blat: inc/flydna.h File Reference

boolean flyCdnaSeq	(	char *	name,
		struct dnaSeq **	retDna,
		struct wormCdnaInfo *	retInfo
	)

Definition at line 77 of file flydna.c.

References cdnaFa, cdnaSnof, FALSE, faReadNext(), flyFaCommentIntoInfo(), mustOpen(), SEEK_SET, snofFindOffset(), snofMustOpen(), and TRUE.

00080 {
00081 long offset;
00082 char *faComment;
00083 char **pFaComment = (retInfo == NULL ? NULL : &faComment);
00084 static struct snof *cdnaSnof = NULL;
00085 static FILE *cdnaFa;
00086 
00087 if (cdnaSnof == NULL)
00088         cdnaSnof = snofMustOpen("c:/biodata/fly/cDna/allcdna");
00089 if (cdnaFa == NULL)
00090         cdnaFa = mustOpen("c:/biodata/fly/cDna/allcdna.fa", "rb");
00091 if (!snofFindOffset(cdnaSnof, name, &offset))
00092     return FALSE;
00093 fseek(cdnaFa, offset, SEEK_SET);
00094 if (!faReadNext(cdnaFa, name, TRUE, pFaComment, retDna))
00095     return FALSE;
00096 flyFaCommentIntoInfo(faComment, retInfo);
00097 return TRUE;
00098 }

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void flyChromNames	(	char ***	retNames,
		int *	retNameCount
	)

Definition at line 48 of file flydna.c.

References ArraySize, and chromNames.

00050 {
00051 *retNames = chromNames;
00052 *retNameCount = ArraySize(chromNames);
00053 }

char* flyFeaturesDir ( )

Definition at line 101 of file flydna.c.

00103 {
00104 return "C:/biodata/fly/features/";
00105 }

void flyFreeNt4Genome ( struct nt4Seq *** pNt4Seq )

Definition at line 35 of file flydna.c.

References ArraySize, freeNt4(), freez(), and ntFileNames.

00037 {
00038 struct nt4Seq **pSeq;
00039 int i;
00040 
00041 if ((pSeq = *pNt4Seq) == NULL)
00042         return;
00043 for (i=0; i<ArraySize(ntFileNames); ++i)
00044         freeNt4(&pSeq[i]);
00045 freez(pNt4Seq);
00046 }

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void flyLoadNt4Genome	(	struct nt4Seq ***	retNt4Seq,
		int *	retNt4Count
	)

Definition at line 20 of file flydna.c.

References ArraySize, chromNames, loadNt4(), needMem(), and ntFileNames.

00022 {
00023 struct nt4Seq **pSeq;
00024 int i;
00025 
00026 pSeq = needMem(ArraySize(ntFileNames) * sizeof(pSeq[0]) );
00027 for (i=0; i<ArraySize(ntFileNames); ++i)
00028         {
00029         pSeq[i] = loadNt4(ntFileNames[i], chromNames[i]);
00030         }
00031 *retNt4Seq = pSeq;
00032 *retNt4Count = ArraySize(ntFileNames);
00033 }

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FILE* flyOpenGoodAli ( )

Definition at line 107 of file flydna.c.

References cdaOpenVerify().

00110 {
00111 return cdaOpenVerify("C:/biodata/fly/cDNA/good.ali");
00112 }

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Functions
void	flyLoadNt4Genome (struct nt4Seq **retNt4Seq, int retNt4Count)
void	flyFreeNt4Genome (struct nt4Seq ***pNt4Seq)
void	flyChromNames (char **retNames, int retNameCount)
boolean	flyCdnaSeq (char name, struct dnaSeq retDna, struct wormCdnaInfo retInfo)
char *	flyFeaturesDir ()
FILE *	flyOpenGoodAli ()

inc/flydna.h File Reference

Functions

Function Documentation