inc/cda.h File Reference

#include "memgfx.h"
#include "fuzzyFind.h"

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Data Structures
struct	cdaBlock
struct	cdaAli
Functions
boolean	cdaCloneIsReverse (struct cdaAli *cda)
char	cdaCloneStrand (struct cdaAli *cda)
char	cdaDirChar (struct cdaAli *cda, char chromStrand)
char *	cdaLoadString (FILE *f)
void	cdaReadBlock (FILE *f, struct cdaBlock *block)
FILE *	cdaOpenVerify (char *fileName)
cdaAli *	cdaLoadOne (FILE *f)
void	cdaFixChromStartEnd (struct cdaAli *cda)
void	cdaCoalesceBlocks (struct cdaAli *ca)
void	cdaCoalesceFast (struct cdaAli *ca)
void	cdaShowAlignmentTrack (struct memGfx *mg, int xOff, int yOff, int width, int height, Color goodColor, Color badColor, int dnaSize, int dnaOffset, struct cdaAli *cda, char repeatChar)
void	cdaRcOne (struct cdaAli *cda, int dnaStart, int baseCount)
void	cdaRcList (struct cdaAli *cdaList, int dnaStart, int baseCount)
void	cdaFreeAli (struct cdaAli *ca)
void	cdaFreeAliList (struct cdaAli **pList)
cdaAli *	cdaAliFromFfAli (struct ffAli *aliList, DNA *needle, int needleSize, DNA *hay, int haySize, boolean isRc)
void	cdaWrite (char *fileName, struct cdaAli *cdaList)

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Function Documentation

struct cdaAli* cdaAliFromFfAli	(	struct ffAli *	aliList,
		DNA *	needle,
		int	needleSize,
		DNA *	hay,
		int	haySize,
		boolean	isRc
	)			[read]

Definition at line 437 of file cda.c.

References AllocVar, cdaAli::baseCount, cdaAli::blockCount, cdaAli::blocks, cdaFixChromStartEnd(), countAlis(), cdaAli::direction, dnaScoreMatch(), ffAli::hEnd, ffAli::hStart, leftGood(), needMem(), ffAli::nEnd, ffAli::nStart, cdaAli::orientation, reverseComplement(), ffAli::right, rightGood(), roundingScale(), and cdaAli::strand.

{
int count = countAlis(aliList);
struct cdaAli *cda;
struct cdaBlock *blocks;
struct ffAli *fa;
int score;
int bases;

if (isRc)
    reverseComplement(needle, needleSize);
AllocVar(cda);
cda->baseCount = needleSize;
cda->strand = (isRc ? '-' : '+');
cda->direction = '+';   /* Actually we don't know. */
cda->orientation = (isRc ? -1 : 1);
cda->blockCount = count;
cda->blocks = blocks = needMem(count * sizeof(blocks[0]));

for (fa = aliList; fa != NULL; fa = fa->right)
    {
    blocks->nStart = fa->nStart - needle;
    blocks->nEnd = fa->nEnd - needle;
    blocks->hStart = fa->hStart - hay;
    blocks->hEnd  = fa->hEnd - hay;
    blocks->startGood = leftGood(fa);
    blocks->endGood = rightGood(fa);
    bases = fa->nEnd - fa->nStart;
    score = dnaScoreMatch(fa->nStart, fa->hStart, bases);
    blocks->midScore = roundingScale(255, score, bases);
    ++blocks;
    }
cdaFixChromStartEnd(cda);
if (isRc)
    {
    reverseComplement(needle, needleSize);
    }
return cda;
}

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boolean cdaCloneIsReverse

(

struct cdaAli *

cda

)

Definition at line 174 of file cda.c.

References cdaAli::direction, and cdaAli::strand.

Referenced by cdaCloneStrand(), and cdaDirChar().

{
boolean isReverse = (cda->direction == '-');
if (cda->strand == '-')
    isReverse = !isReverse;
return isReverse;
}

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char cdaCloneStrand

(

struct cdaAli *

cda

)

Definition at line 183 of file cda.c.

References cdaCloneIsReverse().

{
return cdaCloneIsReverse(cda) ? '-' : '+';
}

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void cdaCoalesceBlocks

(

struct cdaAli *

ca

)

Definition at line 310 of file cda.c.

References cdaCoalesceAll(), and TRUE.

{
cdaCoalesceAll(ca, TRUE);
}

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void cdaCoalesceFast

(

struct cdaAli *

ca

)

Definition at line 316 of file cda.c.

References cdaCoalesceAll(), and FALSE.

{
cdaCoalesceAll(ca, FALSE);
}

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char cdaDirChar	(	struct cdaAli *	cda,
		char	chromStrand
	)

Definition at line 189 of file cda.c.

References cdaCloneIsReverse().

