inc/dnaseq.h File Reference

#include "dnautil.h"
#include "bits.h"

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Data Structures
struct	dnaSeq
Defines
#define	dnaSeqFree   freeDnaSeq
#define	dnaSeqFreeList   freeDnaSeqList
Typedefs
typedef dnaSeq	bioSeq
typedef dnaSeq	aaSeq
Functions
dnaSeq *	newDnaSeq (DNA *dna, int size, char *name)
dnaSeq *	cloneDnaSeq (struct dnaSeq *seq)
void	freeDnaSeq (struct dnaSeq **pSeq)
void	freeDnaSeqList (struct dnaSeq **pSeqList)
aaSeq *	translateSeqN (struct dnaSeq *inSeq, unsigned offset, unsigned size, boolean stop)
aaSeq *	translateSeq (struct dnaSeq *inSeq, unsigned offset, boolean stop)
boolean	seqIsDna (bioSeq *seq)
boolean	seqIsLower (bioSeq *seq)
bioSeq *	whichSeqIn (bioSeq **seqs, int seqCount, char *letters)
Bits *	maskFromUpperCaseSeq (bioSeq *seq)
hash *	dnaSeqHash (struct dnaSeq *seqList)

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Define Documentation

#define dnaSeqFree   freeDnaSeq

Definition at line 38 of file dnaseq.h.

Referenced by gfIndexNibsAndTwoBits(), gfPcrOneViaNet(), and searchOneIndex().

#define dnaSeqFreeList   freeDnaSeqList

Definition at line 42 of file dnaseq.h.

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Typedef Documentation

typedef struct dnaSeq aaSeq

Definition at line 28 of file dnaseq.h.

typedef struct dnaSeq bioSeq

Definition at line 27 of file dnaseq.h.

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Function Documentation

struct dnaSeq* cloneDnaSeq

(

struct dnaSeq *

seq

)

[read]

Definition at line 29 of file dnaseq.c.

References bitClone(), cloneString(), CloneVar, dnaSeq::dna, dnaSeq::mask, dnaSeq::name, needHugeMem(), and dnaSeq::size.

{
struct dnaSeq *seq = CloneVar(orig);
seq->name = cloneString(seq->name);
seq->dna = needHugeMem(seq->size+1);
memcpy(seq->dna, orig->dna, seq->size+1);
seq->mask = NULL;
if (orig->mask != NULL)
    {
    seq->mask = bitClone(orig->mask, seq->size);
    }
return seq;
}

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struct hash* dnaSeqHash

(

struct dnaSeq *

seqList

)

[read]

Definition at line 163 of file dnaseq.c.

References digitsBaseTwo(), hashAddUnique(), hashNew, dnaSeq::name, dnaSeq::next, hash::size, and slCount().

{
int size = slCount(seqList)+1;
int sizeLog2 = digitsBaseTwo(size);
struct hash *hash = hashNew(sizeLog2);
struct dnaSeq *seq;
for (seq = seqList; seq != NULL; seq = seq->next)
    hashAddUnique(hash, seq->name, seq);
return hash;
}

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void freeDnaSeq

(

struct dnaSeq **

pSeq

)

Definition at line 44 of file dnaseq.c.

References bitFree(), dnaSeq::dna, freeMem(), freez(), dnaSeq::mask, and dnaSeq::name.

Referenced by freeDnaSeqList(), gfAddTilesInNib(), gfAlignStrand(), gfCountTilesInNib(), gfCountTilesInTwoBit(), gfIndexTransNibsAndTwoBits(), searchOneIndex(), and trans3Free().

{
struct dnaSeq *seq = *pSeq;
if (seq == NULL)
    return;
freeMem(seq->name);
freeMem(seq->dna);
bitFree(&seq->mask);
freez(pSeq);
}

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void freeDnaSeqList

(

struct dnaSeq **

pSeqList

)

Definition at line 56 of file dnaseq.c.

References freeDnaSeq(), and dnaSeq::next.

