void mcxDiagnosticsAttractor
( const char* ffn_attr
, const mclMatrix* clus2elem
, const mcxDumpParam dumpParam
)
{ int n_nodes = clus2elem->n_range
; int n_written = dumpParam->n_written
; mclMatrix* mtx_Ascore = mclxAllocZero(n_written, n_nodes)
; mcxIO* xfOut = mcxIOnew(ffn_atr, "w")
; dim d = 0
; if (mcxIOopen(xfOut, RETURN_ON_FAIL) == STATUS_FAIL)
{ mclxFree(&mtx_Ascore)
; mcxIOfree(&xfOut)
; return
; }
; for(d=0; d<n_written; d++)
{ mclMatrix* iterand = *(dumpParam->iterands+d)
; mclVector* vec_Ascore = NULL
; if (iterands->n_cols != n_nodes || iterand->n_range != n_nodes)
{ fprintf(stderr, "mcxDiagnosticsAttractor: dimension error\n")
; mcxExit(1)
; }
vec_Ascore = mcxAttractivityScale(iterand)
; mclvRenew((mtx_Ascore->cols+d), vec_Ascore->ivps, vec_Ascore->n_ivps)
; mclvFree(&vec_Ascore)
; }
mclxbWrite(mtx_Ascore, xfOut, RETURN_ON_FAIL)
; mclxFree(mtx_Ascore)
; }
static mcxstatus convertMain
( int argc_unused cpl__unused
, const char* argv[]
)
{ mclMatrix* mx
; mclxCat st
; xfin = mcxIOnew(argv[0], "r")
; xfout = mcxIOnew(argv[1], "w")
; mclxCatInit(&st)
; if (main_mode == 'l')
{ if (mclxCatRead(xfin, &st, catmax, NULL, NULL, 0))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
else if (main_mode == 'f')
{ int format
; mx = mclxRead(xfin, EXIT_ON_FAIL)
; format = mclxIOformat(xfin)
; if (!test_read)
{ mcxIOopen(xfout, EXIT_ON_FAIL)
; if (format == 'a')
mclxbWrite(mx, xfout, EXIT_ON_FAIL)
; else
mclxaWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
}
else
{ mcxbits bits
= main_mode == 'c'
? MCLX_REQUIRE_DOMTREE | MCLX_CATREAD_CLUSTERSTACK
: main_mode == 's'
? MCLX_REQUIRE_DOMSTACK | MCLX_CATREAD_CLUSTERTREE
: 0
; mcxIOopen(xfout, EXIT_ON_FAIL)
; if (mclxCatRead(xfin, &st, catmax, NULL, NULL, bits))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_NONE, EXIT_ON_FAIL)
; }
return 0
; }
int main
( int argc
, const char* argv[]
)
{ int a = 0
; mcxTing* argtxt = mcxTingEmpty(NULL, 10)
; if (0)
mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; opInitialize() /* symtable etc */
; globInitialize() /* hdltable etc */
; if (argc == 1)
{ mcxTing* ops = mcxTingEmpty(NULL, 20)
; mcxIO *xfin = mcxIOnew("-", "r")
; mcxIOopen(xfin, EXIT_ON_FAIL)
; fprintf
( stdout
, "At your service: "
"'[/<op>] help', '[/<str>] grep', 'ops', 'info', and 'quit'.\n"
)
; while (1)
{ int ok
; mcxTing* line = mcxTingEmpty(NULL, 30)
; fprintf(stdout, "> ")
; fflush(stdout)
; if (STATUS_OK != mcxIOreadLine(xfin, line, MCX_READLINE_BSC))
{ fprintf(stdout, "curtains!\n")
; mcxTingFree(&line)
; break
; }
mcxTingAppend(ops, line->str)
; mcxTingFree(&line)
; ok = zsDoSequence(ops->str)
; if (ok && (v_g & V_STACK))
zsList(0)
; mcxTingEmpty(ops, 20)
; }
}
else
{ for (a=1;a<argc;a++)
{ mcxTingWrite(argtxt, argv[a])
; if (!zgUser(argtxt->str))
mcxExit(1)
; }
}
mcxTingFree(&argtxt)
; return 0
; }
mcxstatus mcxIOtestOpen
( mcxIO* xf
, mcxOnFail ON_FAIL
)
{ if (!xf->fp && mcxIOopen(xf, ON_FAIL) != STATUS_OK)
{ mcxErr
("mcxIO", "cannot open file <%s> in mode %s", xf->fn->str, xf->mode)
; return STATUS_FAIL
; }
return STATUS_OK
; }
void write_clustering
( mclx* cl
, const mclx* clprev
, mcxIO* xfcone
, mcxIO* xfstack
, const char* plexprefix
, int multiplex_idx
, const mclAlgParam* mlp
)
{
/* this branch is also taken for dispatch mode */
if (plexprefix)
{ mcxTing* clname = mcxTingPrint(NULL, "%s.%03d", plexprefix, multiplex_idx)
; mcxIO* xfout = mcxIOnew(clname->str, "w")
; if (dispatch_g && mlp && !mcxIOopen(xfout, RETURN_ON_FAIL))
fprintf(xfout->fp, "# %s\n", mlp->cline->str)
; mclxaWrite(cl, xfout, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; mcxTingFree(&clname)
; mcxIOfree(&xfout)
; }
if (subcluster_g || dispatch_g)
return
; if (xfstack)
mclxaWrite(cl, xfstack, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfcone && !clprev)
mclxaWrite(cl, xfcone, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; else if (xfcone)
{ mclx* clprevt = mclxTranspose(clprev)
; mclx* contracted = mclxCompose(clprevt, cl, 0)
; mclxMakeCharacteristic(contracted)
; mclxaWrite(contracted, xfcone, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; mclxFree(&clprevt)
; mclxFree(&contracted)
; }
}
mcxstatus mcxIOreadFile
( mcxIO *xf
, mcxTing *filetxt
)
{ struct stat mystat
; size_t sz = 4096
; ssize_t r
; const char* me = "mcxIOreadFile"
; mcxTingEmpty(filetxt, 0)
; if (inbuffer(xf))
buffer_spout(xf, me)
; if (!xf->stdio)
{ if (stat(xf->fn->str, &mystat))
mcxIOerr(xf, me, "cannae stat file")
; else
sz = mystat.st_size
; }
if (!xf->fp && mcxIOopen(xf, RETURN_ON_FAIL))
{ mcxIOerr(xf, me, "cannae open file")
; return STATUS_FAIL
; }
if (xf->ateof)
return STATUS_OK
/* fixme; ting count overflow */
; if (!(filetxt = mcxTingEmpty(filetxt, sz)))
return STATUS_NOMEM
; while ((r = mcxIOappendChunk(xf, filetxt, sz, 0)) > 0 && !xf->ateof)
; if (r <0)
return STATUS_FAIL /* fixme; look closer at error */
; return STATUS_OK
; }
mcxstatus mcxIOreadLine
( mcxIO *xf
, mcxTing *dst
, mcxbits flags
)
{ int a
; dim ll
; mcxbool chomp = flags & MCX_READLINE_CHOMP ? TRUE : FALSE
; mcxbool skip = flags & MCX_READLINE_SKIP_EMPTY ? TRUE : FALSE
; mcxbool par = flags & MCX_READLINE_PAR ? TRUE : FALSE
; mcxbool dot = flags & MCX_READLINE_DOT ? TRUE : FALSE
; mcxbool bsc = flags & MCX_READLINE_BSC ? TRUE : FALSE
; mcxbool repeat = dot || par || bsc ? TRUE : FALSE
; mcxbool continuation = FALSE
; mcxTing* line
; mcxstatus stat = STATUS_OK
; if (!xf->fp && mcxIOopen(xf, RETURN_ON_FAIL))
{ mcxIOerr(xf, "mcxIOreadLine", "is not open")
; return STATUS_FAIL
; }
if (xf->ateof)
return STATUS_DONE
; if (!dst || !mcxTingEmpty(dst, 1))
return STATUS_NOMEM
; if (skip || par)
{ while((a = mcxIOstep(xf)) == '\n')
NOTHING
; if (xf->ateof)
return STATUS_DONE
; else
mcxIOstepback(a, xf)
; }
if (!(line = repeat ? mcxTingEmpty(NULL, 1) : dst))
return STATUS_NOMEM
; while (1)
{ ofs d = mcxIO__rl_rl__(xf, line)
; if (IO_MEM_ERROR == d)
{ stat = STATUS_NOMEM /* fixme grainify error/status */
; break
; }
ll = line->len
; if (!repeat)
break
; else /* must append line to dst */
{ if
( dot
&& !continuation
&& line->str[0] == '.'
