static void erdos_link_together
( mcxIO* xfout
, mclx* mx
, mclv* tails
, mclv* heads
)
{ dim v = 0
; mclv* relevant = mclvInit(NULL)
; fprintf(xfout->fp, "(");
; for (v=0;v<tails->n_ivps;v++)
{ long t = tails->ivps[v].idx
; dim j
; mclv* nb = mclxGetVector(mx, t, EXIT_ON_FAIL, NULL)
; mcldMeet(nb, heads, relevant)
; for (j=0;j<relevant->n_ivps;j++)
{ if (tab_g)
{ long u = relevant->ivps[j].idx
; const char* sx = mclTabGet(tab_g, (long) t, NULL)
; const char* sy = mclTabGet(tab_g, (long) u, NULL)
; if (!sx)
sx = "NAx"
; if (!sy)
sy = "NAy"
; fprintf(xfout->fp, " (%s %s)", sx, sy)
; }
else
fprintf(xfout->fp, " (%ld %ld)", (long) t, (long) relevant->ivps[j].idx)
; }
if (!relevant->n_ivps)
mcxErr(me, "odd, %d has no friends\n", (int) t)
; }
fprintf(xfout->fp, " )\n");
; mclvFree(&relevant)
; }
mcxstatus fire_node_next
( const mclx* mx
, mclv* seen
, mclv *todo
, dim start
)
{ mclv* next = mclvInit(NULL)
; dim i
; mcxstatus s = STATUS_OK
;if(0)fprintf(stderr, "\tnext layer has %d nodes\n", (int) todo->n_ivps)
; for (i=0; i<todo->n_ivps;i++)
{ mclv* ls = mclxGetVector(mx, todo->ivps[i].idx, RETURN_ON_FAIL, NULL)
; if (ls)
{ mcldMerge(next, ls, next)
; if (mclvGetIvp(ls, start, NULL))
{ s = STATUS_FAIL
; break
; }
}
}
mcldMerge(seen, todo, seen) /* add todo to seen */
; mcldMinus(next, seen, next) /* remove seen from next */
; mclvCopy(todo, next) /* copy next to todo */
; mclvFree(&next)
; return s
; }
mclVector* mclvInstantiate
( mclVector* dst_vec
, dim new_n_ivps
, const mclIvp* src_ivps
)
{ mclIvp* new_ivps
; dim old_n_ivps
; if (!dst_vec && !(dst_vec = mclvInit(NULL))) /* create */
return NULL
; old_n_ivps = dst_vec->n_ivps
/* I've had a suspicion that some reallocs might be too lazy
* to reuse shrunk array space.
*/
; if (old_n_ivps / 2 > new_n_ivps)
{ new_ivps = mcxAlloc(new_n_ivps * sizeof new_ivps[0], ENQUIRE_ON_FAIL)
; if (new_ivps && !src_ivps)
memcpy(new_ivps, dst_vec->ivps, new_n_ivps * sizeof new_ivps[0])
; mcxFree(dst_vec->ivps)
; dst_vec->ivps = new_ivps
; }
else
dst_vec->ivps = mcxRealloc(dst_vec->ivps, new_n_ivps * sizeof new_ivps[0], ENQUIRE_ON_FAIL)
; if
( !dst_vec->ivps
&& new_n_ivps
)
{ mcxMemDenied(stderr, "mclvInstantiate", "mclIvp", new_n_ivps)
; return NULL
; }
/* ^ do not free; *dst_vec could be array element */
new_ivps = dst_vec->ivps
; if (!src_ivps) /* resize */
{ dim k = old_n_ivps
; while (k < new_n_ivps)
{ mclpInit(new_ivps + k)
; k++
; }
}
else if (src_ivps && new_n_ivps) /* copy */
memcpy(new_ivps, src_ivps, new_n_ivps * sizeof(mclIvp))
; dst_vec->n_ivps = new_n_ivps
; return dst_vec
; }
/* current dst content is thrown away if fltbinary not used */
mclv* mclvFromPAR
( mclv* dst
, mclpAR* par
, mcxbits warnbits
, void (*ivpmerge)(void* ivp1, const void* ivp2)
, double (*fltbinary)(pval val1, pval val2)
)
{ mcxbool warn_re = warnbits & MCLV_WARN_REPEAT_ENTRIES
; mcxbool warn_rv = warnbits & MCLV_WARN_REPEAT_VECTORS
; mclp* ivps = par->ivps
; dim n_ivps = par->n_ivps
