added pipeline commands which involved change to command factory and command class...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index b5357b38e1e3bf892ef7f0cd9ffcfb7b7de4ec8a..20b11a85ac05e57b453906475d73ab4fd2ecb2e0 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,40 +13,48 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
 
 class TrimSeqsCommand : public Command {
 public:
        TrimSeqsCommand(string);
+       TrimSeqsCommand();
        ~TrimSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
 
        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<string>&);
-       bool stripQualThreshold(Sequence&, ifstream&);
-       bool cullQualAverage(Sequence&, ifstream&);
-       int stripBarcode(Sequence&, int&);
-       int stripForward(Sequence&, int&);
-       bool stripReverse(Sequence&);
+       void getOligos(vector<string>&, vector<string>&);
+       int stripBarcode(Sequence&, QualityScores&, int&);
+       int stripForward(Sequence&, QualityScores&, int&);
+       bool stripReverse(Sequence&, QualityScores&);
        bool cullLength(Sequence&);
        bool cullHomoP(Sequence&);
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
-       int countDiffs(string, string);//, int, int&, int);
+       int countDiffs(string, string);
+       map<string, vector<string> > outputTypes;
 
        bool abort;
        string fastaFile, oligoFile, qFileName, outputDir;
        
        bool flip, allFiles, qtrim;
-       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, qThreshold, qAverage, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+       int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
+       int qWindowSize, qWindowStep;
+       double qRollAverage, qThreshold, qWindowAverage, qAverage;
        vector<string> revPrimer, outputNames;
+       set<string> filesToRemove;
        map<string, int> barcodes;
        vector<string> groupVector;
        map<string, int> primers;
@@ -56,9 +64,9 @@ private:
        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<string>, vector<string>, linePair*, linePair*);     
+       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>&);
        
 };