&& ( ll == 2
|| (ll == 3 && line->str[1] == '\r')
)
/* fixme still not fully covering */
)
break
/* do not attach the single-dot-line */
; if (par && !continuation && ll == 1)
break
/* do not attach the second newline */
; if (!mcxTingNAppend(dst, line->str, line->len))
{ stat = STATUS_NOMEM
; break
; }
continuation = bsc && (ll > 1 && *(line->str+ll-2) == '\\')
; if (continuation)
mcxTingShrink(dst, -2)
; if (!par && !dot && (bsc && !continuation))
break
; if (xf->ateof)
break
; }
}
if (repeat)
mcxTingFree(&line)
; if (stat)
return stat /* fixme; should we not check chomp first ? */
/* fixme _: \n\r ? */
; if (chomp && dst->len && *(dst->str+dst->len-1) == '\n')
mcxTingShrink(dst, -1)
; if (xf->ateof && !dst->len)
return STATUS_DONE
; return STATUS_OK
; }
static mcxstatus meetMain
( int argc
, const char* argv[]
)
{ mcxIO **xfmcs = NULL
; mclMatrix *lft = NULL
; mclMatrix *rgt = NULL
; mclMatrix *dst = NULL
; int a = 0
; int n_mx = 0
; int j
; dim o, m, e
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_YES)
; mclx_app_init(stderr)
; xfmcs = (mcxIO**) mcxAlloc
( (argc)*sizeof(mcxIO*)
, EXIT_ON_FAIL
)
; mcxIOopen(xfout, EXIT_ON_FAIL)
; for(j=a;j<argc;j++)
{ xfmcs[n_mx] = mcxIOnew(argv[j], "r")
; n_mx++
; }
if (!n_mx)
mcxDie(1, me, "at least one clustering matrix required")
/* Fixme: do a decent initialization with lft = clmTop() *before*
* this loop (removing the need for ugly tmp assignment), but that requires
* we know the correct domain to pass to it. For that, we need to peak into
* the first matrix.
*/
; for (j=0;j<n_mx;j++)
{ mclMatrix* tmp = mclxRead (xfmcs[j], EXIT_ON_FAIL)
; if (clmEnstrict(tmp, &o, &m, &e, ENSTRICT_SPLIT_OVERLAP))
report_partition("clmmeet", tmp, xfmcs[j]->fn, o, m, e)
, mcxExit(1)
; if (!lft)
{ lft = tmp
; continue
; }
else
rgt = tmp
; if (!MCLD_EQUAL(lft->dom_rows, rgt->dom_rows))
mcxDie
( 1
, me
, "domains not equal (files %s/%s)"
, xfmcs[j-1]->fn->str
, xfmcs[j]->fn->str
)
; mcxIOclose(xfmcs[j])
; dst = clmMeet(lft, rgt)
; lft = dst
; mclxFree(&rgt)
; }
mclxColumnsRealign(lft, mclvSizeRevCmp)
; mclxWrite(lft, xfout, MCLXIO_VALUE_NONE, EXIT_ON_FAIL)
; mclxFree(&lft)
; mcxIOfree(&xfout)
; free(xfmcs)
; return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO
*xfcl = NULL
, *xfctrl = NULL
, *xfcoarse= NULL
, *xfbase = NULL
, *xfcone = NULL
, *xfstack = NULL
; mclx* mxbase, *cl, *cl_coarse, *clprev, *clctrl = NULL
; mcxTing* shared = mcxTingNew("-I 4 -overlap split")
; mcxbool root = TRUE
; mcxbool have_bootstrap = FALSE
; const char* plexprefix = NULL
; const char* stem = "mcl"
; mcxbool same = FALSE
; mcxbool plex = TRUE
; mcxbool add_transpose = FALSE
; const char* b2opts = NULL
; const char* b1opts = NULL
; mcxbits write_modes = 0
; mclAlgParam* mlp = NULL
; mcxstatus status = STATUS_OK
; mcxstatus parse_status = STATUS_OK
; int multiplex_idx = 1
; int N = 0
; int n_ite = 0
; dim n_components = 0, n_cls = 0
; int a = 1, i= 0
; int n_arg_read = 0
; int delta = 0
; mcxOption* opts, *opt
; mcxTing* cline = mcxOptArgLine(argv+1, argc-1, '\'')
; mclgTF* transform = NULL
; mcxTing* transform_spec = NULL
; double iaf = 0.84
; mclx_app_init(stderr)
; if (0)
mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; else
mcxLogLevelSetByString("xf4g1")
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; if (argc == 2 && argv[1][0] == '-' && mcxOptIsInfo(argv[1], options))
delta = 1
; else if (argc < 2)
{ help(options, shared)
; exit(0)
; }
opts = mcxOptExhaust
(options, (char**) argv, argc, 2-delta, &n_arg_read, &parse_status)
; if (parse_status != STATUS_OK)
{ mcxErr(me, "initialization failed")
; exit(1)
; }
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: help(options, shared)
; exit(0)
;
case MY_OPT_APROPOS
: help(options, shared)
; exit(0)
; break
;
case MY_OPT_NMAX
: N = atoi(opt->val)
; break
;
case MY_OPT_Z
: help(NULL, shared)
; exit(0)
; break
;
case MY_OPT_SHARED
: mcxTingPrintAfter(shared, " %s", opt->val)
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(opt->val)
; break
;
case MY_OPT_B1
: b1opts = opt->val
; break
;
case MY_OPT_B2
: b2opts = opt->val
; break
;
case ALG_OPT_SETENV
: mcxSetenv(opt->val)
; break
;
case ALG_OPT_QUIET
: mcxLogLevelSetByString(opt->val)
; break
;
case MY_OPT_HDP
: hdp_g = atof(opt->val)
; break
;
case MY_OPT_ADDTP
: add_transpose = TRUE
; break
;
case MY_OPT_ANNOT /* only used in command-line copying */
: break
;
case MY_OPT_IAF
: iaf = atof(opt->val) / 100
; break
;
case MY_OPT_WRITE
: if (strstr(opt->val, "stack"))
write_modes |= OUTPUT_STACK
; if (strstr(opt->val, "cone"))
write_modes |= OUTPUT_CONE
; if (strstr(opt->val, "levels"))
write_modes |= OUTPUT_STEPS
; if (strstr(opt->val, "coarse"))
write_modes |= OUTPUT_COARSE
; if (strstr(opt->val, "base"))
write_modes |= OUTPUT_BASE
; break
;
case MY_OPT_BASENAME
: xfbase = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_COARSE
: xfcoarse = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_CONE
: xfcone = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_ROOT
: root = strchr("1yY", (u8) opt->val[0]) ? TRUE : FALSE
; break
;
case MY_OPT_STACK
: xfstack = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_STEM
: stem = opt->val
; break
;
case MY_OPT_MULTIPLEX
: plex = strchr("yY1", (unsigned char) opt->val[0]) ? TRUE : FALSE
; break
;
case MY_OPT_DISPATCH
: dispatch_g = TRUE
; break
;
case MY_OPT_INTEGRATE
: integrate_g = TRUE
; break
;
case MY_OPT_CONTRACT
: break
;
case MY_OPT_SUBCLUSTERX
: subclusterx_g = TRUE, subcluster_g = TRUE
; break
;
case MY_OPT_SUBCLUSTER
: subcluster_g = TRUE
; break
;
case MY_OPT_CONTROL
: xfctrl = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_CL
: xfcl = mcxIOnew(opt->val, "r")
; have_bootstrap = TRUE
; break
;
case MY_OPT_VERSION
: app_report_version(me)
; exit(0)
;
default
: mcxExit(1)
;
}
}
mcxOptFree(&opts)
; a = 2 + n_arg_read
; if (a < argc)
{ if (strcmp(argv[a], "--"))
mcxDie
( 1
, me
, "trailing %s options require standalone '--' separator (found %s)"
, integrate_g ? "integrate" : "mcl"
, argv[a]
)
; a++
; }
if (subcluster_g + dispatch_g + integrate_g > 1)
mcxDie(1, me, "too many modes!")
