added modify names parameter to set.dir

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index c45405f42455de7bbdf93d7f2c391756d0700a05..5ae6b9c482fe6b4022bb4d4c5d4ae2e79ea3aad8 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -18,22 +18,28 @@ class ParseFastaQCommand : public Command {
 public:
        ParseFastaQCommand(string);
        ParseFastaQCommand();
-       ~ParseFastaQCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       ~ParseFastaQCommand() {}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "fastq.info";          }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+       string getDescription()         { return "reads a fastq file and creates a fasta and quality file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
 
        vector<string> outputNames;     
-       map<string, vector<string> > outputTypes;
-       string outputDir, fastaQFile;
-       bool abort;
+       string outputDir, fastaQFile, format;
+       bool abort, fasta, qual, pacbio;
        
        vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif