard<std::mutex> guard(currentProtector); return sabundfile; }
string getNameFile() { lock_guard<std::mutex> guard(currentProtector); return namefile; }
string getGroupFile() { lock_guard<std::mutex> guard(currentProtector); return groupfile; }
string getOrderFile() { lock_guard<std::mutex> guard(currentProtector); return orderfile; }
string getOrderGroupFile() { lock_guard<std::mutex> guard(currentProtector); return ordergroupfile; }
string getTreeFile() { lock_guard<std::mutex> guard(currentProtector); return treefile; }
string getSharedFile() { lock_guard<std::mutex> guard(currentProtector); return sharedfile; }
string getRelAbundFile() { lock_guard<std::mutex> guard(currentProtector); return relabundfile; }
string getCLRFile() { lock_guard<std::mutex> guard(currentProtector); return clrfile; }
string getDesignFile() { lock_guard<std::mutex> guard(currentProtector); return designfile; }
string getFastaFile() { lock_guard<std::mutex> guard(currentProtector); return fastafile; }
string getSFFFile() { lock_guard<std::mutex> guard(currentProtector); return sfffile; }
string getQualFile() { lock_guard<std::mutex> guard(currentProtector); return qualfile; }
string getOligosFile() { lock_guard<std::mutex> guard(currentProtector); return oligosfile; }
string getSampleFile() { lock_guard<std::mutex> guard(currentProtector); return samplefile; }
string getAccnosFile() { lock_guard<std::mutex> guard(currentProtector); return accnosfile; }
string getTaxonomyFile() { lock_guard<std::mutex> guard(currentProtector); return taxonomyfile; }
string getFlowFile() { lock_guard<std::mutex> guard(currentProtector); return flowfile; }
string getContigsReportFile(){ lock_guard<std::mutex> guard(currentProtector); return contigsreportfile; }
string getBiomFile() { lock_guard<std::mutex> guard(currentProtector); return biomfile; }
string getCountFile() { lock_guard<std::mutex> guard(currentProtector); return countfile; }
string getSummaryFile() { lock_guard<std::mutex> guard(currentProtector); return summaryfile; }
string getFileFile() { lock_guard<std::mutex> guard(currentProtector); return filefile; }
string getConsTaxonomyFile(){ lock_guard<std::mutex> guard(currentProtector); return constaxonomyfile; }
void setListFile(string f) { lock_guard<std::mutex> guard(currentProtector); listfile = util.getFullPathName(f); }
void setBiomFile(string f) { lock_guard<std::mutex> guard(currentProtector); biomfile = util.getFullPathName(f); }
void setFlowFile(string f) { lock_guard<std::mutex> guard(currentProtector); flowfile = util.getFullPathName(f); }
void setContigsReportFile(string f) { lock_guard<std::mutex> guard(currentProtector); contigsreportfile = util.getFullPathName(f); }
void setSummaryFile(string f) { lock_guard<std::mutex> guard(currentProtector); summaryfile = util.getFullPathName(f); }
void setTreeFile(string f) { lock_guard<std::mutex> guard(currentProtector); treefile = util.getFullPathName(f); }
void setGroupFile(string f) { lock_guard<std::mutex> guard(currentProtector); groupfile = util.getFullPathName(f); setGroupMode("group"); }
void setCountFile(string f) { lock_guard<std::mutex> guard(currentProtector); countfile = util.getFullPathName(f); setGroupMode("count"); }
void setPhylipFile(string f) { lock_guard<std::mutex> guard(currentProtector); phylipfile = util.getFullPathName(f); }
void setColumnFile(string f) { lock_guard<std::mutex> guard(currentProtector); columnfile = util.getFullPathName(f); }
void setNameFile(string f) { lock_guard<std::mutex> guard(currentProtector); namefile = util.getFullPathName(f); }
void setRabundFile(string f) { lock_guard<std::mutex> guard(currentProtector); rabundfile = util.getFullPathName(f); }
void setSabundFile(string f) { lock_guard<std::mutex> guard(currentProtector); sabundfile = util.getFullPathName(f); }
void setSharedFile(string f) { lock_guard<std::mutex> guard(currentProtector); sharedfile = util.getFullPathName(f); }
void setRelAbundFile(string f) { lock_guard<std::mutex> guard(currentProtector); relabundfile = util.getFullPathName(f); }
void setCLRFile(string f) { lock_guard<std::mutex> guard(currentProtector); clrfile = util.getFullPathName(f); }
void setOrderFile(string f) { lock_guard<std::mutex> guard(currentProtector); orderfile = util.getFullPathName(f); }
void setOrderGroupFile(string f) { lock_guard<std::mutex> guard(currentProtector); ordergroupfile = util.getFullPathName(f); }
void setDesignFile(string f) { lock_guard<std::mutex> guard(currentProtector); designfile = util.getFullPathName(f); }
void setFastaFile(string f) { lock_guard<std::mutex> guard(currentProtector); fastafile = util.getFullPathName(f); }
void setSFFFile(string f) { lock_guard<std::mutex> guard(currentProtector); sfffile = util.getFullPathName(f); }
void setQualFile(string f) { lock_guard<std::mutex> guard(currentProtector); qualfile = util.getFullPathName(f); }
void setOligosFile(string f) { lock_guard<std::mutex> guard(currentProtector); oligosfile = util.getFullPathName(f); }
void setAccnosFile(string f) { lock_guard<std::mutex> guard(currentProtector); accnosfile = util.getFullPathName(f); }
void setTaxonomyFile(string f) { lock_guard<std::mutex> guard(currentProtector); taxonomyfile = util.getFullPathName(f); }
void setConsTaxonomyFile(string f) { lock_guard<std::mutex> guard(currentProtector); constaxonomyfile = util.getFullPathName(f); }
void setProgramPath(string f) { lock_guard<std::mutex> guard(currentProtector); mothurProgramPath = util.getFullPathName(f); }
void setFileFile(string f) { lock_guard<std::mutex> guard(currentProtector); filefile = util.getFullPathName(f); }
void setSampleFile(string f) { lock_guard<std::mutex> guard(currentProtector); samplefile = util.getFullPathName(f); }
//current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes/hasCurrentFiles. add a get and set function.
