removed unused copy constructors and comments within comments that where causing...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index d40cfe3c5604d66009ba22b568b0df71f3688faa..b6050f2ee58a3db6f56714e7f313fa9ed93b77b5 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -20,44 +20,40 @@ 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"; }
+       string getDescription()         { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 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);
-       map<string, vector<string> > outputTypes;
 
-       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;
+       bool flip, allFiles, qtrim, keepforward;
+       int numFPrimers, numRPrimers, numLinkers, numSpacers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, comboStarts;
        int qWindowSize, qWindowStep, keepFirst, removeLast;
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
        vector<string> revPrimer, outputNames;
@@ -65,19 +61,22 @@ private:
        map<string, int> barcodes;
        vector<string> groupVector;
        map<string, int> primers;
+    vector<string>  linker;
+    vector<string>  spacer;
        map<string, int> combos;
        map<string, int> groupToIndex;
        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