working on pam

[mothur.git] / makefastqcommand.h

diff --git a/makefastqcommand.h b/makefastqcommand.h
index fd893ad590f2f8ed8590b4741a8a11e8ec0db484..e3e0b70b087b17e5d6299052cb06567e9b7c9f69 100644 (file)
--- a/makefastqcommand.h
+++ b/makefastqcommand.h
@@ -20,19 +20,26 @@ public:
        MakeFastQCommand(string);       
        MakeFastQCommand();
        ~MakeFastQCommand(){}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.fastq";                          }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
+       string getDescription()         { return "creates a fastq file from a fasta and quality file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
        
-       string fastafile, qualfile, outputDir;
+       string fastafile, qualfile, outputDir, format;
        bool abort;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        string convertQual(vector<int>);