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fffasta.c
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fffasta.c
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/* fffasta.c 12-Feb-1984, 11-Mar-1985, 14-Oct-1985
copyright (c) 1985,1986,1987,1988,1991,1992 William R. Pearson
*/
/*
Sept-1991 release 1.6 uses W. Miller l_band, g_band for optimization
25-Sept-1991 fixed RLOCAL_ALIGN() call in zzlgmata.c
14-Mar-87 added BIGMEM for large memory machines
Mar-87 added TFASTA for translation of DNA
1-Jun-87 added LFASTA for lfasta generation from same file
3-Jun-87 added SFASTA for sfasta generation from same file
28-Jun-87 made modifications for speed a la Warren Gish
changed name to flfasta.c
24-Aug-87 no more modulus counting in dhash(), 2X as
fast on the SUN, now MAXDIAG = MAXTST + MAXLIB;
(ALLOCN0 for modulus counting in LFASTA)
19-Oct-87 modified behavior for nbest > MAXBEST, now
resorts nbest and throws out bottom 25%
also modifying bestcut in the process
12-Nov-87 Added automatic detection of protein/DNA sequences
28-Feb-88 added getopt for options
21-Mar-88 added PAM scores for kfact
25-Mar-88 flag -k for using PAM scores for kfact
30-Mar-88 added menu for libraries
30-Mar-88 combine fasta/fastgb, tfasta/tfastgb
19-May-88 added options for fasta mail processing
-Q - quiet, does not ask for any input
with -Q, has heuristic for number of scores
to display, that number will be less than mshow,
which is set with the -o option.
4-Feb-89 modified libchoice for a variety of different
library formats - no more automatic library setting
20-Nov-89 1.3a fixed bug in pamfact that prevented -k option
from working by default with DNA
5-Jun-90 added optall option
3-Sept-90 use select() instead of sortbest()
allow individual library letters to be concatenated
13-Dec-90 fixed bug in select() due to lack of sentinel.
23-Jan-91 fixed bug in aatran() for short sequences
27-Jan-91 made certain than showbest() is called with nbest>0.
20-May-91 fixed ashow to reflect nshow
7-Dec-92 added -h option to suppress histogram
13-Dec-92 added -e option to scale scores by length
26-Aug-95 added -O option to provide filename for output
*/
/* fastn is a derivative of dfastp for DNA sequences
fastn is designed to search a DNA sequence database
very rapidly. It first looks for diagonals with homology
using a hashing algorithm.
General structure:
Read in the test DNA sequence, build a hash table using
a hash length of ktup. DNA bases will be given values
between 0 and 3 (2 bits) and ktup of 1 to 6 will be allowed
(hash table of 4 to 1024 entries, on larger machines, 4096
(ktup=6) would be acceptable).
Start reading the library. Reading the library, looking up
the hash table and accumulating diagonals will all be done
in one loop. The max n diagonals will be identified and
scanned with the PAM matrix for each library sequence.
