pat's changes to trim.seqs

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index ab692d3ee0dbd3ce77ce158ab9a0e82aca7719e6..a904a10b683ce3fd04784e9ac1a60d02e293c368 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "qualityscores.h"
 
 class TrimSeqsCommand : public Command {
 public:
@@ -29,23 +30,23 @@ private:
                linePair(unsigned long int i, int j) : start(i), num(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);
 
        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;
@@ -57,8 +58,8 @@ 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 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, vector<linePair*>&);
        
 };