Over all structure of the fasta3 program.  (Some functions
are different for translated comparisons FASTX, FASTY, TFASTX, TFASTY.)

main() {	/* complib.c structure */

  /* get command line arguments, set up initial parameter values */
  initenv (argc, argv, &m_msg, &pst,&aa0[0],outtty);

  /* allocate space for sequence arrays */
  /* get the query file name if not on command line */
  /* get query */
  m_msg.n0 = getseq (m_msg.tname,aa0[0], MAXTOT, m_msg.libstr,&pst.dnaseq,
		     &m_msg.sq0off);

  /* reset some parameters if DNA */		     
  resetp (aa0[0], m_msg.n0, &m_msg, &pst);

  /* get a library name if not on command line */
  libchoice(m_msg.lname,sizeof(m_msg.lname),&m_msg);
  /* use library name to build list of library files */
  libselect(m_msg.lname, &m_msg);

  /* get additional options (ktup, prss-window) if not specified */
  query_parm (&m_msg, &pst);

  /* do final parameter initializations */
  last_init(&m_msg, &pst);

  /* set up structures for saved scores[20000], statistics[50000] */
  nbest = 0;
  
  /* initialize the comparison function */
  init_work (aa0[0], m_msg.n0, &pst, &f_str[0]);

  /* open the library */
  for (iln = 0; iln < m_msg.nln; iln++) {
    if (openlib(m_msg.lbnames[iln],m_msg)!=1) {continue;}
  }

  /* get the library sequence and do the comparison */
  while ((n1=GETLIB(aa1ptr,maxt,libstr,&lmark,&lcont))>0) {
    do_work (aa0[itt], m_msg.n0, aa1, n1, itt, &pst, f_str[itt], &rst);

  /* save the scores */
  /* save the scores for statistics */
  }

  /* all done with all libraries */
  process_hist(stats,nstats,pst);

  /* sort the scores by z-value */
  sortbestz (bptr, nbest);

  /* sort the scores by E-value */
  sortbeste (bptr, nbest);

  /* print the histogram */
  prhist (stdout,m_msg,pst,gstring2);

  /* show the high scoring sequences */
  showbest (stdout, aa0, aa1, maxn, bptr, nbest, qlib, &m_msg, pst,
            f_str, gstring2);

  /* show the high-scoring alignments */
  showalign(outfd, aa0, aa1, maxn, bptr, nbest, qlib, m_msg, pst,
	    f_str, gstring2);

  /* thats all folks !!! */
}

================
complib.c	/* version set as mp_verstr */

main()
printsum()	/* prints summary of run (residues, entries, time) */
void fsigint() 	/* sets up interrupt handler for HUP not used */

================
compacc.c

void selectbest() /* select best 15000/20000 based on raw score */
void selectbestz() /* select best 15000/20000 based on z-score */
void sortbest()  /* sort based on raw score */
void sortbestz() /* sort based on z-score */
void sortbeste() /* sort based on E() score - different from z-score for DNA */

prhist()	/* print histogram */

shuffle()	/* shuffle sequence (prss) */
wshuffle()	/* window shuffle */

================
showbest.c

void showbest()	/* present list of high scoring sequences */

================
showalign.c

void showalign() /* show list of high-scoring alignments */
void do_show()	/* show an individual alignment */
void initseq()	/* setup seqc0/seqc1 which contain alignment characters */
void freeseq()	/* free them up */

================
htime.c

time_t s_time()	/* get the time in usecs */
void ptime()	/* print elapsed time */

================
apam.c

initpam ()	/* read in PAM matrix or change default array */
void mk_n_pam()	/* make DNA pam from +5/-3 values */
================
doinit.c

void initenv()	/* read environment variables, general options */
================
initfa.c	/* version set as "verstr" */

alloc_pam()	/* allocate 2D pam array */
initpam2()	/* fill it up from 1D pam triangle */
f_initenv()	/* function-specific environment variables */
f_getopt()	/* function-specific options */
f_getarg()	/* function specific argument - ktup */
resetp()	/* reset scoring matrix, optional parameters for DNA-DNA */
reseta()	/* reset scoring matrix, optional parameters for prot-DNA */
query_parm()	/* ask for additional program arguments (ktup) */
last_init()	/* last chance to set up parameters based on query,lib,parms */
f_initpam()	/* not used - could set parameters from pam matrix */

================
scaleswn.c

process_hist()	/* do statistics calculations */

  proc_hist_r()	/* regression fit z=1, also used by z=5 */
    float find_z() /* gives z-score for score, length, mu, rho, var */
    float find_zr() /* gives z-score for score, length, mu, rho, var */
    fit_llen()	/* first estimate of mu, rho, var */
    fit_llens()	/* second estimate of mu, rho, var, mu2, rho2 */

  proc_hist_r2()  /* regression_i fit z=4 */
    float find_zr2() /* gives z-score for score, length, mu, rho, mu2, rho2 */
    fit_llen2()	/* iterative estimate of mu, rho, var */

  proc_hist_ln()  /* ln()-scaled z=2 */ /* no longer used */
    float find_zl() /* gives z-score from ln()-scaled scores */

  proc_hist_ml() /* estimate lambda, K using Maximum Likelihood */
    float find_ze() /* z-score from lambda, K */