The max PAM score and diagonal positions are then saved
for comparison against the whole library. After all sequences
have been examined, a mean and s.d. are calculated and the
max matches displayed.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
/* cannot use <unistd.h> because of name clash with 'link' */
int isatty(int);
char *refstr="\nPlease cite:\n W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448\n";
char *verstr="v2.1u00 Mar, 2001";
#ifdef TFASTX
char *progstr = "TFASTX";
#else
#ifdef TFASTA
char *progstr = "TFASTA";
#else
#ifdef FASTX
char *progstr = "FASTX";
#else
char *progstr = "FASTA";
#endif
#endif
#endif
#ifdef __MWERKS__
#include <Types.h>
#include <StandardFile.h>
StandardFileReply freply;
Point wpos;
int tval;
char prompt[256];
#define getenv mgetenv
#include <sioux.h>
#endif
#define YES 1
#define NO 0
#define max(a,b) (((a)>(b))?(a):(b))
#define min(a,b) (((a)<(b))?(a):(b))
#ifndef BIGMEM
#define BIGNUM 32000
#define QFILE_SIZE 40
#define LFILE_SIZE 80
#if defined(TFASTA) || defined(FASTX)
#define MAXTRN 5000 /* MAXTRN must be (MAXTST*3+MAXLIB)/3 */
#endif
#ifdef TFASTX
#define MAXTRN 15000
#endif
#if defined(TFASTA) || defined(TFASTX)
#define MAXTST 1000 /* longest test sequence */
#define MAXLIB 8000
#define MAXDIAG (MAXTST+MAXTRN)
#else
#define MAXTST 2000 /* longest test sequence */
#define MAXLIB 8000
#define MAXDIAG (MAXTST+MAXLIB)
#endif
#else
#define BIGNUM 1000000000
#define QFILE_SIZE 256
#define LFILE_SIZE 256
#define MAXTST 10000
#define MAXLIB 50000
#define MAXDIAG (MAXTST+MAXLIB)
#if defined(TFASTA) || defined(FASTX)
#define MAXTRN 30000
#endif
#ifdef TFASTX
#define MAXTRN 90000
#endif
#endif
#ifdef LFASTA
#define MAXSAV 250
#endif
#ifndef MAXSAV
#define MAXSAV 10 /* number of best diagonals saved */
#endif
#define MAXHIST 51 /* number of histogram divisions */
#ifndef BIGMEM
#define MAXBEST 5000 /* number of good matches remembered */
#else
#define MAXBEST 20000
#endif
FILE *outfd; /* fd for output file */
int smark[4];
FILE *tmpfd;
char tmpfname[LFILE_SIZE];
int dataflg=0;
int revflg = 0;
char *compstr="\0";
int lnsflg=0;
int optwid=32, optwidf=0; /* width for band optimization */
/* changed in initparm() */
/* globals for matching */
long lmark; /* position in library file from ftell() */
long nlib, onlib;
long ntt, ontt; /* number of library sequences, number of
residues scanned*/
#ifdef LFASTA
int have_stats = 0;
int oneseq;
#endif
#ifdef NCBIBL13
#define LASTLIB NCBIBL13+1 /* this must agree with altlib.h */
#else
#define LASTLIB 10
#endif
#ifndef LFASTA
extern int (*getlib)(), (*ranlib)();
extern int sfnum;
#define GETLIB (*getlib)
#define RANLIB (*ranlib)
#else
extern int getlib(), ranlib();
#define GETLIB getlib
#define RANLIB ranlib
#endif
char libstr[21]; /* partial title from library sequence */
char name0[20], name1[20]; /* for labeling output */
int ixstat; /* >0 if annotations displayed */
#define MAXLF 200 /* number of library names */
#ifdef BIGMEM
