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msequenceserver.h
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msequenceserver.h
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/*
Copyright (C) 2003 Ronald C Beavis, all rights reserved
X! tandem
This software is a component of the X! proteomics software
development project
Use of this software governed by the Artistic license, as reproduced here:
The Artistic License for all X! software, binaries and documentation
Preamble
The intent of this document is to state the conditions under which a
Package may be copied, such that the Copyright Holder maintains some
semblance of artistic control over the development of the package,
while giving the users of the package the right to use and distribute
the Package in a more-or-less customary fashion, plus the right to
make reasonable modifications.
Definitions
"Package" refers to the collection of files distributed by the Copyright
Holder, and derivatives of that collection of files created through
textual modification.
"Standard Version" refers to such a Package if it has not been modified,
or has been modified in accordance with the wishes of the Copyright
Holder as specified below.
"Copyright Holder" is whoever is named in the copyright or copyrights
for the package.
"You" is you, if you're thinking about copying or distributing this Package.
"Reasonable copying fee" is whatever you can justify on the basis of
media cost, duplication charges, time of people involved, and so on.
(You will not be required to justify it to the Copyright Holder, but
only to the computing community at large as a market that must bear
the fee.)
"Freely Available" means that no fee is charged for the item itself,
though there may be fees involved in handling the item. It also means
that recipients of the item may redistribute it under the same
conditions they received it.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that
you duplicate all of the original copyright notices and associated
disclaimers.
2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A
Package modified in such a way shall still be considered the Standard
Version.
3. You may otherwise modify your copy of this Package in any way, provided
that you insert a prominent notice in each changed file stating how and
when you changed that file, and provided that you do at least ONE of the
following:
a. place your modifications in the Public Domain or otherwise make them
Freely Available, such as by posting said modifications to Usenet
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to include your modifications in the Standard Version of the Package.
b. use the modified Package only within your corporation or organization.
c. rename any non-standard executables so the names do not conflict
with standard executables, which must also be provided, and provide
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d. make other distribution arrangements with the Copyright Holder.
4. You may distribute the programs of this Package in object code or
executable form, provided that you do at least ONE of the following:
a. distribute a Standard Version of the executables and library files,
together with instructions (in the manual page or equivalent) on
where to get the Standard Version.
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Package with your modifications.
c. give non-standard executables non-standard names, and clearly
document the differences in manual pages (or equivalent), together
with instructions on where to get the Standard Version.
d. make other distribution arrangements with the Copyright Holder.
5. You may charge a reasonable copying fee for any distribution of
this Package. You may charge any fee you choose for support of
this Package. You may not charge a fee for this Package itself.
However, you may distribute this Package in aggregate with other
(possibly commercial) programs as part of a larger (possibly
commercial) software distribution provided that you do not a
dvertise this Package as a product of your own. You may embed this
Package's interpreter within an executable of yours (by linking);
this shall be construed as a mere form of aggregation, provided that
the complete Standard Version of the interpreter is so embedded.
6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whomever generated
them, and may be sold commercially, and may be aggregated with this
Package. If such scripts or library files are aggregated with this
Package via the so-called "undump" or "unexec" methods of producing
a binary executable image, then distribution of such an image shall
neither be construed as a distribution of this Package nor shall it
fall under the restrictions of Paragraphs 3 and 4, provided that you
do not represent such an executable image as a Standard Version of
this Package.
7. C subroutines (or comparably compiled subroutines in other languages)
supplied by you and linked into this Package in order to emulate
subroutines and variables of the language defined by this Package
shall not be considered part of this Package, but are the equivalent
of input as in Paragraph 6, provided these subroutines do not change
the language in any way that would cause it to fail the regression
tests for the language.
8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
construed as a distribution of this Package.
9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.
10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
The End
*/
// 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