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
; }
void mcxIOrelease
( mcxIO* xf
)
{ if (xf)
{ mcxIOclose(xf)
; if (xf->fn)
mcxTingFree(&(xf->fn))
; if (xf->mode)
mcxFree(xf->mode)
; }
}
static mcxstatus handle_label
( mcxTing** keypp
, unsigned long* z
, map_state* map_z
, mcxbits bits
, const char* mode
)
{ mcxbool strict = bits & MCLXIO_STREAM_GTAB_STRICT
; mcxbool warn = bits & MCLXIO_STREAM_WARN
; mcxbool ro = bits & (MCLXIO_STREAM_GTAB_STRICT | MCLXIO_STREAM_GTAB_RESTRICT)
; mcxbool debug = bits & MCLXIO_STREAM_DEBUG
; mcxstatus status = STATUS_OK
; mcxKV* kv = mcxHashSearch(*keypp, map_z->map, ro ? MCX_DATUM_FIND : MCX_DATUM_INSERT)
; if (!kv) /* ro and not found */
{ if (strict)
{ mcxErr
(module, "label <%s> not found (%s strict)", (*keypp)->str, mode)
; status = STATUS_FAIL
; }
else
{ if (warn) /* restrict */
mcxTell
(module, "label <%s> not found (%s restrict)", (*keypp)->str, mode)
; status = STATUS_IGNORE
; }
}
else if (kv->key != *keypp) /* seen */
{ mcxTingFree(keypp)
; *z = VOID_TO_ULONG kv->val /* fixme theoretical signedness issue */
; }
else /* INSERTed */
{ if (debug)
mcxTell
( module
, "label %s not found (%s extend %lu)"
, (*keypp)->str
, mode
, (map_z->max_seen + 1)
)
; map_z->n_seen++
; map_z->max_seen++
; kv->val = ULONG_TO_VOID map_z->max_seen
; *z = map_z->max_seen /* fixme theoretical signedness issue */
;if(DEBUG3)fprintf(stderr, "hl insert %s <%s> to %d\n", mode, keypp[0]->str, (int) *z)
; status = STATUS_NEW
; }
;if(DEBUG2)fprintf(stderr, "hl final map to %d\n", (int) *z)
; return status
; }
void mcxIOfree
( mcxIO** xfpp
)
{ if (*xfpp)
{ mcxIO* xf = *xfpp
; mcxIOrelease(xf)
; mcxTingFree(&(xf->buffer))
; if (xf->usr && xf->usr_free)
xf->usr_free(xf->usr)
; mcxFree(xf)
; *xfpp = NULL
; }
}
static mcxstatus get_interface
( mclAlgParam** mlpp
, const char* fn_input /* Use this as input or mx_input */
, const char* arg_shared
, const char* arg_extra
, mclx* mx_input /* Use this as input or fn_input */
, mcxbits CACHE
, mcxOnFail ON_FAIL
)
{ mcxTing* spec = mcxTingNew(arg_shared)
; int argc1 = 0
; char** argv1
; mcxstatus status
; mclAlgParam* mymlp = NULL
; mclAlgParam** mymlpp = mlpp ? mlpp : &mymlp
; if (arg_extra)
mcxTingPrintAfter(spec, " %s", arg_extra)
/* warning this clobbers spec->str */
; argv1 = mcxOptParseString(spec->str, &argc1, ' ')
; status
= mclAlgInterface
( mymlpp
, argv1
, argc1
, fn_input
, mx_input
, CACHE
)
; if (status && ON_FAIL == EXIT_ON_FAIL)
mcxExit(1)
; mcxFree(argv1)
; mcxTingFree(&spec)
/* fixfixfixmefixmefffixme: mclAlgInterface might use opt->val
* which points to somewhere in spec->str. Check.
