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"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
-// GroupMap* groupMap;
-
struct linePair {
unsigned long int start;
unsigned long int end;
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
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;
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>&){};
-
};