Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / fasta34 / defs.h

diff --git a/website/archive/binaries/mac/src/fasta34/defs.h b/website/archive/binaries/mac/src/fasta34/defs.h
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+/* Concurrent read version */
+
+/* $Name: fa_34_26_5 $ - $Id: defs.h,v 1.26 2006/06/22 02:35:05 wrp Exp $ */
+
+#ifdef SUNOS
+#include <sys/stdtypes.h>
+#endif
+
+#ifndef IS_BIG_ENDIAN
+#if defined(__BIG_ENDIAN__) || defined(_BIG_ENDIAN)
+#define IS_BIG_ENDIAN
+#else
+#undef IS_BIG_ENDIAN
+#endif
+#endif
+
+#if !defined(MAX_WORKERS) && !defined(PCOMPLIB)
+#define MAX_WORKERS 1
+#endif
+
+/* 3-Oct-2003 - we can now have 2 nucleotide query types, DNA
+   and RNA.  pst.dnaseq can also be SEQT_RNA.
+   ldnaseq can only be DNA */
+
+#define SEQT_DNA 1
+#define SEQT_RNA 3     /* DNA and RNA seqtypes must be odd */
+
+#define SEQT_PROT 0
+#define SEQT_UNK -1
+#define SEQT_OTHER 2
+
+#ifndef DEF_NMLEN
+#define DEF_NMLEN 6
+#endif
+
+/* unfortunately, there is an important relationship between MAXTRN and
+   MAXTST+MAXLIB embedded here.  MAXTRN must be >= (MAXTST+MAXLIB)/3
+   or it will be possible for a translated DNA sequence to be longer
+   than the translation space available */
+
+#define MAX_STR        512 /* standard label/message buffer */
+#define MAX_SSTR 32 /* short string */
+#define MAX_FN  120 /* maximum size of a file name */
+#define MAX_CH 40 /* maximum number of library choices */
+#ifndef SMALLMEM
+#define MAX_LF  500 /* maximum numer of library files */
+#else
+#define MAX_LF  80 /* maximum numer of library files */
+#endif
+
+/* padding at the end of sequences for ALTIVEC, other vector
+   processors */
+#define SEQ_PAD 16
+
+#define MAX_UID 20 /* length of libstr, used for character keys with SQL */
+
+#define AVE_AA_LEN 400
+#define AVE_NT_LEN 5000
+#define MAX_AA_BUF 5000                /* 5000 later */
+#define MAX_NT_BUF 1000                /* 2000 later */
+
+#ifndef SMALLMEM
+#define MAXTST 40000           /* longest query */
+#define MAXLIB 120000          /* longest library */
+#define MAXPLIB        600000          /* longest library with p_comp* */
+#define MIN_RES 2000           /* minimum amount allocated for alignment */
+#ifndef TFAST
+#define MAXTRN  80000          /* buffer for fastx translation */
+#else
+#define MAXTRN 180000          /* buffer for tfastx translation */
+#endif
+#define SEQDUP 1200            /* future - overlap */
+#ifndef PCOMPLIB
+#ifndef MAXBEST
+#define MAXBEST        60000   /* max number of best scores */
+#endif
+#define MAXSTATS 60000
+#else
+#ifndef MAXBEST
+#define MAXBEST        60000   /* max number of best scores */
+#endif
+#define MAXSTATS 60000
+#endif
+#define BIGNUM  1000000000
+#ifndef MAXINT
+#define MAXINT 2147483647
+#endif
+#define MAXLN  120     /* size of a library name */
+#else
+#define MAXTST 1500
+#define MAXLIB 10000
+#define MAXPLIB        100000          /* longest library with p_comp* */
+#define MIN_RES 1000
+#ifndef TFAST
+#define MAXTRN  6000
+#else
+#define MAXTRN 11500
+#endif
+#define SEQDUP 300
+#define MAXBEST 2000
+#define MAXSTATS 20000
+#define BIGNUM  32767
+#define MAXINT  32767
+#define MAXLN  40      /* size of a library name */
+#endif
+#if !defined(TFAST)
+#define MAXTOT (MAXTST+MAXLIB)
+#define MAXDIAG        (MAXTST+MAXLIB)
+#else
+#define MAXTOT (MAXTST+MAXTRN)
+#define MAXDIAG        (MAXTST+MAXTRN)
+#endif
+
+#define MAXPAM 600     /* maximum allowable size of the pam matrix */
+#define PROF_MAX 500
+#define ALF_MAX 30
+
+#ifdef SUPERFAMNUM
+#define NSFCHAR '!'
+#endif
+
+#define max(a,b) (((a) > (b)) ? (a) : (b))
+#define min(a,b) (((a) < (b)) ? (a) : (b))
+
+#define MX_ATYPE 7     /* markx==0,1,2 7=> no alignment */
+#define MX_ASEP  8     /* markx==3  - separate lines */
+#define MX_AMAP  16    /* markx==4,5 - graphic map */
+#define MX_HTML  32    /* markx==6  - HTML */
+#define MX_M9SUMM 64   /* markx==9(c) */
+#define MX_M10FORM 128 /* markx==10 */
+
+/* codes for -m 9 */
+#define SHOW_CODE_ID   1       /* identity only */
+#define SHOW_CODE_ALIGN 2      /* encoded alignment */