added group option to trim.seqs so you can provide your own groupfile instead of...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 93e8c776918ec9fa2d6f661d7c178380a4f47d66..2f8fbd7c499559bf65f9f5393982bd00dddfbcc3 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -14,16 +14,24 @@
 #include "command.hpp"
 #include "sequence.hpp"
 #include "qualityscores.h"
+#include "groupmap.h"
 
 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();
        
 private:
-
+       
+       GroupMap* groupMap;
+       
        struct linePair {
                unsigned long int start;
                unsigned long int end;
@@ -39,9 +47,10 @@ private:
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
        int countDiffs(string, string);
+       map<string, vector<string> > outputTypes;
 
        bool abort;
-       string fastaFile, oligoFile, qFileName, outputDir;
+       string fastaFile, oligoFile, qFileName, groupfile, outputDir;
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -53,6 +62,7 @@ private:
        vector<string> groupVector;
        map<string, int> primers;
        map<string, int> combos;
+       map<string, int> groupToIndex;
        
        vector<int> processIDS;   //processid
        vector<linePair*> lines;