{
boolean isReverse = cdaCloneIsReverse(cda);
if (chromStrand == '-')
    isReverse = !isReverse;
return (isReverse ? '<' : '>');    
}

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void cdaFixChromStartEnd

(

struct cdaAli *

cda

)

Definition at line 65 of file cda.c.

References cdaAli::blockCount, cdaAli::blocks, cdaAli::chromEnd, cdaAli::chromStart, cdaBlock::hEnd, and cdaBlock::hStart.

Referenced by cdaAliFromFfAli(), and cdaLoadOne().

{
int start = 0x7fffffff;
int end = -start;
int count = cda->blockCount;
struct cdaBlock *block = cda->blocks;

while (--count >= 0)
    {
    if (start > block->hStart)
        start = block->hStart;
    if (end < block->hEnd)
        end = block->hEnd;
    ++block;
    }
cda->chromStart = start;
cda->chromEnd = end;
}

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void cdaFreeAli

(

struct cdaAli *

ca

)

Definition at line 238 of file cda.c.

References cdaAli::blocks, freeMem(), and cdaAli::name.

Referenced by cdaFreeAliList().

{
freeMem(ca->blocks);
freeMem(ca->name);
freeMem(ca);
}

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void cdaFreeAliList

(

struct cdaAli **

pList

)

Definition at line 246 of file cda.c.

References cdaFreeAli(), and cdaAli::next.

{
struct cdaAli *ca, *next;
next = *pList;
while ((ca = next) != NULL)
    {
    next = ca->next;
    cdaFreeAli(ca);
    }
*pList = NULL;
}

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struct cdaAli* cdaLoadOne

(

FILE *

f

)

[read]

Definition at line 109 of file cda.c.

References AllocVar, cdaAli::baseCount, cdaAli::blockCount, cdaAli::blocks, cdaFixChromStartEnd(), cdaLoadString(), cdaReadBlock(), chromIx(), cdaAli::chromIx, cdaAli::direction, cdaAli::isEmbryonic, cdaAli::milliScore, mustReadOne, name, cdaAli::name, needMem(), cdaAli::strand, and UBYTE.

Referenced by wormCdaAlisInRange().

{
struct cdaAli *ca;
struct cdaBlock *blocks;
int count;
int i;
char *name;
UBYTE chromIx;

if ((name = cdaLoadString(f)) == NULL)
    return NULL;
AllocVar(ca);
ca->name = name;
mustReadOne(f, ca->isEmbryonic);
mustReadOne(f, ca->baseCount);
mustReadOne(f, ca->milliScore);
mustReadOne(f, chromIx);
ca->chromIx = chromIx;
mustReadOne(f, ca->strand);
mustReadOne(f, ca->direction);
mustReadOne(f, ca->blockCount);
count = ca->blockCount;
ca->blocks = blocks = needMem(count * sizeof(blocks[0]));
for (i=0; i<count; ++i)
    cdaReadBlock(f, &blocks[i]);
cdaFixChromStartEnd(ca);
return ca;
}

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char* cdaLoadString

(

FILE *

f

)

Definition at line 16 of file cda.c.

References mustRead(), needMem(), readOne, and UBYTE.

Referenced by cdaLoadOne().

{
UBYTE size;
char *s;
if (!readOne(f, size))
    return NULL;
s = needMem(size+1);
mustRead(f, s, size);
return s;
}

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FILE* cdaOpenVerify

(

char *

fileName

)

Definition at line 86 of file cda.c.

References aliSig, bits32, errAbort(), mustOpen(), and mustReadOne.

Referenced by flyOpenGoodAli(), and wormOpenGoodAli().

{
FILE *aliFile;
bits32 sig;

aliFile = mustOpen(fileName, "rb");
mustReadOne(aliFile, sig);
if (sig != aliSig)
    errAbort("Bad signature %x on %s", sig, fileName);
return aliFile;
}

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void cdaRcList	(	struct cdaAli *	cdaList,
		int	dnaStart,
		int	baseCount
	)

Definition at line 229 of file cda.c.

References cdaRcOne(), and cdaAli::next.

{
struct cdaAli *cda;
for (cda = cdaList; cda != NULL; cda = cda->next)
    cdaRcOne(cda, dnaStart, baseCount);
}

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void cdaRcOne	(	struct cdaAli *	cda,
		int	dnaStart,
		int	baseCount
	)

Definition at line 199 of file cda.c.

References cdaAli::baseCount, cdaAli::blockCount, cdaAli::blocks, cdaBlock::endGood, cdaBlock::hEnd, cdaBlock::hStart, cdaBlock::nEnd, cdaBlock::nStart, reverseOffset(), cdaBlock::startGood, and UBYTE.

Referenced by cdaRcList().

