chain Struct Reference

#include <chain.h>

Collaboration diagram for chain:

[legend]

Data Fields
chain *	next
cBlock *	blockList
double	score
char *	tName
int	tSize
int	tStart
int	tEnd
char *	qName
int	qSize
char	qStrand
int	qStart
int	qEnd
int	id

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Detailed Description

Definition at line 39 of file chain.h.

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Field Documentation

struct chain* chain::next [read]

Definition at line 42 of file chain.h.

Referenced by chainBlocks(), chainFreeList(), chainWriteAll(), and ssFindBestBig().

struct cBlock* chain::blockList [read]

Definition at line 43 of file chain.h.

Referenced by chainCalcBounds(), chainCalcScore(), chainCalcScoreSubChain(), chainFree(), chainMergeAbutting(), chainReadBlocks(), chainRemovePartialOverlaps(), chainSubsetOnQ(), chainSubsetOnT(), chainSwap(), chainToAxt(), chainToPsl(), chainWrite(), chainWriteLong(), checkChainGaps(), checkChainIncreases(), checkStartBeforeEnd(), fillInMatchEtc(), removeNegativeBlocks(), setChainBounds(), and ssFindBestBig().

double chain::score

Definition at line 44 of file chain.h.

Referenced by chainCmpScore(), chainCmpScoreDesc(), chainReadChainLine(), chainWriteHead(), and ssFindBestBig().

char* chain::tName

Definition at line 45 of file chain.h.

Referenced by axtFromBlocks(), chainCmpTarget(), chainFree(), chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToPsl(), and chainWriteHead().

int chain::tSize

Definition at line 46 of file chain.h.

Referenced by chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToPsl(), and chainWriteHead().

int chain::tStart

Definition at line 48 of file chain.h.

Referenced by chainCalcBounds(), chainCalcScoreSubChain(), chainCmpTarget(), chainReadBlocks(), chainReadChainLine(), chainSwap(), chainToPsl(), chainWriteHead(), and setChainBounds().

int chain::tEnd

Definition at line 48 of file chain.h.

Referenced by chainCalcBounds(), chainFastSubsetOnT(), chainReadBlocks(), chainReadChainLine(), chainSwap(), chainToPsl(), chainWriteHead(), setChainBounds(), and ssFindBestBig().

char* chain::qName

Definition at line 49 of file chain.h.

Referenced by axtFromBlocks(), chainCmpQuery(), chainFree(), chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToPsl(), and chainWriteHead().

int chain::qSize

Definition at line 50 of file chain.h.

Referenced by chainRangeQPlusStrand(), chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToPsl(), and chainWriteHead().

char chain::qStrand

Definition at line 51 of file chain.h.

Referenced by axtFromBlocks(), chainRangeQPlusStrand(), chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToFullPsl(), chainToPsl(), and chainWriteHead().

int chain::qStart

Definition at line 52 of file chain.h.

Referenced by chainCalcBounds(), chainCalcScoreSubChain(), chainCmpQuery(), chainRangeQPlusStrand(), chainReadBlocks(), chainReadChainLine(), chainSwap(), chainToPsl(), chainWriteHead(), and setChainBounds().

int chain::qEnd

Definition at line 52 of file chain.h.

Referenced by chainCalcBounds(), chainRangeQPlusStrand(), chainReadBlocks(), chainReadChainLine(), chainSubsetOnQ(), chainSwap(), chainToPsl(), chainWriteHead(), and setChainBounds().

int chain::id

Definition at line 53 of file chain.h.

Referenced by chainIdNext(), chainReadChainLine(), chainReadUsedSwapLf(), chainSubsetOnQ(), and chainWriteHead().

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

• inc/chain.h

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