fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index c45405f42455de7bbdf93d7f2c391756d0700a05..6feabce848c09c21b2e276df8361ac4d78667f22 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -18,20 +18,23 @@ 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 "parse.fastq";         }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       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;
+       bool abort, fasta, qual;
        
        vector<int> convertQual(string);
 };