removed UWSig and WSig from output if user does not set random=T

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 99103ba25af92565be2e0879c0904603aea5990c..5affc3fbdf7fedc366f7c8294c762e28681d7625 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -20,13 +20,18 @@ class TrimFlowsCommand : public Command {
 public:
        TrimFlowsCommand(string);
        TrimFlowsCommand();
-       ~TrimFlowsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~TrimFlowsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "trim.flows";  }
+       string getCommandCategory()             { return "Hidden";              }
+       string getHelpString(); 
+       string getCitation() { return "no citation"; }
+       string getDescription()         { return "trim.flows"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
@@ -44,13 +49,9 @@ private:
        int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
        int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
 
-       
-       map<string, vector<string> > outputTypes;
        vector<string> outputNames;
        set<string> filesToRemove;
        
-       
-       
        void getOligos(vector<vector<string> >&);               //a rewrite of what is in trimseqscommand.h
        int stripBarcode(Sequence&, int&);                              //largely redundant with trimseqscommand.h
        int stripForward(Sequence&, int&);                              //largely redundant with trimseqscommand.h
@@ -65,7 +66,7 @@ private:
        int numFlows;
        float signal, noise;
        bool fasta;
-       
+       string flowOrder;       
        
        string flowFileName, oligoFileName, outputDir;