added pipeline commands which involved change to command factory and command class...

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index a904a10b683ce3fd04784e9ac1a60d02e293c368..20b11a85ac05e57b453906475d73ab4fd2ecb2e0 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -18,7 +18,12 @@
 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();
        
@@ -26,8 +31,8 @@ private:
 
        struct linePair {
                unsigned long int start;
-               int num;
-               linePair(unsigned long int i, int j) : start(i), num(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
 
        void getOligos(vector<string>&, vector<string>&);
@@ -39,6 +44,7 @@ private:
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
        int countDiffs(string, string);
+       map<string, vector<string> > outputTypes;
 
        bool abort;
        string fastaFile, oligoFile, qFileName, outputDir;
@@ -60,7 +66,7 @@ private:
        
        int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);     
        int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
-       int setLines(string, vector<linePair*>&);
+       int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
        
 };