; if (N && N < argc-a)
mcxErr(me, "-n argument leaves spurious option specifications")
; srandom(mcxSeed(89315))
; signal(SIGALRM, mclSigCatch)
; if (dispatch_g)
plexprefix = "dis"
; else if (!write_modes || (write_modes & OUTPUT_STEPS))
plexprefix = stem
; { mcxTing* tg = mcxTingEmpty(NULL, 30)
; if ((write_modes & OUTPUT_COARSE) && !xfcoarse)
mcxTingPrint(tg, "%s.%s", stem, "coarse")
, xfcoarse = mcxIOnew(tg->str, "w")
; if ((write_modes & OUTPUT_BASE) && !xfbase)
mcxTingPrint(tg, "%s.%s", stem, "base")
, xfbase = mcxIOnew(tg->str, "w")
; if
( (!write_modes || (write_modes & OUTPUT_CONE))
&& !xfcone
)
{ mcxTingPrint(tg, "%s.%s", stem, "cone")
; xfcone = mcxIOnew(tg->str, "w")
; mcxIOopen(xfcone, EXIT_ON_FAIL)
; fprintf(xfcone->fp, "# %s %s\n", argv[0], cline->str)
; }
if ((write_modes & OUTPUT_STACK) && !xfstack)
{ mcxTingPrint(tg, "%s.%s", stem, "stack")
; xfstack = mcxIOnew(tg->str, "w")
; mcxIOopen(xfstack, EXIT_ON_FAIL)
; fprintf(xfstack->fp, "# %s %s\n", argv[0], cline->str)
; }
mcxTingFree(&tg)
; }
if (integrate_g)
{ for (i=a;i<argc;i++)
{ mcxIO* xf = mcxIOnew(argv[i], "r")
; mclx* cl = mclxRead(xf, EXIT_ON_FAIL)
; mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-integrate", n_cls++)
; }
integrate_results(&stck_g)
; if (xfstack)
mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfcone)
mclxCatConify(&stck_g)
, mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; return 0
; }
for (i=a;i<argc;i++)
{ if (get_interface(NULL, argv[1], shared->str, argv[i], NULL, 0, RETURN_ON_FAIL))
mcxDie(1, me, "error while testing mcl options viability (%s)", argv[i])
; }
mcxLog(MCX_LOG_APP, me, "pid %ld", (long) getpid())
/* make sure clusters align with this cluster
* status: does not seem promising.
*/
; if (xfctrl)
clctrl = mclxRead(xfctrl, EXIT_ON_FAIL)
;
/*
* Below: compute cl and mxbase.
*/
; if (xfcl)
{ cl = mclxRead(xfcl, EXIT_ON_FAIL)
; write_clustering
(cl, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, cl, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; mcxIOfree(&xfcl)
; if (!b1opts && !b2opts)
b1opts = ""
; mxbase = get_base(argv[1], NULL, b1opts, b2opts)
; }
else
{ mcxbits CACHE = b1opts || b2opts
? ALG_CACHE_INPUT /* cache, transform later */
: ALG_CACHE_START
; get_interface
( &mlp
, argv[1]
, shared->str
, a < argc ? argv[a] : NULL
, NULL
, CACHE
, EXIT_ON_FAIL
)
; if (a < argc)
a++
; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL)
{ mcxErr(me, "failed at initial run")
; exit(1)
; }
cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result)
; cl_coarse = control_test(cl_coarse, clctrl)
; write_clustering
(cl_coarse, NULL, xfcone, xfstack, plexprefix, multiplex_idx++, mlp)
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, cl_coarse, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; cl = cl_coarse
; n_ite++
; if (b1opts || b2opts)
{ mclx* mx_input = mclAlgParamRelease(mlp, mlp->mx_input)
; mxbase = get_base(NULL, mx_input, b1opts, b2opts)
/* ^ get_base frees mx_input */
; }
else
mxbase = mclAlgParamRelease(mlp, mlp->mx_start)
; }
clprev = cl
; mclAlgParamFree(&mlp, TRUE)
; if (xfbase)
{ dim nre = mclxNrofEntries(mxbase)
; mcxLog(MCX_LOG_APP, me, "base has %lu entries", (ulong) nre)
; mclxaWrite(mxbase, xfbase, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; mcxIOclose(xfbase)
; }
if (subcluster_g || dispatch_g)
iaf = iaf ? 1/iaf : 1.414
; while
( (!dispatch_g && (!N || n_ite < N))
|| (dispatch_g && a < argc)
)
{ mclx* mx_coarse = NULL, *clnext = NULL
; dim dist_new_prev = 0, dist_prev_new = 0
; mclx* clnew = NULL
; mcxbool faith = FALSE
; double inflation = -1.0
; if (subcluster_g)
mx_coarse
= subclusterx_g
? mclxBlockPartition(mxbase, clprev, 50)
: mclxBlockUnion(mxbase, clprev)
/* have to copy mxbase as mx_coarse is freed.
* Even if it were not freed, it is probably transformed.
*/
; else if (dispatch_g)
mx_coarse = mclxCopy(mxbase)
; else
{ mx_coarse = get_coarse(mxbase, clprev, add_transpose)
; if (n_ite == 1)
{ mclx* cc = clmUGraphComponents(mx_coarse, NULL) /* fixme; mx_coarse garantueed UD ? */
; n_components = N_COLS(cc)
; mclxFree(&cc)
; }
}
if (xfcoarse)
write_coarse(xfcoarse, mx_coarse)
; get_interface
( &mlp
, NULL
, shared->str
, a < argc ? argv[a] : NULL
, mx_coarse
, ALG_CACHE_START
, EXIT_ON_FAIL
)
; inflation = mlp->mpp->mainInflation
; BIT_OFF(mlp->modes, ALG_DO_SHOW_PID | ALG_DO_SHOW_JURY)
; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL)
{ mcxErr(me, "failed")
; mcxExit(1)
; }
cl_coarse = mclAlgParamRelease(mlp, mlp->cl_result)
; if (xfcoarse)
mclxaWrite(cl_coarse, xfcoarse, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (dispatch_g || subcluster_g)
clnext = cl_coarse
; else
clnext = mclxCompose(clprev, cl_coarse, 0)
, clnext = control_test(clnext, clctrl)
, mclxFree(&cl_coarse)
; clmSJDistance
(clprev, clnext, NULL, NULL, &dist_prev_new, &dist_new_prev)
; if (dist_prev_new + dist_new_prev)
{ write_clustering
(clnext, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, mlp)
; clnew = clnext
; if (subcluster_g || dispatch_g)
mclxCatPush(&stck_g, clnext, NULL, NULL, mclxCBdomStack, NULL, "dummy-mclcm", n_cls++)
; else
mclxFree(&clprev)
; clprev = clnew
; }
else if
( N_COLS(clnext) > n_components
&& inflation * iaf > 1.2
&& inflation * iaf < 10
)
{ mclxFree(&clnext)
; inflation *= iaf
; mcxTingPrintAfter(shared, " -I %.2f", inflation)
; mcxLog(MCX_LOG_APP, me, "setting inflation to %.2f", inflation)
; faith = TRUE
; }
/* i.e. vanilla mode, contraction */
else if (!subcluster_g && !dispatch_g)
{ mclx* cc
; mclxFree(&clnext)
; mclxAddTranspose(mx_coarse, 1.0)
; cc = clmUGraphComponents(mx_coarse, NULL)
; if (N_COLS(cc) < N_COLS(clprev))
{ mclx* ccback = mclxCompose(clprev, cc, 0)
; write_clustering
(ccback, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; mclxFree(&clprev)
; clprev = ccback
; mcxTell(me, "connected components added as root clustering")
; }
if (root && N_COLS(cc) > 1)
{ mclx* root = mclxCartesian
( mclvCanonical(NULL, 1, 0)
, mclvCopy(NULL, mxbase->dom_cols)
, 1.0
)
; write_clustering
(root, clprev, xfcone, xfstack, plexprefix, multiplex_idx++, NULL)
; mclxFree(&clprev)
; mcxTell(me, "universe added as root clustering")
; clprev = root
; clnew = NULL
; }
mclxFree(&cc)
; }
else if (subcluster_g || dispatch_g)
mclxFree(&clnext)
; mclAlgParamFree(&mlp, TRUE) /* frees mx_coarse */
; if (!clnew && !faith)
{ same = TRUE
; break
; }
a++
; if (dispatch_g && a == argc)
break
; n_ite++
; }
if (same)
mcxLog(MCX_LOG_MODULE, me, "no further contraction: halting")
; if (dispatch_g)
integrate_results(&stck_g)
; else if (subcluster_g)
mclxCatReverse(&stck_g)
; if (dispatch_g || subcluster_g)
{ dim j
; if (xfstack)
mclxCatWrite(xfstack, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfcone && ! mclxCatConify(&stck_g))
mclxCatWrite(xfcone, &stck_g, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; for (j=0;j<stck_g.n_level;j++)
{ mclxAnnot* an = stck_g.level+j
; mclxFree(&an->mx)
; }
mcxFree(stck_g.level)
; }
mcxIOfree(&xfcoarse)
; mcxIOfree(&xfbase)
; mcxIOfree(&xfcone)
; mcxIOfree(&xfstack)
; mcxTingFree(&shared)
; if (!dispatch_g && !subcluster_g) /* fixme fixme fixme */
mclxFree(&clprev)
; mclxFree(&mxbase)
; mclvFree(&start_col_sums_g)
; mcxTingFree(&cline)
; helpful_reminder()
; return STATUS_OK
; }
mclx* mclxIOstreamIn
( mcxIO* xf
, mcxbits bits
, mclpAR* transform
, void (*ivpmerge)(void* ivp1, const void* ivp2)
, mclxIOstreamer* streamer
, mcxOnFail ON_FAIL
)
{ mcxstatus status = STATUS_FAIL
; const char* me = module
; mcxbool symmetric = bits & MCLXIO_STREAM_SYMMETRIC
; mcxbool mirror = bits & MCLXIO_STREAM_MIRROR
; mcxbool abc = bits & MCLXIO_STREAM_ABC ? TRUE : FALSE
; mcxbool one23 = bits & MCLXIO_STREAM_123 ? TRUE : FALSE
; mcxbool etc = bits & (MCLXIO_STREAM_ETC | MCLXIO_STREAM_ETC_AI) ? TRUE : FALSE
; mcxbool longlist = bits & (MCLXIO_STREAM_ETCANY | MCLXIO_STREAM_235ANY) ? TRUE : FALSE
; mcxTing* linebuf = mcxTingEmpty(NULL, 100)
; map_state map_c = { NULL, NULL, -1 , 0}
; map_state map_r = { NULL, NULL, -1 , 0}
; stream_state iface
; etc_state etcstate
; unsigned long n_ite = 0
; mclx* mx = NULL
; if (!ivpmerge)
ivpmerge = mclpMergeMax
; if (symmetric)
iface.map_c = &map_c /* this bit of hidgery-pokery */
, iface.map_r = &map_c /* is a crucial interfacummathingy */
; else
iface.map_c = &map_c
, iface.map_r = &map_r
;if(DEBUG2)fprintf(stderr, "%s abc\n", abc ? "yes" : "no")
; etcstate.etcbuf = NULL
; etcstate.etcbuf_ofs = 0
; etcstate.etcbuf_check = 0
; etcstate.x_prev = ULONG_MAX /* note we depend on ULONG_MAX + 1 == 0 */
; etcstate.n_y = 0
/* fixme incomplete and distributed initialization of iface */
; iface.pars = NULL
; iface.pars_n_alloc = 0
; iface.pars_n_used = 0
;if(DEBUG3)fprintf(stderr, "1 + max c %lu\n", (ulong) (iface.map_c->max_seen+1))
/* fixme: put the block below in a subroutine */
; while (1)
{ if (abc + one23 + longlist > TRUE) /* OUCH */
{ mcxErr(module, "multiple stream formats specified")
; break
; }
if (!symmetric && streamer->tab_sym_in)
{ mcxErr(module, "for now disallowed, single tab, different domains")
; break
; }
if ((!one23 && !abc && !longlist))
{ mcxErr(module, "not enough to get going")
; break
; }
/* These have maps associated with them.
