X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsefastaqcommand.h;h=96fcb7d6799358ff4e10f930d1ad4165763b46a0;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=c45405f42455de7bbdf93d7f2c391756d0700a05;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index c45405f..96fcb7d 100644
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -18,22 +18,27 @@ 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 getOutputFileNameTag(string, string);
+	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;
+	string outputDir, fastaQFile, format;
+	bool abort, fasta, qual;
 	
 	vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif