removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 7458dbe60b90f52c900e3ffd8fb645ccce0d0e86..0514a53edc62362d3b95118d5d5e501fd2ef0b2e 100644 (file)
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -20,13 +20,15 @@ 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(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
@@ -44,13 +46,9 @@ 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