* Note that bitsp may be changed (by filling in
* somewhat underspecified settings).
* todo hierverder: etc case supported below ?
*/
if (abc || etc)
stream_state_set_map(symmetric, &iface, streamer, &bits)
; if (xf->fp == NULL && (mcxIOopen(xf, ON_FAIL) != STATUS_OK))
{ mcxErr(me, "cannot open stream <%s>", xf->fn->str)
; break
; }
status = STATUS_OK
; break
; }
iface.bits = bits
; if (!status)
while (1)
{ unsigned long x = 876543210, y = 876543210
; double value = 0
; n_ite++
; iface.x = 0
; iface.y = 0
; if (n_ite % 20000 == 0)
fputc('.', stderr) /* fixme conditional to sth */
; if (n_ite % 1000000 == 0)
fprintf(stderr, " %ldM\n", (long) (n_ite / 1000000))
/*
* - the read routines largely manage iface, including
* map_c->max_seen and map_r->max_seen. It would be
* nice to encapsulate that management in a single
* place. Note the read_abc requirement that sometimes
* a label may need to be deleted from a hash. The fact
* that handle_label (called by read_etc and read_abc)
* also manages max_seen complicate encapsulation though.
*
* - read_etc manages its line buffer.
*/
; status
= one23 ? read_123(xf, linebuf, &iface, streamer, &value, bits)
: abc ? read_abc(xf, linebuf, &iface, &value)
: longlist ? read_etc(xf, &iface, &etcstate, &value)
: STATUS_FAIL
; x = iface.x
; y = iface.y
/* considerme: etc status ignore could still expand column range.
* do we change the status and deal with not incorporating the row,
* or do we keep status, and change realloc/ignore logic below?
*/
;if(0)fprintf(stderr, "#x now %lu status %s\n", (ulong) (iface.map_c->max_seen+1), MCXSTATUS(status))
/* etc/235 are special in that with NEW x and IGNORE y
* we respect x
* fixme: should not do that for auto-increment
*/
; if (status == STATUS_IGNORE) /* maybe restrict mode */
{ if
( longlist
&& iface.statusx == STATUS_NEW
&& iface.map_c->max_seen+1 > iface.pars_n_used /* note mixed-sign comparison */
)
{ if ((status = pars_realloc(&iface, iface.map_c->max_seen+1)))
break
; }
continue
; }
else if (status) /* FAIL or DONE */
break
; if
( iface.map_c->max_seen >= iface.pars_n_used /* note mixed-sign comparison */
&& (status = pars_realloc(&iface, iface.map_c->max_seen+1))
)
break
; status = STATUS_FAIL /* fixme restructure logic, mid-re-initialization is ugly */
; if
( bits & (MCLXIO_STREAM_LOGTRANSFORM | MCLXIO_STREAM_NEGLOGTRANSFORM) )
{ if (bits & MCLXIO_STREAM_LOGTRANSFORM)
value = value > 0 ? log(value) : -PVAL_MAX
; else if (bits & MCLXIO_STREAM_NEGLOGTRANSFORM)
value = value > 0 ? -log(value) : PVAL_MAX
; if (bits & MCLXIO_STREAM_LOG10)
value /= log(10)
; }
if (transform)
{ mclp bufivp
; bufivp.idx = 0
; bufivp.val = value
; value = mclpUnary(&bufivp, transform)
; }
/* fixme: below we have canonical dependence, index as offset */
if (value)
{ if(DEBUG3)fprintf(stderr, "attempt to extend %d\n", (int) x)
; if (mclpARextend(iface.pars+x, y, value))
{ mcxErr(me, "x-extend fails")
; break
; }
if (mirror && mclpARextend(iface.pars+y, x, value))
{ mcxErr(me, "y-extend fails")
; break
; }
}
status = STATUS_OK
; }
if (n_ite >= 1000000 && n_ite % 5000000)
fputc('\n', stderr)
; mcxTingFree(&(etcstate.etcbuf))
; if (status == STATUS_FAIL || ferror(xf->fp))
mcxErr(me, "error occurred (status %d lc %d)", (int) status, (int) xf->lc)
; else
{ mx = make_mx_from_pars(streamer, &iface, ivpmerge, bits)
; status = mx ? STATUS_OK : STATUS_FAIL
; }
mcxTingFree(&linebuf)
; free_pars(&iface)
; if (status == STATUS_FAIL)
{ if (ON_FAIL == EXIT_ON_FAIL)
mcxDie(1, me, "fini")
; }
/* with 123, etcai there is simply no column tab
* todo: perhaps create a dummy one (integers).
