added command descriptions

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 215b1a2f69bf717e11e2a8f25ce1761e7c0951f9..5affc3fbdf7fedc366f7c8294c762e28681d7625 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -20,19 +20,22 @@ 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;
 
-//     GroupMap* groupMap;
-       
        struct linePair {
                unsigned long int start;
                unsigned long int end;
@@ -41,12 +44,13 @@ private:
        int comboStarts;
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
-       vector<linePair*> qLines;
-       map<string, vector<string> > outputTypes;
+
+       vector<unsigned long int> getFlowFileBreaks();
+       int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
+       int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+
        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
@@ -54,15 +58,15 @@ private:
        bool stripReverse(Sequence&);                                   //largely redundant with trimseqscommand.h
        bool compareDNASeq(string, string);                             //largely redundant with trimseqscommand.h
        int countDiffs(string, string);                                 //largely redundant with trimseqscommand.h
-
        
        bool allFiles;
-//     int processors;
+       int processors;
        int numFPrimers, numRPrimers;
-       int totalFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+       int numFlows;
        float signal, noise;
        bool fasta;
-       
+       string flowOrder;       
        
        string flowFileName, oligoFileName, outputDir;
 
@@ -77,12 +81,6 @@ private:
        map<string, int> combos;                        //needed here?
        map<string, int> groupToIndex;          //needed here?
        
-       
-       int driverCreateTrim(string, string, string, string);
-       
-//     int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>){};
-       int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&){};
-       
 };