string getProcessors() { lock_guard<std::mutex> guard(currentProtector); return processors; }
int setProcessors(string p);
string getProgramPath() { lock_guard<std::mutex> guard(currentProtector); return mothurProgramPath; }
//default paths = MOTHUR_FILES
vector<string> getDefaultPath() { lock_guard<std::mutex> guard(currentProtector); return defaultPath; }
void setDefaultPath(vector<string>);
vector<string> getToolsPath() { lock_guard<std::mutex> guard(currentProtector); return toolsPath; }
void setToolsPath(vector<string>);
string getTestFilePath() { lock_guard<std::mutex> guard(currentProtector); return testFilePath; }
void setTestFilePath(string);
string getHomePath() { lock_guard<std::mutex> guard(currentProtector); return homePath; }
void setHomePath(string);
vector<string> getPaths() { lock_guard<std::mutex> guard(currentProtector); return paths; } //environment variable 'PATH' values
void setPaths(vector<string>);
string getOutputDir() { lock_guard<std::mutex> guard(currentProtector); return outputDir; }
void setOutputDir(string f) { lock_guard<std::mutex> guard(currentProtector); outputDir = util.getFullPathName(f); }
vector<string> getInputDir() { lock_guard<std::mutex> guard(currentProtector); return inputDir; }
void setInputDir(vector<string> f);
void setFileName(string);
string getReleaseDate() { lock_guard<std::mutex> guard(currentProtector); return releaseDate; }
void setReleaseDate(string r) { lock_guard<std::mutex> guard(currentProtector); releaseDate = r; }
string getVersion() { lock_guard<std::mutex> guard(currentProtector); return version; }
void setVersion(string r) { lock_guard<std::mutex> guard(currentProtector); version = r; }
vector< vector<string> > getLocations();
bool getMothurCalling() { lock_guard<std::mutex> guard(currentProtector); return mothurCalling; }
void setMothurCalling(bool t) { lock_guard<std::mutex> guard(currentProtector); mothurCalling = t; }
void printCurrentFiles(string); //string="" for just to logfile.
void clearCurrentFiles();
set<string> getCurrentTypes();
bool hasCurrentFiles();
string getGroupMode() { lock_guard<std::mutex> guard(currentProtector); return groupMode; }
string getTestDirectory() { lock_guard<std::mutex> guard(currentProtector); return testDirectory; }
void setTestDirectory(string t) { lock_guard<std::mutex> guard(currentProtector); testDirectory = t; }
private:
MothurOut* m;
Utils util;
vector<string> paths, defaultPath, toolsPath, inputDir; //paths stored in PATH environment variables, defaultPaths = MOTHUR_FILES, toolsPath = MOTHUR_TOOLS
string logFileName, mothurProgramPath, homePath;
string outputDir, releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, filefile, testFilePath, contigsreportfile, clrfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, countfile, summaryfile, constaxonomyfile, groupMode, testDirectory, sharedHeaderMode, samplefile;
bool mothurCalling;
void setGroupMode(string t) { groupMode = t; }
static CurrentFile* instance;
CurrentFile( const CurrentFile& ); // Disable copy constructor
void operator=( const CurrentFile& ); // Disable assignment operator
std::mutex currentProtector;
CurrentFile() {
m = MothurOut::getInstance();
testFilePath = "";
outputDir= "";
accnosfile = "";
filefile = "";
phylipfile = "";
columnfile = "";
listfile = "";
rabundfile = "";
sabundfile = "";
namefile = "";
phylipfile = "";
columnfile = "";
listfile = "";
rabundfile = "";
sabundfile = "";
namefile = "";
groupfile = "";
designfile = "";
orderfile = "";
treefile = "";
sharedfile = "";
ordergroupfile = "";
relabundfile = "";
clrfile = "";
fastafile = "";
qualfile = "";
sfffile = "";
oligosfile = "";
groupfile = "";
designfile = "";
orderfile = "";
treefile = "";
sharedfile = "";
ordergroupfile = "";
relabundfile = "";
fastafile = "";
qualfile = "";
sfffile = "";
oligosfile = "";
accnosfile = "";
taxonomyfile = "";
constaxonomyfile = "";
samplefile = "";
unsigned concurentThreadsSupported = std::thread::hardware_concurrency();
if (concurentThreadsSupported < 1) { concurentThreadsSupported = 1; } //in case thread errors
processors = toString(concurentThreadsSupported);
flowfile = "";
biomfile = "";
countfile = "";
summaryfile = "";
contigsreportfile = "";
groupMode = "group";
sharedHeaderMode = "otu";
mothurCalling = false;
}
~CurrentFile() { instance = 0; }
};
/***********************************************/
#endif
|