*/
if
( !status
&& (abc || (bits & (MCLXIO_STREAM_ETC | MCLXIO_STREAM_ETC_AI)))
)
{ if (symmetric)
streamer->tab_sym_out = make_tab(iface.map_c)
; else
{ if (!(bits & MCLXIO_STREAM_ETC_AI))
streamer->tab_col_out = make_tab(iface.map_c)
;if(0)fprintf(stderr, "%p x %p\n", (void*) iface.map_c->map, (void*) iface.map_c->tab)
;if(0)mcxHashStats(stdout, iface.map_c->map)
; streamer->tab_row_out = make_tab(iface.map_r)
; }
}
mcxHashFree(&(iface.map_c->map), mcxTingRelease, NULL)
; if (!symmetric)
mcxHashFree(&(iface.map_r->map), mcxTingRelease, NULL)
; return mx
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO* xf_tab = NULL
; mcxIO* xf_tabr = NULL
; mcxIO* xf_tabc = NULL
; mcxIO* xf_restrict_tab = NULL
; mcxIO* xf_restrict_tabr = NULL
; mcxIO* xf_restrict_tabc = NULL
; mcxIO* xf_mx = mcxIOnew("-", "r")
; mcxIO* xfout = NULL
; const char* fndump = "-"
; mclTab* tabr = NULL
; mclTab* tabc = NULL
; mclTab* restrict_tabr = NULL
; mclTab* restrict_tabc = NULL
; mcxbool transpose = FALSE
; mcxbool lazy_tab = FALSE
; mcxbool write_tabc = FALSE
; mcxbool write_tabr = FALSE
; mcxbool cat = FALSE
; mcxbool tree = FALSE
; mcxbool skel = FALSE
; mcxbool newick = FALSE
; mcxbits newick_bits = 0
; mcxbits cat_bits = 0
; dim catmax = 1
; dim n_max = 0
; dim table_nlines = 0
; dim table_nfields = 0
; int split_idx = 1
; int split_inc = 1
; const char* split_stem = NULL
; const char* sort_mode = NULL
; mcxTing* line = mcxTingEmpty(NULL, 10)
; mcxbits modes = MCLX_DUMP_VALUES
; mcxbits mode_dump = MCLX_DUMP_PAIRS
; mcxbits mode_part = 0
; mcxbits mode_loop = MCLX_DUMP_LOOP_ASIS
; mcxbits mode_matrix = 0
; int digits = MCLXIO_VALUE_GETENV
; mcxOption* opts, *opt
; mcxstatus parseStatus = STATUS_OK
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_YES)
; mclx_app_init(stderr)
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)
; if (!opts)
exit(0)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 0, 0, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_TAB
: xf_tab = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_TABC
: xf_tabc = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_TABR
: xf_tabr = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_OUTPUT
: fndump = opt->val
; break
;
case MY_OPT_SEP_LEAD
: sep_lead_g = opt->val
; break
;
case MY_OPT_SEP_FIELD
: sep_row_g = opt->val
; break
;
case MY_OPT_SEP_CAT
: sep_cat_g = opt->val
; break
;
case MY_OPT_SEP_VAL
: sep_val_g = opt->val
; break
;
case MY_OPT_PREFIXC
: prefixc_g = opt->val
; break
;
case MY_OPT_RESTRICT_TAB
: xf_restrict_tab = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RESTRICT_TABC
: xf_restrict_tabc = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RESTRICT_TABR
: xf_restrict_tabr = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_LAZY_TAB
: lazy_tab = TRUE
; break
;
case MY_OPT_NO_VALUES
: BIT_OFF(modes, MCLX_DUMP_VALUES)
; break
;
case MY_OPT_DUMP_RLINES
: mode_dump = MCLX_DUMP_LINES
; BIT_ON(modes, MCLX_DUMP_NOLEAD)
; break
;
case MY_OPT_DUMP_VLINES
: mode_dump = MCLX_DUMP_LINES
; BIT_ON(modes, MCLX_DUMP_LEAD_VALUE)
; break
;
case MY_OPT_DUMP_LINES
: mode_dump = MCLX_DUMP_LINES
; break
;
case MY_OPT_OMIT_EMPTY
: BIT_ON(modes, MCLX_DUMP_OMIT_EMPTY)
; break
;
case MY_OPT_SORT
: sort_mode = opt->val
; break
;
case MY_OPT_NO_LOOPS
: mode_loop = MCLX_DUMP_LOOP_NONE
; break
;
case MY_OPT_CAT_LIMIT
: n_max = atoi(opt->val)
; break
;
case MY_OPT_SPLIT_STEM
: split_stem = opt->val
; sep_cat_g = NULL
; break
;
case MY_OPT_FORCE_LOOPS
: mode_loop = MCLX_DUMP_LOOP_FORCE
; break
;
case MY_OPT_SKEL
: skel = TRUE
; break
;
case MY_OPT_WRITE_TABC
: write_tabc = TRUE
; break
;
case MY_OPT_DIGITS
: digits = strtol(opt->val, NULL, 10)
; break
;
case MY_OPT_WRITE_TABR
: write_tabr = TRUE
; break
;
case MY_OPT_DUMP_RDOM
: transpose = TRUE
; skel = TRUE
; mode_dump = MCLX_DUMP_LINES
; break
;
case MY_OPT_DUMP_CDOM
: skel = TRUE
; mode_dump = MCLX_DUMP_LINES
; break
;
case MY_OPT_IMX
: mcxIOnewName(xf_mx, opt->val)
; break
;
case MY_OPT_ICL
: mcxIOnewName(xf_mx, opt->val)
; mode_dump = MCLX_DUMP_LINES
; BIT_ON(modes, MCLX_DUMP_NOLEAD)
; BIT_OFF(modes, MCLX_DUMP_VALUES)
; break
;
case MY_OPT_TREECAT
: mcxIOnewName(xf_mx, opt->val)
; tree = TRUE
; cat_bits |= MCLX_PRODUCE_DOMSTACK
; break
;
case MY_OPT_CAT
: mcxIOnewName(xf_mx, opt->val)
; cat = TRUE
; break
;
case MY_OPT_DUMP_MATRIX
: mode_matrix |= MCLX_DUMP_MATRIX
; break
;
case MY_OPT_TRANSPOSE
: transpose = TRUE
; break
;
case MY_OPT_DUMP_UPPER
: mode_part = MCLX_DUMP_PART_UPPER
; break
;
case MY_OPT_DUMP_UPPERI
: mode_part = MCLX_DUMP_PART_UPPERI
; break
;
case MY_OPT_DUMP_LOWER
: mode_part = MCLX_DUMP_PART_LOWER
; break
;
case MY_OPT_DUMP_LOWERI
: mode_part = MCLX_DUMP_PART_LOWERI
; break
;
case MY_OPT_DUMP_NOLEAD
: BIT_ON(modes, MCLX_DUMP_NOLEAD)
; break
;
case MY_OPT_NEWICK_MODE
: if (strchr(opt->val, 'N'))
newick_bits |= (MCLX_NEWICK_NONL | MCLX_NEWICK_NOINDENT)
; if (strchr(opt->val, 'I'))
newick_bits |= MCLX_NEWICK_NOINDENT
; if (strchr(opt->val, 'B'))
newick_bits |= MCLX_NEWICK_NONUM
; if (strchr(opt->val, 'S'))
newick_bits |= MCLX_NEWICK_NOPTHS
; newick = TRUE
; break
;
case MY_OPT_DUMP_NEWICK
: newick = TRUE
; break
;
case MY_OPT_DUMP_TABLE
: mode_dump = MCLX_DUMP_TABLE
; break
;
case MY_OPT_TABLE_NFIELDS
: table_nfields = atoi(opt->val)
; break
;
case MY_OPT_TABLE_NLINES
: table_nlines = atoi(opt->val)
; break
;
case MY_OPT_DUMP_PAIRS
: mode_dump = MCLX_DUMP_PAIRS
; break
; }
}
; if (skel)
cat_bits |= MCLX_READ_SKELETON
; modes |= mode_loop | mode_dump | mode_part | mode_matrix
; xfout = mcxIOnew(fndump, "w")
; mcxIOopen(xfout, EXIT_ON_FAIL)
; mcxIOopen(xf_mx, EXIT_ON_FAIL)
; if (cat || tree)
catmax = n_max ? n_max : 0
; if ((write_tabc || write_tabr) && !xf_tab)
mcxDie(1, me, "need a single tab file (-tab option) with --write-tabc or --write-tabr")
; if (xf_tab && mcxIOopen(xf_tab, RETURN_ON_FAIL))
mcxDie(1, me, "no tab")
; else
{ if (xf_tabr && mcxIOopen(xf_tabr, RETURN_ON_FAIL))
mcxDie(1, me, "no tabr")
; if (xf_tabc && mcxIOopen(xf_tabc, RETURN_ON_FAIL))
mcxDie(1, me, "no tabc")
; }
{ if (xf_restrict_tab && mcxIOopen(xf_restrict_tab, RETURN_ON_FAIL))
mcxDie(1, me, "no restriction tab")
; else
{ if (xf_restrict_tabr && mcxIOopen(xf_restrict_tabr, RETURN_ON_FAIL))
mcxDie(1, me, "no restriction tabr")
; if (xf_restrict_tabc && mcxIOopen(xf_restrict_tabc, RETURN_ON_FAIL))
mcxDie(1, me, "no restriction tabc")
; }
/* fixme: below is pretty boilerplate, happens in other places as well */
if (xf_restrict_tab)
{ if (!(restrict_tabr = mclTabRead (xf_restrict_tab, NULL, RETURN_ON_FAIL)))
mcxDie(1, me, "error reading restriction tab")
; restrict_tabc = restrict_tabr
