addition of trim.flows

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
new file mode 100644 (file)
index 0000000..215b1a2
--- /dev/null
+++ b/trimflowscommand.h
@@ -0,0 +1,89 @@
+#ifndef TRIMFLOWSCOMMAND_H
+#define TRIMFLOWSCOMMAND_H
+
+/*
+ *  trimflowscommand.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 12/22/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "command.hpp"
+#include "sequence.hpp"
+#include "flowdata.h"
+#include "groupmap.h"
+
+class TrimFlowsCommand : public Command {
+public:
+       TrimFlowsCommand(string);
+       TrimFlowsCommand();
+       ~TrimFlowsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();
+       
+private:
+       bool abort;
+
+//     GroupMap* groupMap;
+       
+       struct linePair {
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+       };
+       int comboStarts;
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
+       vector<linePair*> qLines;
+       map<string, vector<string> > outputTypes;
+       vector<string> outputNames;
+       set<string> filesToRemove;
+
+       
+       
+       void getOligos(vector<vector<string> >&);               //a rewrite of what is in trimseqscommand.h
+       int stripBarcode(Sequence&, int&);                              //largely redundant with trimseqscommand.h
+       int stripForward(Sequence&, int&);                              //largely redundant with trimseqscommand.h
+       bool stripReverse(Sequence&);                                   //largely redundant with trimseqscommand.h
+       bool compareDNASeq(string, string);                             //largely redundant with trimseqscommand.h
+       int countDiffs(string, string);                                 //largely redundant with trimseqscommand.h
+
+       
+       bool allFiles;
+//     int processors;
+       int numFPrimers, numRPrimers;
+       int totalFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       float signal, noise;
+       bool fasta;
+       
+       
+       string flowFileName, oligoFileName, outputDir;
+
+
+       map<string, int> barcodes;
+       map<string, int> primers;
+       vector<string> revPrimer;
+
+       vector<string> primerNameVector;        //needed here?
+       vector<string> barcodeNameVector;       //needed here?
+
+       map<string, int> combos;                        //needed here?
+       map<string, int> groupToIndex;          //needed here?
+       
+       
+       int driverCreateTrim(string, string, string, string);
+       
+//     int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>){};
+       int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&){};
+       
+};
+
+
+#endif