prt Class Reference

#include <prt.h>

List of all members.

Public Member Functions
	prt (const string &infile)
bool	next ()
void	clear ()
void	processID ()
vector< string >	getAC ()
string	getSWID ()
void	writeAce (ostream &os1, ostream &os2)
ostream &	writeSeq (ostream &os, const int len=75)
void	writeMappedTag (ostream &os)
Static Public Member Functions
static void	init ()
Static Public Attributes
static const int	content_idx = 5
static const int	ftdescript_idx = 34
static const int	cc_dash = 74
static map< string, string >	field = map<string,string>()
static string	record_separator = "//"
static map< string, string >	swtag2ace = map<string,string>()
static string	swtag2ace_str [] = {"DE", "Title", "OG", "Organelle", "CC", "DB_remark"}
Private Member Functions
void	read_upto (const string &code)
void	tossccJunk ()
Private Attributes
ifstream	input
map< string, string >	record
string	next_line
string	dates [3]
string	seq
vector< ref >	papers
vector< vector< string > >	dbxref
vector< vector< string > >	feature
string	swpid
char	type
char	swprt_status
int	length
Static Private Attributes
static set< string >	orgset = set<string>()
static set< string >	papset = set<string>()

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Constructor & Destructor Documentation

prt::prt

(

const string &

infile

)

construct a stream of prt objects from a file of swissprot records, so that you can iterator through the objects.

References input.

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Member Function Documentation

bool prt::next

(

)

References ref::bad(), cc_dash, clear(), content_idx, dates, dbxref, ftdescript_idx, input, ref::next(), next_line, papers, processID(), read_upto(), record, remove_end_mark(), replace(), separate(), seq, split(), string(), and tossccJunk().

Referenced by main().

void prt::clear

(

)

References dbxref, papers, record, and seq.

Referenced by next().

void prt::processID

(

)

for processing all EMBL entries

References length, record, split(), swpid, swprt_status, and type.

Referenced by next().

vector< string > prt::getAC

(

)

References erase(), record, and split().

Referenced by writeAce().

string prt::getSWID

(

)

[inline]

References swpid.

Referenced by main().

void prt::writeAce	(	ostream &	os1,
		ostream &	os2
	)

all those defined in swtag2ace /////////////

gene names more complicated //////////

References dbtime::aceTime(), dates, dbxref, erase(), getAC(), length, orgset, papers, papset, dbtime::readsw(), record, replace(), split(), substr(), toupper(), writeMappedTag(), and writeSeq().

Referenced by main().

ostream & prt::writeSeq	(	ostream &	os,
		const int	len = 75
	)

References seq.

Referenced by writeAce().

void prt::writeMappedTag

(

ostream &

os

)

References record, and swtag2ace.

Referenced by writeAce().

void prt::init

(

)

[static]

References swtag2ace, and swtag2ace_str.

Referenced by main().

void prt::read_upto

(

const string &

code

)

[private]

next_line should contain the first line of the record with the same line code

References content_idx, input, next_line, record, record_separator, and separate().

Referenced by next().

void prt::tossccJunk

(

)

[private]

read and discard upto the dash line; next_line will contain one line after the dashed line.

References cc_dash, content_idx, input, next_line, and string().

Referenced by next().

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Member Data Documentation

const int prt::content_idx = 5 [static]

the following two line are initialized here instead of the definition file

Referenced by next(), ref::next(), read_upto(), separate(), and tossccJunk().

const int prt::ftdescript_idx = 34 [static]

Referenced by next().

const int prt::cc_dash = 74 [static]

Referenced by next(), and tossccJunk().

map< string, string > prt::field = map<string,string>() [static]

string prt::record_separator = "//" [static]

Referenced by read_upto().

map< string, string > prt::swtag2ace = map<string,string>() [static]

Two-letter code tag translated to Ace tag

Referenced by init(), and writeMappedTag().

string prt::swtag2ace_str = {"DE", "Title", "OG", "Organelle", "CC", "DB_remark"} [static]

Referenced by init().

ifstream prt::input [private]

Referenced by next(), prt(), read_upto(), and tossccJunk().

map<string,string> prt::record [private]

All two-letter code => content

Referenced by clear(), getAC(), next(), processID(), read_upto(), writeAce(), and writeMappedTag().

string prt::next_line [private]

Referenced by next(), read_upto(), and tossccJunk().

string prt::dates[3] [private]

Referenced by next(), and writeAce().

string prt::seq [private]

Actual protein sequence string

Referenced by clear(), next(), and writeSeq().

vector<ref> prt::papers [private]

Referenced by clear(), next(), and writeAce().

vector< vector<string> > prt::dbxref [private]

Referenced by clear(), next(), and writeAce().

vector< vector<string> > prt::feature [private]

string prt::swpid [private]

Referenced by getSWID(), and processID().

char prt::type [private]

Referenced by processID().

char prt::swprt_status [private]

Referenced by processID().

int prt::length [private]

Referenced by processID(), and writeAce().

set< string > prt::orgset = set<string>() [static, private]

for keeping records of organism key

Referenced by writeAce().

set< string > prt::papset = set<string>() [static, private]

Referenced by writeAce().

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The documentation for this class was generated from the following files:

• seqconv/sptoace/prt.h
• seqconv/sptoace/prt.cpp