ssBundle Struct Reference

#include <supStitch.h>

Collaboration diagram for ssBundle:

[legend]

Data Fields
ssBundle *	next
ssFfItem *	ffList
bioSeq *	qSeq
bioSeq *	genoSeq
int	genoIx
int	genoContigIx
void *	data
boolean	isProt
trans3 *	t3List
boolean	avoidFuzzyFindKludge

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Detailed Description

Definition at line 40 of file supStitch.h.

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Field Documentation

struct ssBundle* ssBundle::next [read]

Definition at line 44 of file supStitch.h.

Referenced by addToBigBundleList(), dumpBuns(), findBundle(), and ssBundleFreeList().

struct ssFfItem* ssBundle::ffList [read]

Definition at line 45 of file supStitch.h.

Referenced by addToBigBundleList(), alignComponents(), dumpBuns(), foldInExtras(), gfAlignSomeClumps(), gfAlignTrans(), gfFindAlignAaTrans(), gfTransTransFindBundles(), refineBundle(), refineSmallExonsInBundle(), saveAlignments(), ssBundleFree(), and ssStitch().

bioSeq* ssBundle::qSeq

Definition at line 46 of file supStitch.h.

Referenced by alignComponents(), dumpBuns(), fastMapClumpsToBundles(), foldInExtras(), gfAlignSomeClumps(), gfAlignTrans(), gfClumpsToBundles(), gfFindAlignAaTrans(), gfTransTransFindBundles(), refineSmallExonsInBundle(), saveAlignments(), smallMiddleExons(), and ssStitch().

bioSeq* ssBundle::genoSeq

Definition at line 47 of file supStitch.h.

Referenced by addToBigBundleList(), alignComponents(), dumpBuns(), findBundle(), foldInExtras(), gfAlignSomeClumps(), gfAlignTrans(), gfClumpsToBundles(), gfFindAlignAaTrans(), gfTransTransFindBundles(), refineSmallExonsInBundle(), saveAlignments(), smallMiddleExons(), and ssStitch().

int ssBundle::genoIx

Definition at line 48 of file supStitch.h.

int ssBundle::genoContigIx

Definition at line 49 of file supStitch.h.

void* ssBundle::data

Definition at line 50 of file supStitch.h.

boolean ssBundle::isProt

Definition at line 51 of file supStitch.h.

Referenced by addToBigBundleList(), gfAlignSomeClumps(), gfAlignTrans(), gfFindAlignAaTrans(), saveAlignments(), smallMiddleExons(), and ssStitch().

struct trans3* ssBundle::t3List [read]

Definition at line 52 of file supStitch.h.

Referenced by gfAlignTrans(), gfFindAlignAaTrans(), smallMiddleExons(), and ssStitch().

boolean ssBundle::avoidFuzzyFindKludge

Definition at line 53 of file supStitch.h.

Referenced by addToBigBundleList(), foldInExtras(), and ssStitch().

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

• inc/supStitch.h

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