inc/aliType.h File Reference

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Enumerations
enum	gfType {   gftDna = 0, gftRna = 1, gftProt = 2, gftDnaX = 3,   gftRnaX = 4 }
enum	ffStringency { ffExact = 0, ffCdna = 1, ffTight = 2, ffLoose = 3 }
Functions
char *	gfTypeName (enum gfType type)
enum gfType	gfTypeFromName (char *name)

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Enumeration Type Documentation

enum ffStringency

Enumerator:

ffExact
ffCdna
ffTight
ffLoose

Definition at line 22 of file aliType.h.

    {
    ffExact = 0,        /* Only an exact match will do. */

    ffCdna = 1,         /* Near exact.  Tolerate long gaps in target (genomic) */
    ffTight = 2,        /* Near exact.  Not so tolerant of long gaps in target. */
    ffLoose = 3,        /* Less exact. */
    };

enum gfType

Enumerator:

gftDna
gftRna
gftProt
gftDnaX
gftRnaX

Definition at line 6 of file aliType.h.

    {
    gftDna = 0,         /* DNA (genomic) */
    gftRna = 1,         /* RNA */
    gftProt = 2,         /* Protein. */
    gftDnaX = 3,                /* Genomic DNA translated to protein */
    gftRnaX = 4,         /* RNA translated to protein */
    };

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Function Documentation

enum gfType gfTypeFromName

(

char *

name

)

Definition at line 19 of file aliType.c.

References errAbort(), gftDna, gftDnaX, gftProt, gftRna, gftRnaX, and sameWord.

Referenced by gfClient(), main(), pslxFileOpen(), and pslxFileOpenWithMetaConfig().

{
if (sameWord(name, "DNA")) return gftDna;
if (sameWord(name, "RNA")) return gftRna;
if (sameWord(name, "protein")) return gftProt;
if (sameWord(name, "prot")) return gftProt;
if (sameWord(name, "DNAX")) return gftDnaX;
if (sameWord(name, "RNAX")) return gftRnaX;
errAbort("Unknown sequence type '%s'", name);
return 0;
}

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char* gfTypeName

(

enum gfType

type

)

Definition at line 7 of file aliType.c.

References gftDna, gftDnaX, gftProt, gftRna, gftRnaX, and internalErr.

Referenced by pslxWriteHead().

{
if (type == gftDna) return "DNA";
if (type == gftRna) return "RNA";
if (type == gftProt) return "protein";
if (type == gftDnaX) return "DNAX";
if (type == gftRnaX) return "RNAX";
internalErr();
return NULL;
}

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