Referenced by blat(), gfAlignTrans(), gfAlignTransTrans(), and gfMakeOoc().

{
struct dnaSeq *seq, *next;

for (seq = *pSeqList; seq != NULL; seq = next)
    {
    next = seq->next;
    freeDnaSeq(&seq);
    }
*pSeqList = NULL;
}

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Bits* maskFromUpperCaseSeq

(

bioSeq *

seq

)

Definition at line 148 of file dnaseq.c.

References bitAlloc(), bitSetOne(), dnaSeq::dna, and dnaSeq::size.

Referenced by blat(), gfLargeIndexSeq(), gfSmallIndexSeq(), and maskQuerySeq().

{
int size = seq->size, i;
char *poly = seq->dna;
Bits *b = bitAlloc(size);
for (i=0; i<size; ++i)
    {
    if (isupper(poly[i]))
        bitSetOne(b, i);
    }
return b;
}

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struct dnaSeq* newDnaSeq	(	DNA *	dna,
		int	size,
		char *	name
	)			[read]

Definition at line 15 of file dnaseq.c.

References cloneString(), and needMem().

Referenced by faReadMixedNext(), and gffReadDnaSeq().

{
struct dnaSeq *seq;

seq = needMem(sizeof(*seq));
if (name != NULL)
    seq->name = cloneString(name);
seq->dna = dna;
seq->size = size;
seq->mask = NULL;
return seq;
}

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boolean seqIsDna

(

bioSeq *

seq

)

Definition at line 80 of file dnaseq.c.

References dnaSeq::dna, isDna(), and dnaSeq::size.

Referenced by doBlat().

{
return isDna(seq->dna, seq->size);
}

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boolean seqIsLower

(

bioSeq *

seq

)

Definition at line 69 of file dnaseq.c.

References dnaSeq::dna, FALSE, dnaSeq::size, and TRUE.

{
int size = seq->size, i;
char *poly = seq->dna;
for (i=0; i<size; ++i)
    if (!islower(poly[i]))
        return FALSE;
return TRUE;
}

aaSeq* translateSeq	(	struct dnaSeq *	inSeq,
		unsigned	offset,
		boolean	stop
	)

Definition at line 124 of file dnaseq.c.

References translateSeqN().

Referenced by trans3New().

{
return translateSeqN(inSeq, offset, 0, stop);
}

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aaSeq* translateSeqN	(	struct dnaSeq *	inSeq,
		unsigned	offset,
		unsigned	size,
		boolean	stop
	)

Definition at line 87 of file dnaseq.c.

References AllocVar, cloneString(), dnaSeq::dna, lookupCodon(), dnaSeq::name, needLargeMem(), and dnaSeq::size.

Referenced by translateSeq().

{
aaSeq *seq;
DNA *dna = inSeq->dna;
AA *pep, aa;
int i, lastCodon;
int actualSize = 0;

assert(offset <= inSeq->size);
if ((inSize == 0) || (inSize > (inSeq->size - offset)))
    inSize = inSeq->size - offset;
lastCodon = offset + inSize - 3;

AllocVar(seq);
seq->dna = pep = needLargeMem(inSize/3+1);
for (i=offset; i <= lastCodon; i += 3)
    {
    aa = lookupCodon(dna+i);
    if (aa == 0)
        {
        if (stop)
            break;
        else
            aa = 'Z';
        }
    *pep++ = aa;
    ++actualSize;
    }
*pep = 0;
assert(actualSize <= inSize/3+1);
seq->size = actualSize;
seq->name = cloneString(inSeq->name);
return seq;
}

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bioSeq* whichSeqIn	(	bioSeq **	seqs,
		int	seqCount,
		char *	letters
	)

Definition at line 132 of file dnaseq.c.

References dnaSeq::dna, internalErr, and dnaSeq::size.

{
aaSeq *seq;
int i;

for (i=0; i<seqCount; ++i)
    {
    seq = seqs[i];
    if (seq->dna <= letters && letters < seq->dna + seq->size)
        return seq;
    }
internalErr();
return NULL;
}

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