; mcxbits sortbits = par->sorted
; dim n_old = dst ? dst->n_ivps : 0
; const char* me = "mclvFromPAR"
; dim n_re = 0, n_rv = 0
; if (!dst)
dst = mclvInit(NULL)
; if (n_ivps)
{ if (dst->n_ivps && fltbinary)
{ mclVector* tmpvec = mclvNew(ivps, n_ivps)
; if (!(sortbits & MCLPAR_SORTED))
mclvSort(tmpvec, NULL)
; if (!(sortbits & MCLPAR_UNIQUE))
n_re = mclvUniqIdx(tmpvec, ivpmerge)
; n_rv += tmpvec->n_ivps
; n_rv += dst->n_ivps
; mclvBinary(dst, tmpvec, dst, fltbinary)
; n_rv -= dst->n_ivps
; mclvFree(&tmpvec)
; }
else
{ if (dst->ivps == ivps)
mcxErr(me, "DANGER dst->ivps == ivps (dst vid %d)", (int) dst->vid)
; mclvRenew(dst, ivps, n_ivps)
; if (!(sortbits & MCLPAR_SORTED))
mclvSort(dst, NULL)
; if (!(sortbits & MCLPAR_UNIQUE))
n_re += mclvUniqIdx(dst, ivpmerge)
; }
}
if (warn_re && n_re)
mcxErr
( me
, "<%ld> found <%ld> repeated entries within %svector"
, (long) dst->vid
, (long) n_re
, n_rv ? "repeated " : ""
)
; if (warn_rv && n_rv)
mcxErr
( me
, "<%ld> new vector has <%ld> overlap with previous amalgam"
, (long) dst->vid
, (long) n_rv
)
; if (warnbits && n_re + n_rv)
mcxErr
( me
, "<%ld> vector went from <%ld> to <%ld> entries"
, (long) dst->vid
, (long) n_old
, (long) dst->n_ivps
)
; return dst
; }
void pairwise_setops
( mclx* mx1
, mclx* mx2
, mcxbits modes
)
{ dim t, u, n_tst = 0
; mclv* cache = mclvInit(NULL)
; mclv* meet = mclvInit(NULL)
; mclv* join = mclvInit(NULL)
; mclv* diff = mclvInit(NULL)
; mcxbool overwrite = modes & MMM_OVERWRITE
; dim n_zero_meet = 0, n_plus_meet = 0
; mclv* (*fn_meet)(const mclv* lft, const mclv* rgt, mclv* dst) = mcldMeet
; mclv* (*fn_minus)(const mclv* lft, const mclv* rgt, mclv* dst) = mcldMinus1
; if (modes & MMM_MEET2)
fn_meet = mcldMeet2
, fn_minus = mcldMinus
/* the point of overwrite is to have
* a lft == dst or rgt == dst pattern.
*/
; for (t=0;t<N_COLS(mx1);t++)
{ for (u=0;u<N_COLS(mx2);u++)
{ mclv* dst = overwrite ? (modes & MMM_RIGHT ? mx1->cols+u : mx2->cols+t) : diff
; if (overwrite)
mclvCopy(cache, dst) /* cache column, reinstate later */
; if (modes & MMM_BINARY)
mclvBinary(mx1->cols+t, mx2->cols+u, dst, fltLaNR)
; else
fn_minus(mx1->cols+t, mx2->cols+u, dst) /* compute t / u */
; if (overwrite)
mclvCopy(diff, dst)
, mclvCopy(dst, cache) /* reinstate column */
/* diff contains t / u */
; dst = overwrite ? dst : meet /* cache column, same as above */
; if (modes & MMM_BINARY)
mclvBinary(mx1->cols+t, mx2->cols+u, dst, fltLaR)
; else
fn_meet(mx1->cols+t, mx2->cols+u, dst)
; if (overwrite)
mclvCopy(meet, dst)
, mclvCopy(dst, cache) /* meet contains t /\ u */
; mcldMerge(diff, meet, join) /* join should be identical to column t */
; if (meet->n_ivps)
n_plus_meet++
; else
n_zero_meet++
; if (modes & MMM_CHECK)
{ mclv* dediff = mclvClone(mx1->cols+t)
; mclv* demeet = mclvClone(mx1->cols+t)
; dim nd = mclvUpdateMeet(dediff, diff, fltSubtract)
; dim nm = mclvUpdateMeet(demeet, meet, fltSubtract)
; if
( diff->n_ivps + meet->n_ivps != mx1->cols[t].n_ivps
