173 lines
4.8 KiB
C
173 lines
4.8 KiB
C
/* File: ureadseq.h
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*
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* Header for module UReadSeq
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*/
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#ifndef UREADSEQ_H
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#define UREADSEQ_H
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typedef char boolean;
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#define NEWLINE '\n'
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#define false 0
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#define true 1
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#define min(a, b) (a < b) ? a : b
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#define max(a, b) (a > b) ? a : b
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#define skipwhitespace(string) \
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{ \
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while (*string <= ' ' && *string != 0) string++; \
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}
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/* NLM strings */
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#define is_upper(c) ('A' <= (c) && (c) <= 'Z')
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#define is_lower(c) ('a' <= (c) && (c) <= 'z')
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#define to_lower(c) ((char)(is_upper(c) ? (c) + ' ' : (c)))
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#define to_upper(c) ((char)(is_lower(c) ? (c) - ' ' : (c)))
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/* readSeq errors */
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#define eFileNotFound -1
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#define eNoData -2
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#define eMemFull -3
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#define eItemNotFound -4
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#define eOneFormat -5
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#define eUnequalSize -6
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#define eFileCreate -7
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#define eUnknownFormat -8
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#define eOptionBad -9
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#define eASNerr -10
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/* magic number for readSeq(whichEntry) to give seq list */
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#define kListSequences -1
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/* sequence types parsed by getseqtype */
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#define kOtherSeq 0
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#define kDNA 1
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#define kRNA 2
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#define kNucleic 3
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#define kAmino 4
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/* formats known to readSeq */
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#define kIG 1
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#define kGenBank 2
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#define kNBRF 3
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#define kEMBL 4
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#define kGCG 5
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#define kStrider 6
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#define kFitch 7
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#define kPearson 8
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#define kZuker 9
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#define kOlsen 10
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#define kPhylip2 11
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#define kPhylip4 12
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#define kPhylip3 kPhylip4
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#define kPhylip kPhylip4
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#define kPlain 13 /* keep this at #13 */
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#define kPIR 14
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#define kMSF 15
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#define kASN1 16
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#define kPAUP 17
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#define kPretty 18
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#define kMaxFormat 18
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#define kMinFormat 1
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#define kNoformat -1 /* format not tested */
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#define kUnknown 0 /* format not determinable */
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/* subsidiary types */
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#define kASNseqentry 51
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#define kASNseqset 52
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#define kPhylipInterleave 61
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#define kPhylipSequential 62
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typedef struct {
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boolean isactive, baseonlynum;
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boolean numright, numleft, numtop, numbot;
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boolean nameright, nameleft, nametop;
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boolean noleaves, domatch, degap;
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char matchchar, gapchar;
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short numline, atseq;
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short namewidth, numwidth;
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short interline, spacer, seqwidth, tab;
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} prettyopts;
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#define gPrettyInit(p) \
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{ \
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p.isactive = false; \
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p.baseonlynum = true; \
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p.numline = p.atseq = 0; \
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p.numright = p.numleft = p.numtop = p.numbot = false; \
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p.nameright = p.nameleft = p.nametop = false; \
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p.noleaves = p.domatch = p.degap = false; \
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p.matchchar = '.'; \
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p.gapchar = '-'; \
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p.namewidth = 8; \
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p.numwidth = 5; \
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p.interline = 1; \
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p.spacer = 10; \
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p.seqwidth = 50; \
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p.tab = 0; \
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}
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#ifdef UREADSEQ_G
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prettyopts gPretty;
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#else
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extern prettyopts gPretty;
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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extern short seqFileFormat(const char *filename, long *skiplines, short *error);
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extern short seqFileFormatFp(FILE *fseq, long *skiplines, short *error);
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extern char *listSeqs(const char *filename, const long skiplines,
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const short format, short *nseq, short *error);
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extern char *readSeq(const short whichEntry, const char *filename,
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const long skiplines, const short format, long *seqlen,
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short *nseq, short *error, char *seqid);
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extern char *readSeqFp(const short whichEntry_, FILE *fp_,
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const long skiplines_, const short format_,
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long *seqlen_, short *nseq_, short *error_,
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char *seqid_);
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extern short writeSeq(FILE *outf, const char *seq, const long seqlen,
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const short outform, const char *seqid);
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extern unsigned long CRC32checksum(const char *seq, const long seqlen,
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unsigned long *checktotal);
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extern unsigned long GCGchecksum(const char *seq, const long seqlen,
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unsigned long *checktotal);
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#ifdef SMALLCHECKSUM
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#define seqchecksum GCGchecksum
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#else
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#define seqchecksum CRC32checksum
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#endif
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extern short getseqtype(const char *seq, const long seqlen);
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extern char *compressSeq(const char gapc, const char *seq, const long seqlen,
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long *newlen);
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#ifdef NCBI
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extern char *listASNSeqs(const char *filename, const long skiplines,
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const short format, short *nseq, short *error);
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extern char *readASNSeq(const short whichEntry, const char *filename,
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const long skiplines, const short format, long *seqlen,
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short *nseq, short *error, char **seqid);
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#endif
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/* patches for some missing string.h stuff */
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extern int Strcasecmp(const char *a, const char *b);
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extern int Strncasecmp(const char *a, const char *b, long maxn);
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#ifdef __cplusplus
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}
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#endif
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#endif /*UREADSEQ_H*/
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