added command descriptions

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 0a34ff303e618839e3fd80583e91f9ab10305ff8..02a88e889654fd2c6d805e64fbd576a3e1ceb5ad 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -12,33 +12,76 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
+#include "sequence.hpp"
+#include "qualityscores.h"
+#include "groupmap.h"
 
 class TrimSeqsCommand : public Command {
 public:
+       TrimSeqsCommand(string);
        TrimSeqsCommand();
-       ~TrimSeqsCommand();
-       int execute();
+       ~TrimSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "trim.seqs";   }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
+       string getDescription()         { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void getOligos();
-       bool stripBarcode(Sequence&, string&);
-       bool stripForward(Sequence&);
-       bool stripReverse(Sequence&);
        
-       GlobalData* globaldata;
+       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 totalBarcodeCount, matchBarcodeCount;
-       int totalFPrimerCount, matchFPrimerCount;
-       int totalRPrimerCount, matchRPrimerCount;
+       void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
+       int stripBarcode(Sequence&, QualityScores&, int&);
+       int stripForward(Sequence&, QualityScores&, int&);
+       bool stripReverse(Sequence&, QualityScores&);
        
+       bool keepFirstTrim(Sequence&, QualityScores&);
+       bool removeLastTrim(Sequence&, QualityScores&);
+
+       bool cullLength(Sequence&);
+       bool cullHomoP(Sequence&);
+       bool cullAmbigs(Sequence&);
+       bool compareDNASeq(string, string);
+       int countDiffs(string, string);
+
+       bool abort;
+       string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
        
-       bool oligos, flip;
-       int forwardPrimerMismatch, reversePrimerMismatch, barcodeMismatch;
-       int numFPrimers, numRPrimers;
-       vector<string> forPrimer, revPrimer;
-       map<string, string> barcodes;
+       bool flip, allFiles, qtrim;
+       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+       int qWindowSize, qWindowStep, keepFirst, removeLast;
+       double qRollAverage, qThreshold, qWindowAverage, qAverage;
+       vector<string> revPrimer, outputNames;
+       set<string> filesToRemove;
+       map<string, int> barcodes;
+       vector<string> groupVector;
+       map<string, int> primers;
+       map<string, int> combos;
+       map<string, int> groupToIndex;
+       vector<string> primerNameVector;        //needed here?
+       vector<string> barcodeNameVector;       //needed here?
+       map<string, int> groupCounts;  
+       map<string, string> nameMap;
 
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
+       vector<linePair*> qLines;
+       
+       int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);  
+       int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
+       int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };
 
 #endif