; mcxIOclose(xf_restrict_tab)
; }
else
{ if (xf_restrict_tabr)
{ if (!(restrict_tabr = mclTabRead(xf_restrict_tabr, NULL, RETURN_ON_FAIL)))
mcxDie(1, me, "error reading restriction tabr")
; mcxIOclose(xf_restrict_tabr)
; }
if (xf_restrict_tabc)
{ if (!(restrict_tabc = mclTabRead(xf_restrict_tabc, NULL, RETURN_ON_FAIL)))
mcxDie(1, me, "error reading restriction tabc")
; mcxIOclose(xf_restrict_tabc)
; }
}
}
/* fixme: restructure code to include bit below */
if (write_tabc || write_tabr)
{ mclv* dom_cols = mclvInit(NULL)
; mclv* dom_rows = mclvInit(NULL)
; mclv* dom = write_tabc ? dom_cols : dom_rows
; if (!(tabc = mclTabRead(xf_tab, NULL, RETURN_ON_FAIL)))
mcxDie(1, me, "error reading tab file")
; if (mclxReadDomains(xf_mx, dom_cols, dom_rows))
mcxDie(1, me, "error reading matrix file")
; mcxIOclose(xf_mx)
/* fixme check status */
; mclTabWrite(tabc, xfout, dom, RETURN_ON_FAIL)
; mcxIOclose(xfout)
; return 0
; }
if (newick)
{ mcxTing* thetree
; mclxCat cat
; if (xf_tab && !(tabr = mclTabRead(xf_tab, NULL, RETURN_ON_FAIL)))
mcxDie(1, me, "error reading tab file")
; mclxCatInit(&cat)
; if
( mclxCatRead
( xf_mx
, &cat
, 0
, NULL
, tabr ? tabr->domain : NULL
, MCLX_CATREAD_CLUSTERTREE | MCLX_ENSURE_ROOT
)
)
mcxDie(1, me, "failure reading file")
; thetree = mclxCatNewick(&cat, tabr, newick_bits)
; fwrite(thetree->str, 1, thetree->len, xfout->fp)
; fputc('\n', xfout->fp)
; mcxIOclose(xfout)
; return 0
; }
while (1)
{ mclxIOdumper dumper
; mclxCat cat
; dim i
; if (xf_tab && !lazy_tab)
cat_bits |= MCLX_REQUIRE_GRAPH
; mclxCatInit(&cat)
; if (mclxCatRead(xf_mx, &cat, catmax, NULL, NULL, cat_bits))
break
; for (i=0;i<cat.n_level;i++)
{ mclx* mx = cat.level[i].mx
; if (restrict_tabr || restrict_tabc)
{ mclx* sub
; sub
= mclxSub
( mx
, restrict_tabc
? restrict_tabc->domain
: mx->dom_cols
, restrict_tabr
? restrict_tabr->domain
: mx->dom_rows
)
; mx = sub
; }
/* noteme fixme dangersign mx now may violate some 'cat' invariant */
if (sort_mode)
{ if (!strcmp(sort_mode, "size-ascending"))
mclxColumnsRealign(mx, mclvSizeCmp)
; else if (!strcmp(sort_mode, "size-descending"))
mclxColumnsRealign(mx, mclvSizeRevCmp)
; else
mcxErr(me, "unknown sort mode <%s>", sort_mode)
; if (catmax != 1)
mcxErr(me, "-sort option and cat mode may fail or corrupt")
; }
if (xf_tab && !tabr)
{ if (!( tabr = mclTabRead
(xf_tab, lazy_tab ? NULL : mx->dom_rows, RETURN_ON_FAIL)
) )
mcxDie(1, me, "consider using --lazy-tab option")
; tabc = tabr
; mcxIOclose(xf_tab)
; }
else
{ if (!tabr && xf_tabr)
{ if (!(tabr = mclTabRead
(xf_tabr, lazy_tab ? NULL : mx->dom_rows, RETURN_ON_FAIL)
) )
mcxDie(1, me, "consider using --lazy-tab option")
; mcxIOclose(xf_tabr)
; }
if (!tabc && xf_tabc)
{ if (!( tabc = mclTabRead
(xf_tabc, lazy_tab ? NULL : mx->dom_cols, RETURN_ON_FAIL)
) )
mcxDie(1, me, "consider using --lazy-tab option")
; mcxIOclose(xf_tabc)
; }
}
; if (transpose)
{ mclx* tp = mclxTranspose(mx)
; mclxFree(&mx)
; mx = tp
; if (tabc || tabr)
{ mclTab* tabt = tabc
; tabc = tabr
; tabr = tabt
; }
}
if (mode_dump == MCLX_DUMP_TABLE)
BIT_ON(modes, MCLX_DUMP_TABLE_HEADER)
; mclxIOdumpSet(&dumper, modes, sep_lead_g, sep_row_g, sep_val_g)
; dumper.table_nlines = table_nlines
; dumper.table_nfields = table_nfields
; dumper.prefixc = prefixc_g
; if (split_stem)
{ mcxTing* ting = mcxTingPrint(NULL, "%s.%03d", split_stem, split_idx)
; mcxIOclose(xfout)
; mcxIOrenew(xfout, ting->str, "w")
; split_idx += split_inc
; }
if
( mclxIOdump
( mx
, xfout
, &dumper
, tabc
, tabr
, digits
, RETURN_ON_FAIL
) )
mcxDie(1, me, "something suboptimal")
; mclxFree(&mx)
; if (sep_cat_g && i+1 < cat.n_level)
fprintf(xfout->fp, "%s\n", sep_cat_g)
; }
break
; }
mcxIOfree(&xf_mx)
; mcxIOfree(&xfout)
; mcxIOfree(&xf_tab)
; mcxIOfree(&xf_tabr)
; mcxIOfree(&xf_tabc)
; mcxTingFree(&line)
; return 0
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO* xfdagreduce = NULL, *xfattr = NULL, *xfdiff = NULL
; double child_diff_lq = 0.2
; double parent_diff_gq = 0.4
; mcxIO* xfimx = mcxIOnew("-", "r"), *xfdag = NULL, *xftab = NULL
; mclTab* tab = NULL
; int q = -1
; mclx* mx
; unsigned char test_mode = 0
; mcxstatus parseStatus = STATUS_OK
; mcxOption* opts, *opt
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; if
(!(opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)))
exit(0)
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_YES)
; mclx_app_init(stderr)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: mcxOptApropos(stdout, me, syntax, 0, 0, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_TEST_CYCLE
: test_mode = 'c'
; break
;
case MY_OPT_TEST_CROSS
: test_mode = 'x'
; break
;
case MY_OPT_DAG_ATTR
: xfattr = mcxIOnew(opt->val, "w")
; mcxIOopen(xfattr, EXIT_ON_FAIL)
; break
;
case MY_OPT_DAG_DIFF
: xfdiff = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_DAG_REDUCE
: xfdagreduce = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_CHILD_DIFF_LQ
: child_diff_lq = atof(opt->val)
; break
;
case MY_OPT_PARENT_DIFF_GQ
: parent_diff_gq = atof(opt->val)
; break
;
case MY_OPT_QUERY
: q = atoi(opt->val)
; break
;
case MY_OPT_TAB
: xftab = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_IMX
: mcxIOnewName(xfimx, opt->val)
; break
;
}
}
; if (xfimx)
mx = mclxRead(xfimx, EXIT_ON_FAIL)
; else
mcxDie(1, me, "need -imx")
; if (xftab)
tab = mclTabRead(xftab, mx->dom_cols, EXIT_ON_FAIL)
; if (test_mode == 'c')
test_for_cycles(mx)
; else if (test_mode == 'x')
test_cross_ratio(mx)
; else if (xfattr)
get_attr(mx, tab, xfattr)
; else if (xfdagreduce)
{ mclxComposeHelper* ch = mclxComposePrepare(mx, mx)
; dim i
; for (i=0;i<N_COLS(mx);i++)
{ mclv* in = mx->cols+i
; mclv* out = mclxVectorCompose(mx, in, NULL, ch)
; mcldMinus(in, out, in)
; mclvFree(&out)
; }
mclxWrite(mx, xfdagreduce, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; mclxComposeRelease(&ch)
; }
else if (xfdiff)
dag_diff_select(mx, tab, xfdiff, child_diff_lq, parent_diff_gq)
; mclxFree(&mx)
; mcxIOfree(&xfimx)
; mcxIOfree(&xfdag)
; mcxIOfree(&xfattr)
; mcxIOfree(&xfdagreduce)
; return 0
; }
static mcxstatus collectMain
( int argc
, const char* argv[]
)
{ aggr* collect = NULL
; int a
; dim i, collect_n = 0
; mclTab* tab = NULL
; double avg = 0.0
; mclx* aggr = NULL, *mx = NULL
/* mcxHash* map = NULL */
; mcxIO* xfout = mcxIOnew(out_g, "w")
; mcxIOopen(xfout, EXIT_ON_FAIL)
; if
( transform_spec
&& (!(transform = mclgTFparse(NULL, transform_spec)))
)
mcxDie(1, me, "input -tf spec does not parse")
; if (xftab_g)
tab = mclTabRead(xftab_g, NULL, EXIT_ON_FAIL)
/* map not used; perhaps someday we want to map labels to indexes?
* in that case, we could also simply reverse the tab when reading ..
