added shhh.seqs command

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 215b1a2f69bf717e11e2a8f25ce1761e7c0951f9..15c698c2ffe6075101ab1105ff60f579c349c425 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -31,8 +31,6 @@ public:
 private:
        bool abort;
 
-//     GroupMap* groupMap;
-       
        struct linePair {
                unsigned long int start;
                unsigned long int end;
@@ -41,11 +39,16 @@ private:
        int comboStarts;
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
-       vector<linePair*> qLines;
+
+       vector<unsigned long int> getFlowFileBreaks();
+       int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
+       int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+
+       
        map<string, vector<string> > outputTypes;
        vector<string> outputNames;
        set<string> filesToRemove;
-
+       
        
        
        void getOligos(vector<vector<string> >&);               //a rewrite of what is in trimseqscommand.h
@@ -54,12 +57,12 @@ private:
        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 processors;
        int numFPrimers, numRPrimers;
        int totalFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int numFlows;
        float signal, noise;
        bool fasta;
        
@@ -77,12 +80,6 @@ private:
        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>&){};
-       
 };