moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
deleted file mode 100644 (file)
index 837435b..0000000
--- a/sffinfocommand.h
+++ /dev/null
@@ -1,114 +0,0 @@
-#ifndef SFFINFOCOMMAND_H
-#define SFFINFOCOMMAND_H
-
-/*
- *  sffinfocommand.h
- *  Mothur
- *
- *  Created by westcott on 7/7/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-
-
-/**********************************************************/
-struct CommonHeader {
-       unsigned int magicNumber;
-       string version;
-       unsigned long long indexOffset;
-       unsigned int indexLength;
-       unsigned int numReads;
-       unsigned short headerLength;
-       unsigned short keyLength;
-       unsigned short numFlowsPerRead;
-       int flogramFormatCode;
-       string flowChars; //length depends on number flow reads
-       string keySequence; //length depends on key length
-       
-       CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; } 
-       ~CommonHeader() { }
-};
-/**********************************************************/
-struct Header {
-       unsigned short headerLength;
-       unsigned short nameLength;
-       unsigned int numBases;
-       unsigned short clipQualLeft;
-       unsigned short clipQualRight;
-       unsigned short clipAdapterLeft;
-       unsigned short clipAdapterRight;
-       string name; //length depends on nameLength
-       string timestamp;
-       string region;
-       string xy;
-       
-       Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
-       ~Header() { } 
-};
-/**********************************************************/
-struct seqRead {
-       vector<unsigned short> flowgram;
-       vector<unsigned int> flowIndex;
-       string bases;
-       vector<unsigned int> qualScores;
-       
-       seqRead() { } 
-       ~seqRead() { } 
-};
-/**********************************************************/
-
-class SffInfoCommand : public Command {
-       
-public:
-       SffInfoCommand(string);
-       SffInfoCommand();
-       ~SffInfoCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "sffinfo";                                     }
-       string getCommandCategory()             { return "Sequence Processing";         }
-       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, sfftxtFilename, outputDir, accnosName;
-       vector<string> filenames, outputNames, accnosFileNames;
-       bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
-       int mycount;
-       set<string> seqNames;
-    
-       //extract sff file functions
-       int extractSffInfo(string, string);
-       int readCommonHeader(ifstream&, CommonHeader&);
-       int readHeader(ifstream&, Header&);
-       int readSeqData(ifstream&, seqRead&, int, int);
-       int decodeName(string&, string&, string&, string);
-       
-       int printCommonHeader(ofstream&, CommonHeader&); 
-       int printHeader(ofstream&, Header&);
-       int printSffTxtSeqData(ofstream&, seqRead&, Header&);
-       int printFlowSeqData(ofstream&, seqRead&, Header&);
-       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&);
-};
-
-/**********************************************************/
- 
-#endif
-
-