, map = mclTabHash(tab)
*/
; if (!collect_g)
mcxDie(1, me, "require one of --paste, --add-column, --add-matrix")
; if (argc)
{ if (collect_g == 'm')
{ mcxIO* xf = mcxIOnew(argv[0], "r")
; mcxIOopen(xf, EXIT_ON_FAIL)
; aggr = mclxRead(xf, EXIT_ON_FAIL)
; mcxIOfree(&xf)
; }
else
collect_n = do_a_file(&collect, argv[0], 0)
; }
if (tab && collect_n != N_TAB(tab) + (header_g ? 1 : 0))
mcxErr
( me
, "tab has differing size (%lu vs %lu), continuing anyway"
, (ulong) N_TAB(tab)
, (ulong) (collect_n ? collect_n -1 : 0)
)
; for (a=1;a<argc;a++)
{ if (collect_g == 'm')
{ mcxIO* xf = mcxIOnew(argv[a], "r")
; mcxIOopen(xf, EXIT_ON_FAIL)
; mx = mclxRead(xf, EXIT_ON_FAIL)
; mclxAugment(aggr, mx, fltop_g)
; mcxIOfree(&xf)
; mclxFree(&mx)
; }
else
do_a_file(&collect, argv[a], collect_n)
; }
if (collect_g == 'm')
{ if (transform)
mclgTFexec(aggr, transform)
; if (mcx_wb_g)
mclxbWrite(aggr, xfout, EXIT_ON_FAIL)
; else
mclxWrite(aggr, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; mcxIOclose(xfout)
; exit(0)
; }
/* fimxe: dispatch on binary_g */
for (i=0;i<collect_n;i++)
{ const char* lb = collect[i].label
; if (!i && collect[i].columns && collect_g != 'p')
{ fprintf(xfout->fp, "%s\t%s\n", lb, collect[i].columns->str)
; continue
; }
if (tab && (!header_g || i > 0))
{ unsigned u = atoi(lb)
; lb = mclTabGet(tab, u, NULL)
; if (TAB_IS_NA(tab, lb))
mcxDie(1, me, "no label found for index %ld - abort", (long) u)
; }
if (summary_g)
avg += collect[i].val
; else
{ if (collect_g == 'p')
fprintf(xfout->fp, "%s%s\n", lb, collect[i].columns->str)
; else
fprintf(xfout->fp, "%s\t%.8g\n", lb, collect[i].val)
; }
}
if (summary_g && collect_n)
{ dim middle1 = (collect_n-1)/2, middle2 = collect_n/2
; qsort(collect, collect_n, sizeof collect[0], aggr_cmp_val)
; avg /= collect_n
; fprintf /* --summary option is a bit rubbish interface-wise */
( xfout->fp
, "%g %g %g %g\n"
, collect[0].val
, (collect[middle1].val + collect[middle2].val) / 2
, collect[collect_n-1].val
, avg
)
; }
return STATUS_OK
; }
static dim do_a_file
( aggr** collectpp
, const char* fname
, dim collect_n
)
{ mcxIO* xf = mcxIOnew(fname, "r")
; mcxTing* buf = mcxTingEmpty(NULL, 100)
; mcxTing* lbl = mcxTingEmpty(NULL, 100)
; mcxstatus status = STATUS_OK
; aggr* collect = *collectpp
; dim ct = 0, collect_alloc = 0
; if (!collect_n)
collect_alloc = 100
, collect = mcxNAlloc(collect_alloc, sizeof collect[0], NULL, EXIT_ON_FAIL)
; mcxIOopen(xf, EXIT_ON_FAIL)
; while (STATUS_OK == (status = mcxIOreadLine(xf, buf, MCX_READLINE_CHOMP)))
{ double val
; const char* tabchar = NULL
; mcxbool get_header = collect_g != 'p' && !ct ? TRUE : FALSE
; mcxTingEnsure(lbl, buf->len)
/* if header_g && !ct && !paste create/check label */
/* body of this while loop does too many things, refactor */
; if (collect_g == 'p' || get_header)
{ if (!(tabchar = strchr(buf->str, '\t')))
mcxDie(1, me, "paste error at line %d file %s (no tab)", (int) xf->lc, fname)
; mcxTingNWrite(lbl, buf->str, tabchar - buf->str)
; }
else
{ if (2 != sscanf(buf->str, "%s%lg", lbl->str, &val))
mcxDie(1, me, "parse error at line %d file %s", (int) xf->lc, fname)
; lbl->len = strlen(lbl->str)
; }
if (!collect_n)
{ if (ct >= collect_alloc)
{ dim collect_realloc = collect_alloc * 1.44
; collect = mcxNRealloc(collect, collect_realloc, collect_alloc, sizeof collect[0], NULL, EXIT_ON_FAIL)
; collect_alloc = collect_realloc
; }
collect[ct].label = mcxTingStr(lbl)
; collect[ct].val = collect_g == 'p' || get_header ? 0.0 : val
; collect[ct].columns
= collect_g == 'p' || get_header
? mcxTingNew(tabchar + (get_header ? 1 : 0))
: NULL
; }
else
{ if (ct >= collect_n)
mcxDie(1, me, "additional lines in file %s", fname)
; if (strcmp(collect[ct].label, lbl->str))
mcxDie
( 1
, me
, "label conflict %s/%s at line %d in file %s"
, collect[ct].label
, lbl->str
, (int) xf->lc, fname
)
; if (get_header) /* only need to check identity */
{ if (strcmp(tabchar+1, collect[ct].columns->str))
mcxDie(1, me, "different columns <%s> and <%s>", collect[ct].columns->str, tabchar+1)
; }
else if (collect_g == 'p') /* tack it on */
mcxTingNAppend(collect[ct].columns, tabchar, buf->len - lbl->len)
; else
collect[ct].val += val
; }
ct++
; }
if (collect_n)
{ if (ct != collect_n)
mcxDie(1, me, "not enough lines in file %s", fname)
; }
else
{ if (!ct)
mcxDie(1, me, "empty file(s)")
; *collectpp = collect
; }
mcxIOfree(&xf)
; return ct
; }
static mcxstatus mateMain
( int argc_unused cpl__unused
, const char* argv[]
)
{ mcxIO* xfx, *xfy
; mclx* mx, *my, *meet, *teem, *myt
; dim x, y
; mcxIOopen(xfout, EXIT_ON_FAIL)
; xfx = mcxIOnew(argv[0], "r")
; mx = mclxRead(xfx, EXIT_ON_FAIL)
; mcxIOclose(xfx)
; xfy = mcxIOnew(argv[1], "r")
; my = mclxRead(xfy, EXIT_ON_FAIL)
; myt = mclxTranspose(my)
; if (!MCLD_EQUAL(mx->dom_rows, my->dom_rows))
mcxDie(1, me, "domains are not equal")
; meet= mclxCompose(myt, mx, 0, 0) /* fixme thread interface */
; teem= mclxTranspose(meet)
; if (legend)
fprintf
( xfout->fp
, "%-10s %6s %6s %6s %6s %6s %6s %6s\n"
, "overlap"
, "x-idx"
, "y-idx"
, "meet"
, "xdiff"
, "ydiff"
, "x-size"
, "y-size"
)
; for (x=0;x<N_COLS(meet);x++)
{ mclv* xvec = meet->cols+x
; long X = xvec->vid
; long xsize = mx->cols[x].n_ivps
; if (one2many && xvec->n_ivps < 2)
continue
; for (y=0;y<N_COLS(teem);y++)
{ mclv* yvec = teem->cols+y
; long Y = yvec->vid
; long ysize = my->cols[y].n_ivps
; double twinfac
; long meetsize
; mclp* ivp = mclvGetIvp(yvec, X, NULL)
; if (!ivp)
continue
/*
* meet size, left diff, right diff, right size.
