+++ /dev/null
-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 !!! */
-}
-\f
-================
-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 */
-
git://source.jalview.org / jabaws.git / blobdiff