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#ifndef DISTANCECOMMAND_H
#define DISTANCECOMMAND_H
/*
* distancecommand.h
* Mothur
*
* Created by Sarah Westcott on 5/7/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "validcalculator.h"
#include "calculator.h"
#include "sequencedb.h"
#include "ignoregaps.h"
#include "eachgapdist.h"
#include "eachgapignore.h"
#include "onegapdist.h"
#include "onegapignore.h"
#include "jtt.hpp"
#include "writer.h"
#include "proteindb.hpp"
#include "pmb.hpp"
#include "pam.hpp"
#include "kimura.hpp"
/**************************************************************************************************/
struct distanceData {
long long startLine, endLine, numNewFasta, count;
float cutoff;
StorageDatabase* db;
StorageDatabase* oldFastaDB;
MothurOut* m;
OutputWriter* threadWriter;
string outputFileName, calc;
bool countends, prot;
Utils util;
distanceData(){}
distanceData(OutputWriter* ofn) {
threadWriter = ofn;
m = MothurOut::getInstance();
}
distanceData(string ofn) {
outputFileName = ofn;
m = MothurOut::getInstance();
}
void setVariables(int s, int e, float c, StorageDatabase*& dbsp, StorageDatabase*& oldfn, string Est, bool met, long long num, bool cnt) {
startLine = s;
endLine = e;
cutoff = c;
db = dbsp;
oldFastaDB = oldfn;
calc = Est;
prot = met;
numNewFasta = num;
countends = cnt;
count = 0;
}
};
/**************************************************************************************************/
class DistanceCommand : public Command {
public:
DistanceCommand(string);
DistanceCommand(StorageDatabase*&, string, double, string, int); //used by mothur's splitMatrix class to avoid rereading files
~DistanceCommand() = default;
vector<string> setParameters();
string getCommandName() { return "dist.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
string getDescription() { return "calculate the pairwaise distances between aligned sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
StorageDatabase* db;
string output, fastafile, calc, oldfastafile, column;
int processors;
long long numNewFasta, numSeqs, numDistsBelowCutoff;
float cutoff;
bool abort, countends, fitCalc, prot, compress;
vector<string> outputNames;
void createProcesses(string);
bool sanityCheck();
};
#endif
/**************************************************************************************************/
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