added citation function to commands

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index e2b0687e2108bc2f6bc95201917dd08d67f757bf..c5a94839cd82427c193e3e78a71c8e8434636653 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,51 +13,73 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
+#include "groupmap.h"
 
 class TrimSeqsCommand : public Command {
 public:
        TrimSeqsCommand(string);
-       ~TrimSeqsCommand();
-       int execute();
-       void help();
+       TrimSeqsCommand();
+       ~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"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-
+       
+       GroupMap* groupMap;
+       
        struct linePair {
-               int start;
-               int num;
-               linePair(long int i, int j) : start(i), num(j) {}
+               unsigned long int start;
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+       
+       void getOligos(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&);
 
-       void getOligos(vector<string>&);
-       bool stripQualThreshold(Sequence&, ifstream&);
-       bool cullQualAverage(Sequence&, ifstream&);
-       bool stripBarcode(Sequence&, int&);
-       bool stripForward(Sequence&);
-       bool stripReverse(Sequence&);
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
-       int countDiffs(string, string);//, int, int&, int);
+       int countDiffs(string, string);
 
        bool abort;
-       string fastaFile, oligoFile, qFileName, outputDir;
+       string fastaFile, oligoFile, qFileName, groupfile, outputDir;
        
        bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs;
-       vector<string> forPrimer, revPrimer, outputNames;
+       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;  
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        vector<linePair*> qLines;
        
-       int driverCreateTrim(string, string, string, string, string, vector<string>, linePair*, linePair*);     
-       int createProcessesCreateTrim(string, string, string, string, string, vector<string>);
-       int setLines(string, vector<linePair*>&);
-       
+       int driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);   
+       int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
+       int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };
 
 #endif