#define MAXLN QFILE_SIZE /* size of a library name */
#else
#define MAXLN QFILE_SIZE
#endif
char *lbnarr; /* name array of libraries to be opened in list */
char *lbnames[MAXLF]; /* names of libraries to be opened */
int nln; /* number of library files */
#ifndef LFASTA
int deftype=0; /* default library type */
#endif
int libfn; /* current library file being searched */
char ldname[LFILE_SIZE];
unsigned char *aa0, *aa1; /* amino acid sequence data */
#if defined(TFASTA)
unsigned char *aa10;
int nframe=6;
#endif
#ifdef FASTX
#define XFACT 10
unsigned char *aa0x, *aa0y;
int n0x, n0x31, n0x32;
#else
#ifdef TFASTX
#define XFACT 10
unsigned char *aa10, *aa1y;
int nframe=2;
int n1x31, n1x32;
#else
#define XFACT 0
#endif
#endif
int maxn, maxt; /* max space for lib sequence */
int n0, n1, nd, noff; /* length of aa0, length of aa1, n0+n1,
diagonal offset */
long sq0off=1, sq1off=1;
long loffset = 0l; /* offset into sequence */
struct dstruct { /* diagonal structure for saving current run */
int score; /* hash score of current match */
int start; /* start of current match */
int stop; /* end of current match */
struct beststr *dmax; /* location in vmax[] where best score data saved */
} *diag;
#ifdef I86BUG
#define L2DSTR 3 /* log(2) of sizeof dstruct for I86 bug in many 'C'
compilers */
#endif
struct beststr {
int score; /* pam score with segment optimization*/
int score0; /* pam score of best single segment */
int gscore; /* opt score */
int sscore; /* score used for sort */
float zscore;
float escore;
int n1; /* length of library sequence */
long lseek; /* position in library file */
int dp; /* diagonal of match */
int start; /* start of match in lib seq */
int stop; /* end of match in lib seq */
int cont; /* offset into sequence */
int frame;
int lib; /* library for current sequence */
}
#ifndef FAR_PTR
*bbp, /* pointer for fbest */
*bestptr, /* temp pointer */
**bptr, /* array of pointers for sorting */
*best, /* array of best score data */
#else
huge * bbp,
huge * best,
huge * bestptr, /* temp pointer */
huge * huge * bptr,
#endif
vmax[MAXSAV], /* best matches saved for one sequence */
*vptr[MAXSAV];
/* delete this: float *Evalue; */
#ifdef LFASTA
int lcrc0[2*MAXSAV];
int lcrc1[2*MAXSAV];
int maxcrc=2*MAXSAV;
int ncrc;
#endif
int iscore, gscore; /* for displaying scores without showbest */
int cgap; /* gap threshold */
int pgap; /* gap penalty for optimized alignment of diagonals */
int nbest; /* number of sequences better than bestcut in best */
int bestcut=1; /* cut off for getting into MAXBEST */
int optcut=0; /* cut off for optimization */
/* the following are defaults for values that are read by
pam.c from *.mat if SMATRIX is defined */
int histint;
int bestscale=300; /* values for calculating bestcut */
int bestoff=36; /* these values are for BLOSUM50 */
int bkfact=6;
int scfact=3;
int bktup=2;
int ktmax=2;
int bestmax=50;
int pamfact= 1; /* flag for using pam values for kfact */
int dnaseq = 0; /* true if DNA query sequence */