*/
; if (!mlpp)
mclAlgParamFree(mymlpp, TRUE)
; return status
; }
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 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 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
; }
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
; }
static mcxstatus read_abc
( mcxIO* xf
, mcxTing* buf
, stream_state *iface
, double* value
)
{ mcxstatus status = mcxIOreadLine(xf, buf, MCX_READLINE_CHOMP)
; mcxTing* xkey = mcxTingEmpty(NULL, buf->len)
; mcxTing* ykey = mcxTingEmpty(NULL, buf->len)
; mcxbits bits = iface->bits
; mcxbool strict = bits & MCLXIO_STREAM_STRICT
; mcxbool warn = bits & MCLXIO_STREAM_WARN
; mcxbool label_cbits = bits & (MCLXIO_STREAM_CTAB_STRICT | MCLXIO_STREAM_CTAB_RESTRICT)
; mcxbool label_rbits = bits & (MCLXIO_STREAM_RTAB_STRICT | MCLXIO_STREAM_RTAB_RESTRICT)
; mcxbool label_dbits = bits & (MCLXIO_STREAM_WARN | MCLXIO_STREAM_DEBUG)
; const char* printable
; int cv = 0
; iface->statusx = STATUS_OK
; iface->statusy = STATUS_OK
; do
{ int xlen = 0
; int ylen = 0
; if (status)
break
; printable = mcxStrChrAint(buf->str, isspace, buf->len)
; if (printable && (uchar) printable[0] == '#')
{ status = mcxIOreadLine(xf, buf, MCX_READLINE_CHOMP)
; continue
; }
mcxTingEnsure(xkey, buf->len) /* fixme, bit wasteful */
; mcxTingEnsure(ykey, buf->len) /* fixme, bit wasteful */
; cv = strchr(buf->str, '\t')
? sscanf(buf->str, "%[^\t]\t%[^\t]%lf", xkey->str, ykey->str, value)
: sscanf(buf->str, "%s%s%lf", xkey->str, ykey->str, value)
/* WARNING: [xy]key->len have to be set.
* we first check sscanf return value
*/
; if (cv == 2)
*value = 1.0
; else if (cv != 3)
{ if (warn || strict)
mcxErr
( module
, "abc-parser chokes at line %ld [%s]"
, (long) xf->lc
, buf->str
)
; if (strict)
{ status = STATUS_FAIL
; break
; }
status = mcxIOreadLine(xf, buf, MCX_READLINE_CHOMP)
; continue
; }
else if (!(*value <= FLT_MAX)) /* should catch nan, inf */
*value = 1.0
; xlen = strlen(xkey->str)
; ylen = strlen(ykey->str)
; xkey->len = xlen
; ykey->len = ylen
; status
= iface->statusx
= handle_label(&xkey, &(iface->x), iface->map_c, label_cbits | label_dbits, "col")
; if (status == STATUS_FAIL || status == STATUS_IGNORE)
break
; status
= iface->statusy
= handle_label(&ykey, &(iface->y), iface->map_r, label_rbits | label_dbits, "row")
; if (status == STATUS_FAIL || status == STATUS_IGNORE)
break
; status = STATUS_OK /* Note: status can never be STATUS_NEW */
; break
; }
while (1)
;if(DEBUG2) fprintf(stderr, "read_abc status %s\n", MCXSTATUS(status))
; if (status == STATUS_NEW)
mcxErr(module, "read_abc panic, because status == STATUS_NEW")
/* Below we remove the key from the map if it should be
* ignored. It will be freed in the block following this one.
*/
; if
( iface->statusx == STATUS_NEW
&& (iface->statusy == STATUS_FAIL || iface->statusy == STATUS_IGNORE)
)
{ mcxHashSearch(xkey, iface->map_c->map, MCX_DATUM_DELETE)
; iface->map_c->max_seen--
; iface->statusx = STATUS_IGNORE
; }
else if /* Impossible (given that we break when iface->statusx) but defensive */
( iface->statusy == STATUS_NEW
&& (iface->statusx == STATUS_FAIL || iface->statusx == STATUS_IGNORE)
)
{ mcxHashSearch(ykey, iface->map_r->map, MCX_DATUM_DELETE)
; iface->map_r->max_seen--
; iface->statusy = STATUS_IGNORE
; }
/* NOTE handle_label might have set either to NULL but
* that's OK. This is needed because handle_label(&xkey)
* might succeed and free xkey (because already present in
* map_c->map); then when handle_label(&ykey) fails we need to
* clean up.
*/
; if (status)
{ mcxTingFree(&xkey) /* kv deleted if iface->statusx == STATUS_NEW */
; mcxTingFree(&ykey) /* kv deleted if iface->statusy == STATUS_NEW */
; }
return status
; }
/* Purpose: read a single x/y combination. The x may be cached
* due to the etc format, where a single line always refers to the same x
* and that x is listed only at the start or line, or omitted with
* the etc-ai and 235-ai formats.
*
* state->x_prev may be used by read_etc in order to obtain the
* current x index.
