X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Fdefs.h;fp=website%2Farchive%2Fbinaries%2Fmac%2Fsrc%2Ffasta34%2Fdefs.h;h=f0851f5988057bdbff0c55692fa8e6e26b74fe80;hb=dbde3fb6f00b9bb770343631a517c0e599db8528;hp=0000000000000000000000000000000000000000;hpb=85f830bbd51a7277994bd4233141016304e210c9;p=jabaws.git diff --git a/website/archive/binaries/mac/src/fasta34/defs.h b/website/archive/binaries/mac/src/fasta34/defs.h new file mode 100644 index 0000000..f0851f5 --- /dev/null +++ b/website/archive/binaries/mac/src/fasta34/defs.h @@ -0,0 +1,134 @@ +/* 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 +#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 */