int dnasw_flg = 0;
int ldnaseq = 0;
int bestfull=0;
int igncnt=0;
int optall=1;
long optcount=0l;
int init1flg=0;
int nsav, lowscor; /* number of saved runs, worst saved
run, score of worst saved run */
long *hist; /* histogram of all score */
int min_hist, max_hist, maxh;
int histflg=1;
int long_info=0; /* long display of library sequence definition */
int dohist=0;
#ifndef LFASTA
int zsflag=1;
extern long num_db_entries, z_calls;
float zs_to_E(float, int);
float zs_to_Ec(float);
float find_zm(int, int), find_z(int, int);
extern float ks_dev;
extern int ks_df;
#else
int zsflag=0;
long num_db_entries;
#endif
static int fact, gm; /* scoring factors */
static int hmask, hmax; /* hash constants */
static int *pamh2; /* pam based kfact array */
static int *link, *harr; /* hash arrays */
static int ktup, kshft, kt1; /* ktuple constants */
int nshow=20, mshow=50, ashow= -1;
int mshow_flg=0;
#ifndef FASTX
float e_cut=10.0; /* threshold for E value display */
#else
float e_cut=5.0;
#endif
int e_cut_set=0; /* flag for set */
char rline[20],sline[20];
char resfile[QFILE_SIZE];
/* output options */
int showall, llen, markx; /* show all of both sequences */
char ttitle[60];
char ltitle[60];
long tstart, tscan, tdone, sstime();
extern int optind;
#ifndef LFASTA
int outtty;
#else
extern int outtty;
float zs_to_E(float zs, int n) {return 0.0;}
float zs_to_Ec(float zs) {return 0.0;}
#endif
char *libenv, *aaenv, *smptr;
char smstr[QFILE_SIZE], sdstr[QFILE_SIZE];
char flstr[QFILE_SIZE];
#ifdef TPLOT
char lvstr[QFILE_SIZE];
#endif
#ifdef __MWERKS__
/* short ouvRef, q0vRef, q1vRef; */
FSSpec ouSpec, q0Spec, q1Spec;
OSErr error;
#define IntroDID 400 /* LFASTA */
#endif
#ifdef LFASTA
#define PgmDID 403
char *iprompt0=" LFASTA compares two sequences\n";
char *iprompt1=" first sequence file name: ";
char *iprompt2=" second sequence file name: ";
#else
char *iprompt1=" query sequence file name: ";
#ifdef TFASTA
#define PgmDID 402
char *iprompt0=" TFASTA translates and searches a DNA sequence data bank\n";
#else
#ifdef FASTX
#define PgmDID 405
char *iprompt0=" FASTX compares a DNA sequence to a protein data bank\n";
#else
#ifdef TFASTX
#define PgmDID 406
char *iprompt0=" TFASTX translates and searches a DNA sequence data bank\n";
#else
#define PgmDID 401
char *iprompt0=" FASTA searches a protein or DNA sequence data bank\n";
#endif
#endif
#endif
#endif
void initenv(int, char **);
int getseq(char *, unsigned char *, int, int *);
#ifdef FASTX
int getntseq(char *, unsigned char *, int, int *);
int check_nt(unsigned char*, int, int *);
#endif
void gettitle(char *, char *, int n);
void revcomp(unsigned char *, int);
void resetp(int);
void reseta(int);
void libchoice(char *, int, char *);
void libselect(char *);
void addfile(char *, char *);
int initpam(char *);
void initpam2();
#if defined(TFASTX) || defined(TFASTA) || defined(FASTX)
void aainit();
int aatran();
int saatran();
extern int pmatch(unsigned char *, int, unsigned char *, int,