  proc_hist_n()   /* no length-scaling z=0 */
    float find_zn() /* gives z-score from mu, var (no scaling) */

  proc_hist_a()   /* Altschul-Gish params z= 3 */
    ag_parm()	/* match pst.pamfile name, look_p() */
    look_p()	/* lookup Lambda, K, H given param struct */
    float find_za()

eq_s()	/* returns (double)score (available for length correction) */
ln_s()	/* returns (double)score * ln(200)/ln(length) */

proc_hist_r()	/* regression fit z=1, also used by z=5 */
alloc_hist()	/* set up arrays for score vs length  */
free_hist()	/* free them */
inithist()	/* calls alloc_hist(), sets some other globals */
addhist()	/* update score vs length hist */ 
inithistz()	/* initialize displayed (z-score) histogram hist[]*/
addhistz()	/* add to hist[], increment num_db_entries */
addhistzp()	/* add to hist[], don't change num_db_entries */
prune_hist()	/* remove scores from score vs length */
update_db_size() /* num_db_entries = nlib - ntrimmed */
set_db_size()	/* -Z db_size; set nlib */

double z_to_E()	/* z-value to E() (extreme value distribution */
double zs_to_E() /* z-score (mu=50, sigma=10) to E() */
double zs_to_bit() /* z-score to BLAST2 bit score */

float E_to_zs()	/* E() to z-score */
double zs_to_Ec() /* z-score to num_db_entries*(1 - P(zs))

summ_stats()	/* put stat summary in string */
vsort()		/* not used, does shell sort */
calc_ks()	/* does Kolmogorov-Smirnoff calculation for histogram */
================
dropnfa.c	/* contains worker comparison functions */

init_work()	/* set up struct f_struct fstr - hash query */
get_param()	/* actually prints parameters to string */
close_work()	/* clean up fstr */
do_work()	/* do a comparison */
  do_fasta()	/* use the fasta() function */
    savemax()	/* save the best region during scan */
    spam()	/* rescan the best regions */
    sconn()	/* try to connect the best regions for initn */
    kssort()	/* sort by score */
    kpsort()	/* sort by left end pos */
    shscore()	/* best self-score */
    dmatch()	/* do band alignment for opt score */
      FLOCAL_ALIGN()	/* fast band score-only */

do_opt()	/* do an "optimized comparison */

do_walign()	/* put an alignment into res[] for calcons() */
  sw_walign()	/* SW alignment driver - find boundaries */
    ALIGN()	/* actual alignment driver */
      nw_align()	/* recursive global alignment */
    CHECK_SCORE()	/* double check */
    DISPLAY()	/* Miller's display routine */

  bd_walign()	/* band alignment driver for DNA */
    LOCAL_ALIGN()	/* find boundaries in band */
    B_ALIGN()		/* produce band alignment  */
      bg_align()	/* recursively produce band alignment */
    BCHECK_SCORE()	/* double check */

calcons()	/* calculate ascii alignment  seqc0,seqc1 from res[]*/
calc_id()	/* calculate % identity with no alignment */
================
nxgetaa.c

getseq()	/* get a query (prot or DNA) */
getntseq()	/* get a nt query (for fastx, fasty) */
gettitle()	/* get a description */

int openlib()	/* open a library */
closelib()	/* close it */
GETLIB()	/* get a fasta-format next library entry */
RANLIB()	/* jump back in, get description, position for getlib() */

lgetlib()	/* get a Genbank flat-file format next library entry */
lranlib()	/* jump back in, get description, position for lgetlib() */

pgetlib()	/* get CODATA format next library entry */
pranlib()	/* jump back in, get description, position for lgetlib() */

egetlib()	/* get EMBL format next library entry */
eranlib()	/* jump back in, get description, position for egetlib() */

igetlib()	/* get Intelligenetics format next library entry */
iranlib()	/* jump back in, get description, position for igetlib() */

vgetlib()	/* get PIR/VMS/GCG format next library entry */
vranlib()	/* jump back in, get description, position for vgetlib() */

gcg_getlib()	/* get GCG binary format next library entry */
gcg_ranlib()	/* jump back in, get description, position for gcg_getlib() */

int scanseq()	/* find %ACGT */

revcomp()	/* do reverse complement */
sf_sort()	/* sort superfamily numbers */
================
c_dispn.c

discons()	/* display alignment from seqc0, seqc1 */
disgraph()	/* display graphical representation, -m 4,5 */
aancpy()	/* copy a binary sequence to ascii */
r_memcpy()
l_memcpy()
iidex()		/* lookup ascii-encoding of residue */
cal_coord()	/* calculate coordinates of alignment ends */

================
ncbl_lib.c

ncbl_openlib()
ncbl_closelib()
ncbl_getliba()
ncbl_getlibn()
ncbl_ranlib()
src_ulong_read()
src_long_read()
src_char_read()
src_fstr_read()
newname()

================
lib_sel.c

getlnames()
libchoice()
libselect()
addfile()
ulindex()

================
nrand48.c

irand(time)	/* initialize random number generator */
nrand(n)	/* get a number 0 - n */

================
url_subs.c

void do_url1()	/* setup search links */