fixed bug with trim.seqs allfiles=t

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index d40cfe3c5604d66009ba22b568b0df71f3688faa..40c221a0ec61c051099d081f15dd87bea135a163 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -20,13 +20,16 @@ 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();
+       ~TrimSeqsCommand(){}
+       
+       vector<string> setParameters();
+       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()); }  
        
 private:
        
@@ -38,7 +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&);
@@ -51,10 +54,9 @@ private:
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
        int countDiffs(string, string);
-       map<string, vector<string> > outputTypes;
 
        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;
@@ -70,13 +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>&);
 };