unsigned char *, int, int);
#endif
void initparm();
void hashaa(unsigned char *, int, int);
void allocdiag(int);
void initbest(int);
int openlib(char *, char *);
void sortbest(), sortbeste();
void sortbestz();
void ksort(struct beststr *v[], int n, int (*cmp)(int));
void kssort(struct beststr *v[], int n);
void kpsort(struct beststr *v[], int n);
int shscore(unsigned char *, int);
void allochash(int, int);
void dhash();
void freehash();
void savemax();
int spam();
int sconn();
void process_hist(int n0, struct beststr **bptr, int nbest);
void addhistz(float, int);
void ptime(FILE *, long);
void closelib();
void prhist(FILE *);
void showbest();
void showalign(int);
void selectz(int, int);
#ifndef LFASTA
int dmatch(int, int);
#else
int dmatch(int, int,int);
#endif
#ifdef TPLOT
void openplt();
void drawdiag();
void closeplt();
#endif
int smatch(unsigned char *, int, unsigned char *, int, int);
#ifdef LFASTA
void showlocal(int);
#endif
#include "upam.gbl" /* includes pam array */
int main(argc, argv)
int argc; char **argv;
{
char tname[QFILE_SIZE], lname[LFILE_SIZE], llname[LFILE_SIZE], qline[QFILE_SIZE];
int itemp, iln,i;
#ifdef FASTX
int last_n0;
unsigned char *fs, *fd;
#endif
char *getenv(), *cptr, *bp;
#ifdef __MWERKS__
SIOUXSettings.showstatusline=FALSE;
#ifdef TPLOT
InitGraf(&qd.thePort);
SIOUXSettings.asktosaveonclose=FALSE;
#else
SIOUXSettings.asktosaveonclose=TRUE;
#endif
SIOUXSettings.autocloseonquit=TRUE;
argc = ccommand(&argv);
if (GetResource('DLOG',PgmDID)==(Handle)0 &&
OpenResFile("\pFASTA.rsrc")<0) {
SysBeep(100);
fprintf(stderr," WARNING FASTA.rsrc file could not be found\n");
}
InitEvent();
/* GetVol((unsigned char *)prompt,&ouvRef); */
error=HGetVol(NULL,&ouSpec.vRefNum, &ouSpec.parID);
if (error != noErr) {
fprintf(stderr," cannot get current directory\n");
exit(1);
}
wpos.h=50; wpos.v=100;
#endif
#ifndef LFASTA
#ifdef UNIX
outtty=isatty(1);
#else
outtty=1;
#endif
#endif
initenv(argc,argv);
#ifdef __MWERKS__
if (!outtty) SIOUXSettings.asktosaveonclose=FALSE;
#endif
if (dataflg && (tmpfd=fopen(tmpfname,"w"))==NULL) {
fprintf(stderr," cannot open temp file: %s\n",tmpfname);
dataflg=0;
}
#if defined(TFASTA) || defined(TFASTX)
aainit();
dnaseq = -1; /* force to protein */
ldnaseq = 1;
if (sqtype[0]=='D') {
fprintf(stderr," tfasta compares a protein to a translated\n\
DNA sequence library. Do not use a DNA scoring matrix.\n");
exit(1);
}
#endif
if ((aa0=calloc((size_t)MAXTST+MAXLIB,sizeof(char)))==0) {
fprintf(stderr," cannot allocate sequence array\n");
exit(1);
}
maxn = MAXTST+MAXLIB;
#ifdef FASTX
if ((aa0x=calloc((size_t)MAXTRN,sizeof(char)))==0) {
fprintf(stderr," cannot allocate FASTX translation array I\n");
exit(1);
}
if ((aa0y=calloc((size_t)MAXTRN,sizeof(char)))==0) {
fprintf(stderr," cannot allocate FASTX translation array II\n");
exit(1);
}
#endif
#ifdef TFASTX
if ((aa1y=calloc((size_t)MAXTRN,sizeof(char)))==0) {
fprintf(stderr," cannot allocate TFASTX translation array II\n");
exit(1);
}
#endif
