fixed bug with trim.seqs allfiles=t

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 2d0eabc1aa5a1504d23d1fc146f525504f3213f9..40c221a0ec61c051099d081f15dd87bea135a163 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -26,6 +26,7 @@ public:
        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()); }  
@@ -40,7 +41,7 @@ private:
                linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
        
-       void getOligos(vector<vector<string> >&, vector<vector<string> >&);
+       void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
        int stripBarcode(Sequence&, QualityScores&, int&);
        int stripForward(Sequence&, QualityScores&, int&);
        bool stripReverse(Sequence&, QualityScores&);
@@ -55,7 +56,7 @@ private:
        int countDiffs(string, string);
 
        bool abort;
-       string fastaFile, oligoFile, qFileName, groupfile, outputDir;
+       string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -71,13 +72,14 @@ 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 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 int>&, vector<unsigned long int>&);
 };