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#ifndef SCREENSEQSCOMMAND_H
#define SCREENSEQSCOMMAND_H
/*
* screenseqscommand.h
* Mothur
*
* Created by Pat Schloss on 6/3/09.
* Copyright 2009 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "sequence.hpp"
#include "writer.h"
class ScreenSeqsCommand : public Command {
public:
ScreenSeqsCommand(string);
~ScreenSeqsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "screen.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCommonQuestions();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
int optimizeContigs();
int optimizeAlign();
int createProcesses(string, string, string, map<string, string>&);
int screenSummary(map<string, string>&);
int screenContigs(map<string, string>&);
int screenAlignReport(map<string, string>&);
int runFastaScreening(map<string, string>&);
int screenFasta(map<string, string>&);
int screenReports(map<string, string>&);
string printAccnos(map<string, string>& badSeqNames);
int getSummary();
int getSummaryReport();
bool abort;
string fastafile, namefile, groupfile, alignreport, qualfile, taxonomy, countfile, contigsreport, summaryfile, fileType, badAccnosFile;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, minOverlap, oStart, oEnd, mismatches, maxN, maxInsert;
float minSim, minScore, criteria;
vector<string> outputNames;
vector<string> optimize;
map<string, int> nameMap;
};
/**************************************************************************************************/
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
struct sumScreenData {
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, maxN;
unsigned long long start;
unsigned long long end;
int count;
MothurOut* m;
string goodFName, badAccnosFName, filename;
map<string, string> badSeqNames;
string summaryfile, contigsreport;
Utils util;
OutputWriter* outputWriter;
OutputWriter* accnosWriter;
sumScreenData(){}
sumScreenData(int s, int e, int a, int h, int minl, int maxl, int mn, map<string, string> bs, string f, string sum, string cont, unsigned long long st, unsigned long long en, OutputWriter* oWriter, OutputWriter* aWriter) {
startPos = s;
endPos = e;
minLength = minl;
maxLength = maxl;
maxAmbig = a;
maxHomoP = h;
maxN = mn;
filename = f;
outputWriter = oWriter;
accnosWriter = aWriter;
m = MothurOut::getInstance();
start = st;
end = en;
summaryfile = sum;
contigsreport = cont;
badSeqNames = bs;
count = 0;
}
};
/**************************************************************************************************/
#endif
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