#if defined(TFASTA) || defined(TFASTX)
if ((aa1=calloc((size_t)MAXTRN,sizeof(char)))==0) {
fprintf(stderr," cannot allocate translation array\n");
exit(1);
}
#endif
if (argc-optind < 3) {
#ifndef LFASTA
if (!outtty) {
fprintf(stderr," too few command line arguments with -q\n");
exit(1);
}
#endif
#ifndef __MWERKS__
fputs(iprompt0,stdout);
fprintf(stdout," %s%s\n",verstr,refstr);
l1: fputs(iprompt1,stdout);
fflush(stdout);
if (fgets(tname,sizeof(tname),stdin)==NULL) exit(0);
if (tname[strlen(tname)-1]=='\n') tname[strlen(tname)-1]='\0';
if (tname[0]=='\0') goto l1;
#else
/* NIntroDlog(IntroDID,iprompt0,verstr,refstr,"\0"); */
NIntroDlog(PgmDID,verstr,"\0","\0","\0");
l1: SFileDlog(iprompt1,&freply);
if (freply.sfGood==TRUE) {
PtoCstr((unsigned char *)freply.sfFile.name);
strcpy(tname,(char *)freply.sfFile.name);
/* q0vRef=freply.vRefNum;
SetVol(NULL,q0vRef);
*/
q1Spec.vRefNum = q0Spec.vRefNum = freply.sfFile.vRefNum;
q1Spec.parID = q0Spec.parID = freply.sfFile.parID;
HSetVol(NULL,q0Spec.vRefNum,q0Spec.parID);
}
else exit(0);
#endif
#ifdef FASTX
if ((n0=getntseq(tname,aa0,maxn,&dnaseq))==0) {
fprintf(stderr," %s : %s sequence not found\n",tname,sqtype);
goto l1;
}
#else
if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) {
fprintf(stderr," %s : %s sequence not found\n",tname,sqtype);
goto l1;
}
#endif
#ifndef TFASTX
if (revflg) {
if (sqtype[0]=='D') revcomp(aa0,n0);
else {
fprintf(stderr," can only reverse complement DNA\n");
compstr="\0"; revflg = 0;
}
}
#endif
#ifndef FASTX
resetp(dnaseq);
#else
reseta(dnaseq);
#endif
#ifndef TFASTA
if (dnaseq==1 && n0>(MAXTST+MAXLIB)/3) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
else if (dnaseq==0 && n0>(MAXTST+MAXLIB)/2) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
#else
if (n0 > MAXTST) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
#endif
#ifdef LFASTA
#ifndef __MWERKS__
l2: fputs(iprompt2,stdout);
fflush(stdout);
if (fgets(lname,sizeof(lname),stdin)==NULL) exit(1);
if (lname[strlen(lname)-1]=='\n') lname[strlen(lname)-1]='\0';
if (*lname==0) goto l2;
#else
l2: SFileDlog(iprompt2,&freply);
if (freply.sfGood==TRUE) {
PtoCstr((unsigned char *)freply.sfFile.name);
strcpy(lname,(char *)freply.sfFile.name);
/* q1vRef=freply.vRefNum;
SetVol(NULL,q1vRef);
*/
q1Spec.vRefNum = freply.sfFile.vRefNum;
q1Spec.parID = freply.sfFile.parID;
HSetVol(NULL,q1Spec.vRefNum,q1Spec.parID);
}
else exit(0);
#endif
#else
#ifdef __MWERKS__
HSetVol(NULL,ouSpec.vRefNum,ouSpec.parID);
/* SetVol(NULL,ouvRef); */
#endif
libchoice(lname,sizeof(lname),aaenv);
#endif
libselect(lname);
fprintf(stderr," ktup? (1 to %d) [%d] ",ktmax,ktmax);
if (fgets(qline,sizeof(qline),stdin)==NULL) exit(0);
ktup = ktmax;
if (qline[0]!='\0' && qline[0]!='\n') {
sscanf(qline,"%d",&ktup);
if (ktup < 1 || ktup>ktmax ) {
printf(" warning ktup = %d out of range, reset to %d\n",ktup,ktmax);
ktup = ktmax;
}
}
#ifndef LFASTA
fprintf(stderr," use optimized scores? [%s]: ",(optall?"yes":"no"));
