X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;fp=sffinfocommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=837435b3a6ca4c4c7f2e7e7579141b8fbece342b;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
deleted file mode 100644
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
-
-