added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index d8eb853dae6892711a9004ae9ad670032f47228e..4e72a960a7bb07d4e94df795bea462519f6d777a 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -17,7 +17,7 @@
 struct CommonHeader {
        unsigned int magicNumber;
        string version;
-       unsigned long int indexOffset;
+       unsigned long long indexOffset;
        unsigned int indexLength;
        unsigned int numReads;
        unsigned short headerLength;
@@ -64,21 +64,27 @@ class SffInfoCommand : public Command {
 public:
        SffInfoCommand(string);
        SffInfoCommand();
-       ~SffInfoCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SffInfoCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "sffinfo";                                     }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+       string getDescription()         { return "extract sequences reads from a .sff file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string sffFilename, outputDir, accnosName;
+       string sffFilename, sfftxtFilename, outputDir, accnosName;
        vector<string> filenames, outputNames, accnosFileNames;
        bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+       int mycount;
        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 +98,14 @@ private:
        int printFastaSeqData(ofstream&, seqRead&, Header&);
        int printQualSeqData(ofstream&, seqRead&, Header&);
        int readAccnosFile(string);
-               
+       int parseSffTxt();
+       bool sanityCheck(Header&, seqRead&);
+    
+       //parsesfftxt file functions
+       int parseHeaderLineToInt(ifstream&);
+       vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+       vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+       string parseHeaderLineToString(ifstream&);
 };
 
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