if (fgets(qline,sizeof(qline),stdin)==NULL) exit(0);
if (optall==1 && (*qline=='n' || *qline=='N')) optall = 0;
if (optall==0 && (*qline=='y' || *qline=='Y')) optall = 1;
#endif
}
else { /* all arguments from the command line */
#ifdef TPLOT
fputs(iprompt0,stderr);
fprintf(stderr," %s%s\n",verstr,refstr);
#else
fputs(iprompt0,stdout);
fprintf(stdout," %s%s\n",verstr,refstr);
#endif
strncpy(tname,argv[optind+1],sizeof(tname));
#ifndef FASTX
if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) {
fprintf(stderr," %s : %s sequence not found\n",tname,sqtype);
exit(1);
#else
if ((n0=getntseq(tname,aa0,maxn,&dnaseq))==0) {
fprintf(stderr," %s : %s sequence not found\n",tname,sqtype);
exit(1);
#endif
}
#ifndef TFASTX
if (revflg) {
if (dnaseq) revcomp(aa0,n0);
else {
fprintf(stderr," cannot reverse complement protein sequence\n");
compstr="\0"; revflg = 0;
}
}
#endif
#ifndef FASTX
resetp(dnaseq);
#else
reseta(dnaseq);
#endif
#ifndef TFASTA
if (dnaseq==1 && n0>(MAXTST+MAXLIB)/3) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
else if (dnaseq==0 && n0>(MAXTST+MAXLIB)/2) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
#else
if (n0 > MAXTST) {
fprintf(stderr," query sequence is too long %d %s\n",n0,qsqnam);
exit(1);
}
#endif
strncpy(lname,argv[optind+2],sizeof(lname));
#ifndef LFASTA
libselect(lname);
#else
addfile(lname,"");
#endif
if (argc-optind==4) sscanf(argv[optind+3],"%d",&ktup);
else ktup=ktmax;
if (ktup < 1 || ktup>ktmax ) {
fprintf(stderr," warning ktup = %d out of range, reset to %d\n",
ktup,ktmax);
ktup = ktmax;
}
}
#ifndef LFASTA
if (!outtty)
#ifndef TFASTX
fprintf(stdout," %s%s : %4d %-s\n",tname, compstr, n0, qsqnam);
#else
fprintf(stdout," %s : %4d %-s\n",tname, n0, qsqnam);
#endif /* TFASTX */
#endif /* LFASTA */
#ifdef __MWERKS__
HSetVol(NULL,q0Spec.vRefNum,q0Spec.parID);
/* SetVol(NULL,q0vRef); */
#endif
gettitle(tname,ttitle,50);
if (strlen(ttitle)>0)
if (*ttitle=='>') strncpy(name0,&ttitle[1],6);
else strncpy(name0,ttitle,6);
else
strncpy(name0,tname,6);
name0[6]='\0';
if (revflg) name0[5]='-';
#ifdef __MWERKS__
HSetVol(NULL,ouSpec.vRefNum,ouSpec.parID);
/* SetVol(NULL,ouvRef); */
#endif
#ifdef LFASTA
if (strcmp(tname,lname)==0 && revflg==0) oneseq=1;
#else
if (strlen(ttitle)>0)
#ifndef TFASTX
printf(" %s%s: %d %s\n vs %s library\n",ttitle,compstr,n0,qsqnam,ltitle);
#else
printf(" %s: %d %s\n vs %s library %s\n",ttitle,n0,qsqnam,ltitle,compstr);
#endif
else
#ifndef TFASTX
printf(" %s%s: %d %s vs %s library\n",tname,compstr,n0,qsqnam,ltitle);
#else
printf(" %s: %d %s vs %s library %s\n",tname,n0,qsqnam,ltitle,compstr);
#endif
if (dataflg) {
if (strlen(ttitle)>0)
fprintf(tmpfd,"; %s%s: %d %s\n; vs %s library\n",
ttitle,compstr,n0,qsqnam,ltitle);
else
fprintf(tmpfd,"; %s%s: %d %s vs %s library\n",
tname,compstr,n0,qsqnam,ltitle);
}
#endif
#if !defined(TFASTA) && !defined(TFASTX)
aa1 = aa0 + n0 + 2;
#else
aa10 = aa0 + n0 + 2;
#endif
maxn -= n0 + 3;
initpam2(); /* convert 1-d pam to 2-d pam2 */
initparm();
if (dataflg) {
