removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index d8eb853dae6892711a9004ae9ad670032f47228e..d98edbd3e04f0213a24ed51471d09aab1b74d46a 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -73,12 +73,13 @@ public:
        void help();
        
 private:
-       string sffFilename, outputDir, accnosName;
+       string sffFilename, sfftxtFilename, outputDir, accnosName;
        vector<string> filenames, outputNames, accnosFileNames;
        bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
        set<string> seqNames;
        map<string, vector<string> > outputTypes;
        
+       //extract sff file functions
        int extractSffInfo(string, string);
        int readCommonHeader(ifstream&, CommonHeader&);
        int readHeader(ifstream&, Header&);
@@ -92,7 +93,13 @@ private:
        int printFastaSeqData(ofstream&, seqRead&, Header&);
        int printQualSeqData(ofstream&, seqRead&, Header&);
        int readAccnosFile(string);
-               
+       int parseSffTxt();
+       
+       //parsesfftxt file functions
+       int parseHeaderLineToInt(ifstream&);
+       vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+       vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+       string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/