*/
static mcxstatus read_etc
( mcxIO* xf
, stream_state *iface
, etc_state *state
, double* value
)
{ mcxbits bits = iface->bits
; FILE* stdbug = stdout
; mcxstatus status = STATUS_OK
; mcxTing* ykey = NULL
; mcxTing* xkey = NULL
; const char* printable
; mcxbool label_cbits = bits & (MCLXIO_STREAM_CTAB_STRICT | MCLXIO_STREAM_CTAB_RESTRICT)
; mcxbool label_rbits = bits & (MCLXIO_STREAM_RTAB_STRICT | MCLXIO_STREAM_RTAB_RESTRICT)
; mcxbool label_dbits = bits & (MCLXIO_STREAM_WARN | MCLXIO_STREAM_DEBUG)
; iface->statusx = STATUS_OK
; iface->statusy = STATUS_OK
; iface->x = state->x_prev
; *value = 1.0
;if(DEBUG)fprintf(stdbug, "read_etc initially set x to %d\n", (int) iface->x)
; if (!state->etcbuf)
state->etcbuf = mcxTingEmpty(NULL, 100)
; do
{ int n_char_read = 0
; if (state->etcbuf->len != state->etcbuf_check)
{ mcxErr
( module
, "read_etc sanity check failed %ld %ld"
, (long) state->etcbuf->len
, (long) state->etcbuf_check
)
; status = STATUS_FAIL
; break
; }
/* do we need to read a line ? */
/* -> then set iface->x */
/* fixmefixme: funcify this */
/* iface->x can only be changed in this branch */
/* ************************************************************************** */
if (state->etcbuf_ofs >= state->etcbuf->len)
{ state->etcbuf_ofs = 0
; state->n_y = 0
; if ((status = mcxIOreadLine(xf, state->etcbuf, MCX_READLINE_CHOMP)))
break
; state->etcbuf_check = state->etcbuf->len
; if
( !(printable = mcxStrChrAint(state->etcbuf->str, isspace, -1))
|| (unsigned char) *printable == '#'
)
{ state->etcbuf_ofs = state->etcbuf->len
; iface->statusy = STATUS_IGNORE
; break /* fixme: ^ statusx seems to work as well. cleanify design */
; }
; if (bits & (MCLXIO_STREAM_ETC_AI | MCLXIO_STREAM_235_AI))
{
}
/* In this branch we do not issue handle_label, so we take care of max_seen.
*/
else if (bits & MCLXIO_STREAM_235)
{ if (1 != sscanf(state->etcbuf->str, "%lu%n", &(iface->x), &n_char_read))
{ iface->statusx = STATUS_FAIL
; break
; }
state->etcbuf_ofs += n_char_read
; if (iface->map_c->max_seen+1 < iface->x+1) /* note mixed-sign comparison */
iface->map_c->max_seen = iface->x
; state->x_prev = iface->x
; }
else if (bits & MCLXIO_STREAM_ETC)
{ xkey = mcxTingEmpty(NULL, state->etcbuf->len)
; if (1 != sscanf(state->etcbuf->str, "%s%n", xkey->str, &n_char_read))
break
; state->etcbuf_ofs += n_char_read
; xkey->len = strlen(xkey->str)
; xkey->str[xkey->len] = '\0'
;if(DEBUG3)fprintf(stderr, "max %lu\n", (ulong) iface->map_c->max_seen)
; iface->statusx
= handle_label(&xkey, &(iface->x), iface->map_c, label_cbits | label_dbits, "col")
;if(DEBUG3)fprintf(stderr, "max %lu x %lu\n", (ulong) iface->map_c->max_seen, (ulong) iface->x)
; if (iface->statusx == STATUS_IGNORE || iface->statusx == STATUS_FAIL)
{ /* iface->x = 141414 recentlyadded */
;if(DEBUG3)fprintf(stderr, "max %lu\n", (ulong) iface->map_c->max_seen)
; break
; }
/* ^ Consider what happens when we break here (x label not
* accepted) with map_c->max_seen. Basically x label is
* indepedent of y, so we never need to undo the
* handle_label action.
*/
state->x_prev = iface->x
; }
else
mcxDie(1, module, "strange, really")
; }
/* ************************************************************************** */
if
( !( printable
= mcxStrChrAint(state->etcbuf->str+state->etcbuf_ofs, isspace, -1)
)
|| (uchar) *printable == '#'
)
{ state->etcbuf_ofs = state->etcbuf->len
; /* iface->y = 141414 recentlyadded */
; iface->statusy = STATUS_IGNORE
; break
; }
if (bits & (MCLXIO_STREAM_235_AI | MCLXIO_STREAM_235))
{ if (1 != sscanf(state->etcbuf->str+state->etcbuf_ofs, "%lu%n", &(iface->y), &n_char_read))
{ char* s = state->etcbuf->str+state->etcbuf_ofs
; while(isspace((uchar) s[0]))
s++
; mcxErr
( module
, "unexpected string starting with <%c> on line %lu"
, (int) ((uchar) s[0])
, xf->lc
)
; iface->statusy = STATUS_FAIL
; }
else
{
;if(DEBUG3)fprintf(stdbug, "hit at %d\n", (int) state->etcbuf_ofs);
state->etcbuf_ofs += n_char_read
; if (iface->map_r->max_seen+1 < iface->y+1) /* note mixed-sign comparison */
iface->map_r->max_seen = iface->y
; }
}
else /* ETCANY */
{ ykey = mcxTingEmpty(NULL, state->etcbuf->len)
; if (1 != sscanf(state->etcbuf->str+state->etcbuf_ofs, "%s%n", ykey->str, &n_char_read))
break
; ykey->len = strlen(ykey->str)
; ykey->str[ykey->len] = '\0'
; state->etcbuf_ofs += n_char_read
; iface->statusy
= handle_label(&ykey, &(iface->y), iface->map_r, label_rbits | label_dbits, "row")
; }
/* this won't scale well in terms of organisation if and when
* tabs are allowed with 235 mode, because in that case,
* with 235-ai and restrict-tabr and extend-tabc we will
* need the stuff below duplicated in the 235 branch above.
