1 /* Concurrent read version */
3 /* $Name: fa_34_26_5 $ - $Id: defs.h,v 1.26 2006/06/22 02:35:05 wrp Exp $ */
6 #include <sys/stdtypes.h>
10 #if defined(__BIG_ENDIAN__) || defined(_BIG_ENDIAN)
17 #if !defined(MAX_WORKERS) && !defined(PCOMPLIB)
21 /* 3-Oct-2003 - we can now have 2 nucleotide query types, DNA
22 and RNA. pst.dnaseq can also be SEQT_RNA.
23 ldnaseq can only be DNA */
26 #define SEQT_RNA 3 /* DNA and RNA seqtypes must be odd */
36 /* unfortunately, there is an important relationship between MAXTRN and
37 MAXTST+MAXLIB embedded here. MAXTRN must be >= (MAXTST+MAXLIB)/3
38 or it will be possible for a translated DNA sequence to be longer
39 than the translation space available */
41 #define MAX_STR 512 /* standard label/message buffer */
42 #define MAX_SSTR 32 /* short string */
43 #define MAX_FN 120 /* maximum size of a file name */
44 #define MAX_CH 40 /* maximum number of library choices */
46 #define MAX_LF 500 /* maximum numer of library files */
48 #define MAX_LF 80 /* maximum numer of library files */
51 /* padding at the end of sequences for ALTIVEC, other vector
55 #define MAX_UID 20 /* length of libstr, used for character keys with SQL */
57 #define AVE_AA_LEN 400
58 #define AVE_NT_LEN 5000
59 #define MAX_AA_BUF 5000 /* 5000 later */
60 #define MAX_NT_BUF 1000 /* 2000 later */
63 #define MAXTST 40000 /* longest query */
64 #define MAXLIB 120000 /* longest library */
65 #define MAXPLIB 600000 /* longest library with p_comp* */
66 #define MIN_RES 2000 /* minimum amount allocated for alignment */
68 #define MAXTRN 80000 /* buffer for fastx translation */
70 #define MAXTRN 180000 /* buffer for tfastx translation */
72 #define SEQDUP 1200 /* future - overlap */
75 #define MAXBEST 60000 /* max number of best scores */
77 #define MAXSTATS 60000
80 #define MAXBEST 60000 /* max number of best scores */
82 #define MAXSTATS 60000
84 #define BIGNUM 1000000000
86 #define MAXINT 2147483647
88 #define MAXLN 120 /* size of a library name */
92 #define MAXPLIB 100000 /* longest library with p_comp* */
101 #define MAXSTATS 20000
104 #define MAXLN 40 /* size of a library name */
107 #define MAXTOT (MAXTST+MAXLIB)
108 #define MAXDIAG (MAXTST+MAXLIB)
110 #define MAXTOT (MAXTST+MAXTRN)
111 #define MAXDIAG (MAXTST+MAXTRN)
114 #define MAXPAM 600 /* maximum allowable size of the pam matrix */
122 #define max(a,b) (((a) > (b)) ? (a) : (b))
123 #define min(a,b) (((a) < (b)) ? (a) : (b))
125 #define MX_ATYPE 7 /* markx==0,1,2 7=> no alignment */
126 #define MX_ASEP 8 /* markx==3 - separate lines */
127 #define MX_AMAP 16 /* markx==4,5 - graphic map */
128 #define MX_HTML 32 /* markx==6 - HTML */
129 #define MX_M9SUMM 64 /* markx==9(c) */
130 #define MX_M10FORM 128 /* markx==10 */
133 #define SHOW_CODE_ID 1 /* identity only */
134 #define SHOW_CODE_ALIGN 2 /* encoded alignment */