added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index c5a94839cd82427c193e3e78a71c8e8434636653..137cb735719fba42f0d103af842de80c9930cc3e 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -27,7 +27,8 @@ public:
        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()); }  
        
@@ -36,27 +37,20 @@ private:
        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) {}
+               unsigned long long start;
+               unsigned long long end;
+               linePair(unsigned long long i, unsigned long long 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 getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
        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, outputDir;
+       bool abort, createGroup;
+       string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -72,14 +66,15 @@ private:
        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, 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>&);
+       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 long>&, vector<unsigned long long>&);
 };
 
 #endif