*/
; meetsize = ivp->val
; if (!xsize && !ysize) /* paranoia */
continue
; twinfac = 2 * meetsize / ( (double) (xsize + ysize) )
; if (xfout)
fprintf
( xfout->fp
, "%-10.3f %6ld %6ld %6ld %6ld %6ld %6ld %6ld\n"
, twinfac
, X
, Y
, meetsize
, xsize - meetsize
, ysize - meetsize
, xsize
, ysize
)
; }
}
return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO *xfin = mcxIOnew("-", "r")
; mcxIO *xfout = mcxIOnew("-", "w")
; mclMatrix *mx = NULL
; mclx* cmapx = NULL, *rmapx = NULL
; const char* me = "mcxmap"
; long cshift = 0
; long rshift = 0
; long cmul = 1
; long rmul = 1
; mcxIO* xf_cannc = NULL
; mcxIO* xf_cannr = NULL
; mcxstatus status = STATUS_OK
; mcxbool invert = FALSE
; mcxbool invertr = FALSE
; mcxbool invertc = FALSE
; mcxIO* xf_map_c = NULL, *xf_map_r = NULL, *xf_map = NULL, *xf_tab = NULL
; mcxOption* opts, *opt
; mcxstatus parseStatus = STATUS_OK
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; mclx_app_init(stderr)
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)
; if (!opts)
exit(0)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 0, 0, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_IMX
: mcxIOnewName(xfin, opt->val)
; break
;
case MY_OPT_OUT
: mcxIOnewName(xfout, opt->val)
; break
;
case MY_OPT_MUL
: cmul = atol(opt->val)
; rmul = cmul
; break
;
case MY_OPT_CMUL
: cmul = atol(opt->val)
; break
;
case MY_OPT_RMUL
: rmul = atol(opt->val)
; break
;
case MY_OPT_SHIFT
: cshift = atol(opt->val)
; rshift = atol(opt->val)
; break
;
case MY_OPT_CSHIFT
: cshift = atol(opt->val)
; break
;
case MY_OPT_RSHIFT
: rshift = atol(opt->val)
; break
;
case MY_OPT_MAP
: xf_map = mcxIOnew(opt->val, "r")
; invert = FALSE
; break
;
case MY_OPT_CMAP
: invertc = FALSE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAP
: invertr = FALSE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAPI
: invert = TRUE
; xf_map = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_CMAPI
: invertc = TRUE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAPI
: invertr = TRUE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAKE_MAP
: xf_cannc = mcxIOnew(opt->val, "w")
; xf_cannr = xf_cannc
; break
;
case MY_OPT_MAKE_MAPC
: xf_cannc = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_MAKE_MAPR
: xf_cannr = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_TAB
: xf_tab = mcxIOnew(opt->val, "r")
; break
;
}
}
/* little special case. restructure when it grows */
if (xf_tab)
{ mclTab* tab1, *tab2
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; }
else
mcxDie(1, me, "-tab option requires -map option")
; tab1 = mclTabRead(xf_tab, NULL, EXIT_ON_FAIL)
; if ((tab2 = mclTabMap(tab1, cmapx)))
mclTabWrite(tab2, xfout, NULL, EXIT_ON_FAIL)
; else
mcxDie(1, me, "map file error (subsumption/bijection)")
; return 0
; }
mx = mclxRead(xfin, EXIT_ON_FAIL)
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; rmapx = cmapx
; }
else
{ if (xf_map_c)
{ mcxIOopen(xf_map_c, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map_c, EXIT_ON_FAIL)
; }
else if (cshift || cmul > 1)
cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvMap(NULL, cmul, cshift, mx->dom_cols)
)
; else if (xf_cannc) /* fixme slightly flaky interface */
{ cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvCanonical(NULL, mx->dom_cols->n_ivps, 1.0)
)
; mclxWrite(cmapx, xf_cannc, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
if (xf_map_r)
{ mcxIOopen(xf_map_r, EXIT_ON_FAIL)
; rmapx = mclxRead(xf_map_r, EXIT_ON_FAIL)
; }
else if (rshift || rmul > 1)
rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvMap(NULL, rmul, rshift, mx->dom_rows)
)
; else if (xf_cannr)
{ rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvCanonical(NULL, mx->dom_rows->n_ivps, 1.0)
)
; if (xf_cannr != xf_cannc)
mclxWrite(rmapx, xf_cannr, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; else if (!mclxIsGraph(mx))
mcxErr(me, "row map not written but matrix is not a graph")
; }
}
if (invert && cmapx && cmapx == rmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = rmapx = cmapxi
; }
else
{ if ((invert || invertr) && rmapx)
{ mclx* rmapxi = mclxTranspose(rmapx)
; mclxFree(&rmapx)
; rmapx = rmapxi
; }
if ((invert || invertc) && cmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = cmapxi
; }
}
; status = STATUS_FAIL
; do
{ if (cmapx && mclxMapCols(mx, cmapx))
break
; if (rmapx && mclxMapRows(mx, rmapx))
break
; status = STATUS_OK
; }
while (0)
; if (status)
{ mcxErr(me, "error, nothing written")
; return 1
; }
mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; return 0
; }
static mclx* process_queries
( mcxIO* xq
, mclx* mx
, mclx* mxtp
, mcxIO* xfmx
, mclTab* tab
, mcxIO* xfout
, mcxIO* xfpath
, mcxIO* xfstep
)
{ mcxTing* line = mcxTingEmpty(NULL, 100)
; mcxTing* sa = mcxTingEmpty(NULL, 100)
; mcxTing* sb = mcxTingEmpty(NULL, 100)
; SSPxy* sspo = mclgSSPxyNew(mx, mxtp)
; mcxIOopen(xq, EXIT_ON_FAIL)
; while (1)
{ long a = -1, b = -2, ns = 0
; mcxbool query = FALSE
; if (isatty(fileno(xq->fp)))
fprintf
( stdout
, "\n(ready (expect two %s or : directive))\n"
, tab ? "labels" : "graph indices"
)
; if
( STATUS_OK != mcxIOreadLine(xq, line, MCX_READLINE_CHOMP)
|| !strcmp(line->str, ".")
)
break
; query = (u8) line->str[0] == ':'
; if (query && (line->len == 1 || isspace((unsigned char) line->str[1])))
{ fprintf(xfout->fp, "-->\n")
; fprintf(xfout->fp, ":tf <tf-spec>\n")
; fprintf(xfout->fp, ":top <num>\n")
; fprintf(xfout->fp, ":list <node>\n")
; fprintf(xfout->fp, ":clcf <node>\n")
; fprintf(xfout->fp, ":reread>\n")
; fprintf(xfout->fp, "<--\n")
; continue
; }
mcxTingEnsure(sa, line->len)
; mcxTingEnsure(sb, line->len)
; ns = sscanf(line->str, "%s %s", sa->str, sb->str)
; if (ns == 2)
sa->len = strlen(sa->str)
, sb->len = strlen(sb->str)
; else
sa->len = strlen(sa->str)
, sb->len = 0
, sb->str[0] = '\0'
; if (!query && ns != 2)
{ if (line->len)
fprintf(stderr, "(error expect two nodes or : directive)\n")
; continue
; }
if (query)
{ mx = handle_query(mx, xfmx, sa, sb)
; sspo->mx = mx /* fixme improve ownership handling */
; sspo->mxtp = mx
; fprintf(xfout->fp, "%s\n\n", line->str)
; continue /* fixme improve flow */
; }
else if (tab)
{ mcxKV* kv
; if ((kv = mcxHashSearch(sa, hsh_g, MCX_DATUM_FIND)))
a = VOID_TO_ULONG kv->val /* fixme (> 2G labels) */
; else
{ label_not_found(sa)
; continue
; }
if ((kv = mcxHashSearch(sb, hsh_g, MCX_DATUM_FIND)))
b = VOID_TO_ULONG kv->val /* fixme (> 2G labels) */
; else
{ label_not_found(sb)
; continue
; }
}
else if (mcxStrTol(sa->str, &a, NULL) || mcxStrTol(sb->str, &b, NULL))
{ fprintf(stderr, "(error failed-reading-number)\n")
; continue
; }
if (check_bounds(mx, a))
continue
; if (check_bounds(mx, b))
continue
; fprintf
( xfout->fp
, "\n(lattice\n"
" (anchors %s %s)\n"
, sa->str
, sb->str
)
; if (0 && a == b)
{ fprintf
( xfout->fp
, " (path-length 0)\n"
"(data\n"
)
; }
else
{ mcxstatus thestat = mclgSSPxyQuery(sspo, a, b)
; dim t
; if (thestat)
fprintf(xfout->fp, " (path-length -2)\n(data\n")
; else if (sspo->length < 0) /* not in same component */
fprintf(xfout->fp, " (path-length -1)\n(data\n")
; else
{ fprintf
( xfout->fp
, " (path-length %d)\n"
"(data\n"
, (int) sspo->length
)
; if (sspo->length == 1)
{ if (tab)
fprintf(xfout->fp, "((%s %s))\n", sa->str, sb->str)
; else
fprintf(xfout->fp, "((%ld %ld))\n", (long) a, (long) b)
; }
else
for (t=0; t< N_COLS(sspo->pathmx)-1; t++)
erdos_link_together(xfout, mx, sspo->pathmx->cols+t, sspo->pathmx->cols+t+1)
; fputs(")\n", xfout->fp)
; fprintf(xfout->fp, " (anchors %s %s)\n", sa->str, sb->str)
; fprintf(xfout->fp, " (considered %d)\n", (int) sspo->n_considered)
; fprintf(xfout->fp, " (participants %d)\n", (int) sspo->n_involved)
; fprintf(xfout->fp, " (path-length %d)\n", (int) sspo->length)
; }
}
fprintf(xfout->fp, ")\n\n")
; if (xfpath)
mclxWrite(sspo->pathmx, xfpath, MCLXIO_VALUE_NONE, RETURN_ON_FAIL)
; if (xfstep)
mclxWrite(sspo->stepmx, xfstep, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; mclgSSPxyReset(sspo)
; }
mcxTingFree(&sa)
; mcxTingFree(&sb)
; mcxTingFree(&line)
; mclgSSPxyFree(&sspo)
; return mx
; }