{
struct cdaBlock *block, *endBlock;

for (block = cda->blocks, endBlock = block+cda->blockCount; block < endBlock; ++block)
    {
    int temp;
    UBYTE uc;
    temp = reverseOffset(block->hStart-dnaStart, baseCount) + dnaStart + 1;
    block->hStart = reverseOffset(block->hEnd-dnaStart, baseCount) + dnaStart + 1;
    block->hEnd = temp;
    temp = reverseOffset(block->nStart, cda->baseCount);
    block->nStart = reverseOffset(block->nEnd, cda->baseCount);
    block->nEnd = temp;
    uc = block->startGood;
    block->startGood = block->endGood;
    block->endGood = uc;
    }
block = cda->blocks;
endBlock -= 1;
for (;block < endBlock; ++block, --endBlock)
    {
    struct cdaBlock temp;
    temp = *block;
    *block = *endBlock;
    *endBlock = temp;
    }
}

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void cdaReadBlock	(	FILE *	f,
		struct cdaBlock *	block
	)

Definition at line 42 of file cda.c.

References cdaBlock::endGood, cdaBlock::hEnd, cdaBlock::hStart, cdaBlock::midScore, mustReadOne, cdaBlock::nEnd, cdaBlock::nStart, and cdaBlock::startGood.

Referenced by cdaLoadOne().

{
mustReadOne(f, block->nStart);
mustReadOne(f, block->nEnd);
mustReadOne(f, block->hStart);
block->hEnd = block->hStart + (block->nEnd - block->nStart);
mustReadOne(f, block->startGood);
mustReadOne(f, block->endGood);
mustReadOne(f, block->midScore);
}

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void cdaShowAlignmentTrack	(	struct memGfx *	mg,
		int	xOff,
		int	yOff,
		int	width,
		int	height,
		Color	goodColor,
		Color	badColor,
		int	dnaSize,
		int	dnaOffset,
		struct cdaAli *	cda,
		char	repeatChar
	)

Definition at line 323 of file cda.c.

References cdaAli::blockCount, cdaAli::blocks, cdaBlock::endGood, cdaBlock::hEnd, cdaBlock::hStart, MG_WHITE, mgDrawBox(), mgFontCharWidth(), mgSmallFont(), mgTextCentered(), cdaBlock::midScore, cdaBlock::nEnd, cdaBlock::nStart, roundingScale(), and cdaBlock::startGood.

{
struct cdaBlock *block = cda->blocks;
int count = cda->blockCount;
int blockIx;
int scaledHeight = roundingScale(height, dnaSize, width);
MgFont *font = NULL;
int repeatCharWidth = 0;

if (repeatChar)
    {
    font = mgSmallFont();
    repeatCharWidth = mgFontCharWidth(font, repeatChar);
    }

for (blockIx = 0; blockIx < count; ++blockIx)
    {
    int x[4];
    int b[4];
    Color c[3];
    int quarterWid;
    int i;
    int w;

    b[0] = block->hStart;
    b[3] = block->hEnd;
    quarterWid = (b[3]-b[0]+2)>>2;
    if (quarterWid > scaledHeight)
        quarterWid = scaledHeight;
    b[1] = b[0] + quarterWid;
    b[2] = b[3] - quarterWid;

    c[0] = ((block->startGood >= 4 && (blockIx == 0 || block[-1].nEnd == block[0].nStart)) 
        ? goodColor : badColor);
    c[1] = ((block->midScore > 229) ? goodColor : badColor);
    c[2] = ((block->endGood >= 4 && (blockIx == count-1 || block[0].nEnd == block[1].nStart))
        ? goodColor : badColor);

    for (i=0; i<4; ++i)
        x[i] = roundingScale(b[i]-dnaOffset, width, dnaSize) + xOff;
    for (i=0; i<3; ++i)
        {
        if ((w = x[i+1] - x[i]) > 0)
            mgDrawBox(mg, x[i], yOff, w, height, c[i]);
        }
    
    if (repeatChar)
        {
        char buf[256];
        int charCount;
        w = x[3] - x[0];
        charCount = w/repeatCharWidth;
        if (charCount >= sizeof(buf))
            charCount = sizeof(buf)-1;
        memset(buf, repeatChar, charCount);
        buf[charCount] = 0;
        mgTextCentered(mg, x[0], yOff, w, height, MG_WHITE, font, buf);
        }
    ++block;
    }
}

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void cdaWrite	(	char *	fileName,
		struct cdaAli *	cdaList
	)

Definition at line 164 of file cda.c.

References cdaCreate(), cdaWriteOne(), and cdaAli::next.

{
FILE *f = cdaCreate(fileName);
struct cdaAli *ca;
for (ca = cdaList; ca != NULL; ca = ca->next)
    cdaWriteOne(f, ca);
fclose(f);
}

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