* what happens here is that we only decide now whether
* the auto-increment is actually happening. It depends
* on there being at least one y that was not rejected.
*/
; if
( (bits & (MCLXIO_STREAM_ETC_AI | MCLXIO_STREAM_235_AI))
&& (iface->statusy == STATUS_OK || iface->statusy == STATUS_NEW)
&& !state->n_y
)
{ iface->x = state->x_prev + 1 /* works first time around */
; iface->map_c->max_seen = state->x_prev + 1
; state->n_y++
; state->x_prev = iface->x
; }
;if(DEBUG2)fprintf(stdbug, "etc handle label we have y %d status %s\n", (int) iface->y, MCXSTATUS(iface->statusy))
; }
while (0)
;if(DEBUG2)fprintf(stdbug, "status %s\n", MCXSTATUS(status))
; do
{ if (status) /* e.g. STATUS_DONE (readline) [or STATUS_IGNORE (#)]*/
break
/* below iface->statusy == STATUS_NEW should be impossible
* given this clause and the code sequence earlier.
*/
; if (iface->statusx == STATUS_FAIL || iface->statusx == STATUS_IGNORE)
{ mcxTingFree(&xkey)
; status = iface->statusx
; break
; }
/* case iface->statusx == STATUS_NEW is *always* honored
*/
; if (iface->statusy == STATUS_FAIL || iface->statusy == STATUS_IGNORE)
{ mcxTingFree(&ykey)
; status = iface->statusy
; break
; }
}
while (0)
; if (status == STATUS_IGNORE || status == STATUS_FAIL)
mcxTingFree(&ykey)
/* fixme, the action in this branch is done in other places too. cleanify design */
; if
( iface->statusx == STATUS_IGNORE
|| !mcxStrChrAint(state->etcbuf->str+state->etcbuf_ofs, isspace, -1)
)
state->etcbuf_ofs = state->etcbuf->len
;if(DEBUG3)fprintf
( stdbug, "read_etc %s return x(%s -> %d stat=%s) y(%s -> %d stat=%s) status %s buf %d %d c_max_seen %lu\n"
, MCXSTATUS(status)
, (xkey ? xkey->str : "-"), (int) iface->x, MCXSTATUS(iface->statusx)
, (ykey ? ykey->str : "-"), (int) iface->y, MCXSTATUS(iface->statusy)
, MCXSTATUS(status), (int) state->etcbuf->len, (int) state->etcbuf_ofs
, (ulong) iface->map_c->max_seen
)
; return status
; }
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
; }
mcxstatus sharedArgHandle
( int optid
, const char* val
, mcxDispHook* hook
, mcxDispBundle* bundle
)
{ mcxTing* full_syntax = mcxTingPrint(NULL, "%s %s", "clm", hook->syntax)
; switch(optid)
{ case CLM_DISP_HELP
: case CLM_DISP_APROPOS
: case CLM_DISP_AMOIXA
:
mcxOptApropos
( stdout
, hook->name
, full_syntax->str
, 15
, 0
, bundle->disp_shared
)
; mcxOptApropos
( stdout
, hook->name
, NULL
, 15
, MCX_OPT_DISPLAY_SKIP
| ( optid == CLM_DISP_AMOIXA
? MCX_OPT_DISPLAY_HIDDEN
: 0
)
, hook->options
)
; mcxExit(0)
; break
;
case CLM_DISP_VERSION
: bundle->disp_version(hook->name)
; mcxExit(0)
; break
;
case CLM_DISP_NOP
: NOTHING
; break
;
case CLM_DISP_TEST
: mcx_test_g = TRUE
; break
;
case CLM_DISP_PROGRESS
: mcx_progress_g = atoi(val)
; break
;
case CLM_DISP_PROGRESS2
: mcx_progress_g = 1
; break
;
case CLM_DISP_DEBUG
: mcx_debug_g = atoi(val)
; break
;
case CLM_DISP_DEBUG2
: mcx_debug_g = -1u
; break
;
case CLM_DISP_SET
: mcxSetenv(val)
; break
;
default
: break
;
}
mcxTingFree(&full_syntax)
; 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
; }