fprintf(tmpfd,"; ktup = %d\n",ktup);
fprintf(tmpfd,"; cutoff = %d; optcut = %d; ggapval %d gdelval %d cgap %d\n",
bestcut,optcut,ggapval,gdelval,cgap);
if (lnsflg) fprintf(tmpfd,"; ln scaling");
}
tstart = sstime();
#ifdef FASTX
if (check_nt(aa0,n0,&i)==0)
{
fprintf(stderr," error - %s has non-nucleotide residues at: %d\n",tname,i);
exit(1);
}
aainit();
last_n0 = 0;
for (itemp=0; itemp<3; itemp++) {
n0x=saatran(aa0,&aa0x[last_n0],n0,itemp);
/*
for (i=0; i<n0x; i++) {
fprintf(stderr,"%c",aa[aa0x[last_n0+i]]);
if ((i%60)==59) fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
*/
last_n0 += n0x+1;
}
/* fprintf(stderr,"\n"); */
n0x = n0;
n0x31 = (n0-2)/3;
n0x32 = n0x31+1+(n0-n0x31-1)/2;
/* we also need a rearranged version,
111111222222233333333 becomes 123123123123123 */
for (fs=aa0x,itemp=0; itemp <3; itemp++,fs++) {
for (fd=&aa0y[itemp]; *fs !=EOSEQ; fd += 3, fs++) *fd = *fs;
*fd=EOSEQ;
}
/*
for (i=0; i<n0x; i++) {
fprintf(stderr,"%c",aa[aa0y[i]]);
if ((i%60)==59) fprintf(stderr,"\n");
}
fprintf(stderr,"\n");
*/
#endif
fact = ktup*scfact;
#ifndef FASTX
hashaa(aa0,n0,ktup); /* hash test sequence */
#else
hashaa(aa0x,n0x,ktup);
#endif
#ifndef ALLOCN0
allocdiag(MAXDIAG);
#else
allocdiag(n0);
#endif
/* inithist(); */ /* initialize histogram, mean, sd */
initbest(MAXBEST+1); /* +1 required for select() */
for (nbest=0; nbest<MAXBEST+1; nbest++)
bptr[nbest] = &best[nbest];
bptr++; best++;
best[-1].score=best[-1].score0=
best[-1].gscore= best[-1].sscore = BIGNUM;
best[-1].zscore = (float)BIGNUM;
nlib = onlib = 0;
ntt = ontt = 0l;
nbest = 0;
#ifdef LFASTA
/* initialize crc array */
for (ncrc=0; ncrc<MAXSAV; ncrc++) lcrc0[ncrc]=lcrc1[ncrc]= -1;
ncrc = 0;
#ifdef __MWERKS__
HSetVol(NULL,q1Spec.vRefNum,q1Spec.parID);
/* SetVol(NULL,q1vRef); */
#endif
gettitle(lname,ltitle,50);
#ifdef __MWERKS__
HSetVol(NULL,ouSpec.vRefNum,ouSpec.parID);
/* SetVol(NULL,ouvRef); */
#endif
#endif
for (iln=0; iln<nln; iln++) {
libfn = iln;
#ifdef __MWERKS__
HSetVol(NULL,q1Spec.vRefNum,q1Spec.parID);
/* SetVol(NULL,q1vRef); */
#endif
if ((itemp=openlib(lbnames[iln],"\0"))>0) {
#ifndef TPLOT
fprintf(stdout," searching %s library\n",lbnames[iln]);
#endif
dhash();
}
if (itemp== -9) {
printf(" %8ld %s in %5ld sequences\n",ntt-ontt,
sqnam,nlib-onlib);
ontt=ntt; onlib=nlib; continue;
}
if (itemp<0) break;
#ifndef LFASTA
closelib();
#endif
}
tscan = sstime();
#ifdef PROGRESS
#ifdef UNIX
if (outtty)
#endif
if (nlib >= 200) fprintf(stderr," Done!\n");
#endif
#ifndef LFASTA
if (!dohist) {
if (nbest < 20) {
zsflag = 0;
histflg = 0;
}
else if (zsflag) process_hist(n0,bptr,nbest);
}
if (dataflg) {
fprintf(tmpfd,"; %8ld %s in %5ld sequences; scan time: ",
ntt,sqnam,nlib);
ptime(tmpfd,tscan-tstart);
fputs("\n",tmpfd);
if (optall)
fprintf(tmpfd,"; %ld optimizations performed\n",optcount);
}
prhist(stdout); /* print histogram, statistics */
#endif
#ifdef __MWERKS__
HSetVol(NULL,ouSpec.vRefNum,ouSpec.parID);
/* SetVol(NULL,ouvRef); */
#endif
free(diag);
freehash();