inc/chainBlock.h File Reference

#include "chain.h"

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Typedefs
typedef int(*)	GapCost (int dq, int dt, void *gapData)
typedef int(*)	ConnectCost (struct cBlock *a, struct cBlock *b, void *gapData)
Functions
chain *	chainBlocks (char *qName, int qSize, char qStrand, char *tName, int tSize, struct cBlock **pBlockList, ConnectCost connectCost, GapCost gapCost, void *gapData, FILE *details)

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Typedef Documentation

typedef int(*) ConnectCost(struct cBlock *a, struct cBlock *b, void *gapData)

Definition at line 17 of file chainBlock.h.

typedef int(*) GapCost(int dq, int dt, void *gapData)

Definition at line 13 of file chainBlock.h.

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Function Documentation

struct chain* chainBlocks	(	char *	qName,
		int	qSize,
		char	qStrand,
		char *	tName,
		int	tSize,
		struct cBlock **	pBlockList,
		ConnectCost	connectCost,
		GapCost	gapCost,
		void *	gapData,
		FILE *	details
	)			[read]

Definition at line 392 of file chainBlock.c.

References chainCmpScore(), findBestPredecessors(), kdLeafCmpT(), kdLeafCmpTotal(), kdTreeMake(), lm, lmAllocVar, lmCleanup(), lmInit(), cBlock::next, chain::next, peelChains(), cBlock::score, scoreBlocks(), slAddHead, slSort(), cBlock::tEnd, and cBlock::tStart.

Referenced by ssFindBestBig().

{
struct kdTree *tree;
struct kdLeaf *leafList = NULL, *leaf;
struct cBlock *block;
struct chain *chainList = NULL, *chain;
struct lm *lm;

/* Empty lists will be problematic later, so deal with them here. */
if (*pBlockList == NULL)
   return NULL;

/* Make a leaf for each block. */
lm = lmInit(0);  /* Memory for tree, branches and leaves. */
for (block = *pBlockList; block != NULL; block = block->next)
    {
    /* Watch out for 0-length blocks in input: */
    if (block->tStart == block->tEnd)
        continue;
    lmAllocVar(lm, leaf);
    leaf->cb = block;
    leaf->totalScore = block->score;
    slAddHead(&leafList, leaf);
    }

/* Figure out chains. */
slSort(&leafList, kdLeafCmpT);
tree = kdTreeMake(leafList, lm);
findBestPredecessors(tree, leafList, connectCost, gapCost, gapData);
slSort(&leafList, kdLeafCmpTotal);
chainList = peelChains(qName, qSize, qStrand, tName, tSize, leafList, details);

/* Rescore chains (since some truncated) */
for (chain = chainList; chain != NULL; chain = chain->next)
    chain->score = scoreBlocks(chain->blockList, connectCost, gapData);
slSort(&chainList,  chainCmpScore);

/* Clean up and go home. */
lmCleanup(&lm);
*pBlockList = NULL;
return chainList;
}

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