msequenceserver.h

/*
 Copyright (C) 2003 Ronald C Beavis, all rights reserved
 X! tandem 
 This software is a component of the X! proteomics software
 development project

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*/



// msequenceserver seems to be a class that returns proteins
// (represented here by msequence objects), reading them as necessary
// from fasta file(s).



#ifndef MSEQUENCESERVER_H
#define MSEQUENCESERVER_H

// File version: 2003-07-01

/*
 * msequenceserver takes a sequence list file (in FASTA format) and uses it to load an
 * msequencecontainer object with a set of amino acid sequences and descriptions. the container
 * can be loaded repeatedly until the end-of-file is reached. the next list file path in a 
 * deque of file names is then extracted and the process continues until the last
 * sequence from the last file in the deque is read into the msequencecontainer.
 */
typedef map<string,size_t> DESMAP;

class msequenceCollection;

class msequenceServer
{
public:
	msequenceServer(void);
	virtual ~msequenceServer(void);
		
	size_t m_tColMax;		// Maximum size of a sequence collection
	size_t m_tStartAt;	// Ordinal number of the first sequence retreived
	string m_strPath;		// Full path name to the current FASTA file
	string m_strStatus;    // Status string for debugging
	string m_strFirst;
	string m_strTaxonPath;	// Path to the taxonomy translation file
	string m_strTaxon;		// Taxon to model
	msequenceCollection *m_pCol;   // Sequence collection ring

	deque<string> m_dstrFasta;	// List of FASTA files
	vector<string> m_vstrFasta;
	vector<string> m_vstrDesc;

	enum {
		FASTA = 0,
		XBANG = 1,
		UNKNOWN = 0xFFFFFFFF,
	} mfiletypes;

	bool clear(void);
	bool done(void);		// true if all sequences retrieved
	bool error(void);	// true if object in any error state
	double get_time(void); // returns the elapsed time
	virtual long load_file(const string &_p,const string &_t);
	bool initialize(const size_t _t);
	unsigned long next(const bool _b);		// Method to retrieve ASequenceCollection object
	unsigned long next_pro(const bool _b);		// Method to retrieve ASequenceCollection object
	bool started(void);  // true if object was correctly started
	bool working(void);	// true if retrieving sequence
protected:
// Status indicators
	bool m_bStarted; // true if the server is processing files
	bool m_bDone; // true if the last sequence has been read
	bool m_bError; // true if the server is in an error condition
	double m_dTime; // the elapsed time taken to read sequences
	FILE *m_pInput; // a pointer to an input file
	unsigned long m_lFileType;
// Initializing/termination method
	char *m_pLine;
	unsigned long m_lSize;
	bool finish(void);
	unsigned long mac_rev(const unsigned long _l);
	unsigned long next_l(void);		// Method to retrieve ASequenceCollection object
	bool start(void);
};

#include "p3msequenceserver.h"

#endif