added kruskwalliscommand to Xcode project and fixed parameter issues.

[mothur.git] / parsefastaqcommand.h

diff --git a/parsefastaqcommand.h b/parsefastaqcommand.h
index 4481b98bb23bdbcd47a6059b2df0904c176ae9bf..b4d90e542a98f329dd166a93c54d57852e0f54dd 100644 (file)
--- a/parsefastaqcommand.h
+++ b/parsefastaqcommand.h
@@ -23,8 +23,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "parse.fastq";         }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        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"; }
 
@@ -34,10 +35,11 @@ public:
 private:
 
        vector<string> outputNames;     
-       string outputDir, fastaQFile;
+       string outputDir, fastaQFile, format;
        bool abort, fasta, qual;
        
        vector<int> convertQual(string);
+    vector<char> convertTable;
 };
 
 #endif