ProgParam Struct Reference

List of all members.

Public Member Functions
	ProgParam ()
void	setHost1 (const string &h1)
void	setHost2 (const string &h2)
void	setDatabase1 (const string &d1)
void	setDatabase2 (const string &d2)
bool	valid () const
	ProgParam ()
	ProgParam ()
bool	enough ()
Public Attributes
string	host
string	host1
string	host2
string	db
string	db1
string	db2
string	id1
string	id2
string	alntab
float	entropycut
int	exolpcut
double	exolpfrcut
double	avgidencut
string	fptoptab
string	fpdetailtab
string	outab
string	oufile
int	fpmaxlen
string	intab
Friends
ostream &	operator<< (ostream &ous, const ProgParam &par)

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Detailed Description

rtfp r join rtfungal_footprint_detail d using (qid,tid,fpnum,tdb) "

fptoptab is the output from picktopfootprint program.

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Constructor & Destructor Documentation

ProgParam::ProgParam

(

)

[inline]

ProgParam::ProgParam

(

)

[inline]

ProgParam::ProgParam

(

)

[inline]

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Member Function Documentation

void ProgParam::setHost1

(

const string &

h1

)

[inline]

References host1.

void ProgParam::setHost2

(

const string &

h2

)

[inline]

References host2.

void ProgParam::setDatabase1

(

const string &

d1

)

[inline]

References db1.

void ProgParam::setDatabase2

(

const string &

d2

)

[inline]

References db2.

bool ProgParam::valid

(

)

const

References alntab, db1, db2, host1, host2, id1, and id2.

Referenced by main().

bool ProgParam::enough

(

)

only check intab and outab for not emptyness

References intab, and outab.

Referenced by main().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const ProgParam &	par
	)			[friend]

only check intab and outab for not emptyness

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Member Data Documentation

string ProgParam::host

Referenced by main().

string ProgParam::host1

Referenced by bufferAllProteins(), main(), setHost1(), and valid().

string ProgParam::host2

Referenced by bufferAllProteins(), main(), setHost2(), and valid().

string ProgParam::db

Referenced by main().

string ProgParam::db1

Referenced by bufferAllProteins(), main(), setDatabase1(), and valid().

string ProgParam::db2

Referenced by bufferAllProteins(), main(), setDatabase2(), and valid().

string ProgParam::id1

Referenced by bufferAllProteins(), main(), and valid().

string ProgParam::id2

Referenced by bufferAllProteins(), main(), and valid().

string ProgParam::alntab

Referenced by bufferAllProteins(), main(), and valid().

float ProgParam::entropycut

according to fungal sequence alignment the distribution of entropy is as follows: entrop10 is floor(10xentropy) +---------+----------+ | entro10 | count | +---------+----------+ | 9 | 1 | | 10 | 1 | | 11 | 1 | | 12 | 4 | | 13 | 3 | | 14 | 14 | | 15 | 84 | | 16 | 108 | | 17 | 1001 | | 18 | 1079 | | 19 | 3104 | | 20 | 4240 | | 21 | 5163 | | 22 | 11638 | | 23 | 26835 | | 24 | 68991 | | 25 | 217339 | | 26 | 719777 | | 27 | 3460944 | | 28 | 10136982 | | 29 | 792906 | +---------+----------+ So 2.7 is a good cut off <2.7

Referenced by bufferAllProteins(), and main().

int ProgParam::exolpcut

Referenced by mergeNeighbor(), and operator<<().

double ProgParam::exolpfrcut

fraction of overlap as compared to the shorter of the footprint

Referenced by mergeNeighbor(), and operator<<().

double ProgParam::avgidencut

Referenced by mergeNeighbor(), and operator<<().

string ProgParam::fptoptab

footprint top picked by the program picktopfootprint

Referenced by main(), mergeNeighbor(), and operator<<().

string ProgParam::fpdetailtab

footprint detail table

Referenced by main(), mergeNeighbor(), and operator<<().

string ProgParam::outab

contains the merged footprint summary

Referenced by enough(), main(), mergeNeighbor(), operator<<(), and topfp().

string ProgParam::oufile

if oufile is empty then the program will not output a file containing the results of this unique operation This file conains the exon details.

if oufile is empty then the program will not output a file containing the results of this unique operation

Referenced by main(), mergeNeighbor(), operator<<(), and topfp().

int ProgParam::fpmaxlen

Referenced by topfp().

string ProgParam::intab

Referenced by enough(), main(), and topfp().

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

• seqaln/src/dbaln_fungalrmsimp.cpp
• seqaln/Utility/mergefootprint.cpp
• seqaln/Utility/picktopfootprint.cpp