GenModel.h File Reference

#include <string>
#include <vector>
#include "Range.h"
#include <iostream>
#include <cassert>
#include "bioseq.h"
#include <map>
#include <set>

Go to the source code of this file.

Classes
class	PointOutChain
class	Badinput
class	InvalidModel
class	Noschain
class	lessByChainDirectionPtr
class	lessByChainDirection
class	lessChainPtr
class	Alnchain
class	Alnchainid
class	GenModel
Functions
void	string2Vector (vector< int > &v, const string &str)
bool	nonincreasingVector (const vector< int > &v)
bool	nondecreasingVector (const vector< int > &v)
bool	allLessVector (const vector< int > &v1, const vector< int > &v2)
void	errorMessageFix1 (Noschain &c1, Noschain &c2, int status, int end)
int	comparePlusChainFirstBefore (Noschain &c1, Noschain &c2)
int	comparePlusChainIdenticalLeft (Noschain &c1, Noschain &c2)
int	compareMinusChainFirstBefore (Noschain &c1, Noschain &c2)
int	compareMinusChainMinusIdenticalRight (Noschain &c1, Noschain &c2)
void	readandstoreGmap (const string &inputFile, map< string, set< Alnchainid *, lessChainPtr > > &alnseg, map< int, int > &pathstat)
	helper functions
void	readandstoreGmap (istream &ins, map< string, set< Alnchainid *, lessChainPtr > > &alnseg, map< int, int > &pathstat)
void	archiveAln (map< string, set< Alnchainid *, lessChainPtr > > &alnseg, const string &file)
void	archiveAln (map< string, set< Alnchainid *, lessChainPtr > > &alnseg, ostream &ous)
Variables
int	FUZZYMARGIN

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Function Documentation

bool allLessVector	(	const vector< int > &	v1,
		const vector< int > &	v2
	)

Referenced by Noschain::Noschain().

void archiveAln	(	map< string, set< Alnchainid *, lessChainPtr > > &	alnseg,
		ostream &	ous
	)

stream version more flexible

void archiveAln	(	map< string, set< Alnchainid *, lessChainPtr > > &	alnseg,
		const string &	file
	)

Simply stores the Alnchainid object with the toString() method exons(b1-e1,b2-e2, ...) TAB identity TAB coverage TAB estids (id1,id2, ...). The result is sorted on genomic DNA, so genomic DNA is written once at the beginning. GID: chromosome1 1-100,200-300 95 0.9 est1 2-102,202-303 92 0.92 est2

References archiveAln().

Referenced by archiveAln(), and main().

int compareMinusChainFirstBefore	(	Noschain &	c1,
		Noschain &	c2
	)

int compareMinusChainMinusIdenticalRight	(	Noschain &	c1,
		Noschain &	c2
	)

int comparePlusChainFirstBefore	(	Noschain &	c1,
		Noschain &	c2
	)

several helper functions. The noschain compare function is very hard to implement. I have not figured out a simple way to implement this function.

return 0, 1, 2, -2 These are non-member function.

all use a common value fuzzymargin as static constant. I should use a common value in the Range::margin The the caller will have to set this value. The Range::margin has a default of 20. Which should be set to 16. I will use a global constant FUZZYMARGIN. This value can be changed by the user.

int comparePlusChainIdenticalLeft	(	Noschain &	c1,
		Noschain &	c2
	)

void errorMessageFix1	(	Noschain &	c1,
		Noschain &	c2,
		int	status,
		int	end
	)

for debuging

References Noschain::show().

bool nondecreasingVector

(

const vector< int > &

v

)

numbers goes from small to large

Referenced by Noschain::Noschain().

bool nonincreasingVector

(

const vector< int > &

v

)

numbers go from large to small

Referenced by Noschain::Noschain().

void readandstoreGmap	(	istream &	ins,
		map< string, set< Alnchainid *, lessChainPtr > > &	alnseg,
		map< int, int > &	pathstat
	)

stream version

stream version more flexible

References Gmapres::addAlignment(), Gmapres::addPath(), breakString(), getAllInt(), getInt(), Gmapres::storeChain(), and trimLeadingSpace().

void readandstoreGmap	(	const string &	inputFile,
		map< string, set< Alnchainid *, lessChainPtr > > &	alnseg,
		map< int, int > &	pathstat
	)

helper functions

Parameters:

	alnseg	this is the container genomic_id => { exon segments represented by Noschain } The chains are sorted.
	inputFile	is the gmap result in summary format
	pathstat	is a summary of path => count how frequent for a given number of paths, 1 path should dominiate. This is an accumulator.

file version use stream version

References ifstream(), and readandstoreGmap().

Referenced by getInputFromRawGmap(), main(), and readandstoreGmap().

void string2Vector	(	vector< int > &	v,
		const string &	str
	)

Referenced by Noschain::Noschain().

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Variable Documentation

int FUZZYMARGIN

Referenced by cmpEditMinusChainFirstFront(), cmpEditPlusChainFirstFront(), cmpEditPlusChainIdenticalFront(), compareMinusChainFirstBefore(), compareMinusChainIdenticalRight(), compareMultipleWithSingle(), comparePlusChainFirstBefore(), comparePlusChainIdenticalLeft(), frontCompareMinus(), frontComparePlus(), and main().