|| !mcldEquate(join, mx1->cols+t, MCLD_EQT_EQUAL)
|| diff->n_ivps != nd
|| meet->n_ivps != nm
)
{ mclvaDump(mx1->cols+t, stdout, -1, " ", MCLVA_DUMP_HEADER_ON)
; mclvaDump(mx2->cols+u, stdout, -1, " ", MCLVA_DUMP_HEADER_ON)
; mclvaDump(meet, stdout, -1, " ", MCLVA_DUMP_HEADER_ON)
; mclvaDump(diff, stdout, -1, " ", MCLVA_DUMP_HEADER_ON)
; mcxDie(1, me, "rats")
; }
mclvFree(&dediff)
; mclvFree(&demeet)
; }
n_tst++
; }
}
fprintf
( stdout
, "meet was nonempty %.2f\n"
, (double) (n_plus_meet * 1.0f / n_tst)
)
; fprintf
( stdout
, "%d successful tests in %s%s %s mode (checked: %s)\n"
, (int) n_tst
, overwrite ? "overwrite" : "create"
, overwrite ? ( modes & MMM_RIGHT ? "-right" : "-left" ) : ""
, modes & MMM_BINARY
? "generic"
: "update"
, (modes & MMM_CHECK ? "yes" : "no")
)
; fprintf
( stdout
, "meet-can: %10lu\n"
"meet-zip: %10lu\n"
"meet-s/l: %10lu\n"
"diff-can: %10lu\n"
"diff-zip: %10lu\n"
"diff-s/l: %10lu\n"
, (ulong) nu_meet_can
, (ulong) nu_meet_zip
, (ulong) nu_meet_sl
, (ulong) nu_diff_can
, (ulong) nu_diff_zip
, (ulong) nu_diff_sl
)
; mclvFree(&cache)
; mclvFree(&meet)
; mclvFree(&join)
; mclvFree(&diff)
; }
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
; }
dim clmAdjust
( mclx* mx
, mclx* cl
, dim cls_size_max
, mclx** cl_adjustedpp
, mclv** ls_adjustedpp /* nodes that moved around */
, dim* sjd_left
, dim* sjd_right
)
{ dim sum_adjusted = 0, n_ite = 0
; dim dist_curr_adj = 0, dist_adj_curr = 0
; mclx* cl_adj = NULL
; mclx* cl_curr = cl
; mclv* ls_adjusted = mclvInit(NULL)
; clmXScore score_curr, score_adj
; const char* me = "clmAdjust"
; *cl_adjustedpp = NULL
; *ls_adjustedpp = NULL
; while (1)
{ dim n_adjusted
; double cov_curr, cov_adj, frac_curr = 0.0, frac_adj = 0.0
; mclv* cid_affected = NULL, *nid_affected = NULL
; dim o, m, e
; if (n_ite++ >= 100)
break
; mclxColumnsRealign(cl_curr, mclvSizeCmp)
; if
( !(n_adjusted
= clm_clm_adjust
(mx, cl_curr, cls_size_max, &cl_adj, &cid_affected, &nid_affected)
)
)
break
; mcxTell
( me
, "assembled %lu nodes with %lu clusters affected"
, (ulong) n_adjusted
, (ulong) cid_affected->n_ivps
)
; clmXScanInit(&score_curr)
; clmXScanInit(&score_adj)
; clmXScanDomainSet(mx, cl_curr,cid_affected, &score_curr)
; clmXScanDomainSet(mx, cl_adj, cid_affected, &score_adj)
; clmXScoreCoverage(&score_curr, &cov_curr, NULL)
; clmXScoreCoverage(&score_adj , &cov_adj , NULL)
; if (score_curr.n_hits && score_adj.n_hits)
frac_curr = score_curr.sum_i / score_curr.n_hits
, frac_adj = score_adj.sum_i / score_adj.n_hits
; mcxLog
( MCX_LOG_LIST
, me
, "consider (%.5f|%.5f|%lu) vs (%.5f|%.5f|%lu)"
, cov_adj, frac_adj, (ulong) score_adj.n_hits
, cov_curr, frac_curr, (ulong) score_curr.n_hits
)
/* experience tells us that mcl's funneling
* worsens frac
*/
; if (frac_adj <= frac_curr)
{ mclvFree(&cid_affected)
; mclvFree(&nid_affected)
; break
; }
clmEnstrict(cl_adj, &o, &m, &e, 0)
; clmSJDistance(cl_curr, cl_adj, NULL, NULL, &dist_curr_adj, &dist_adj_curr)
; mcxLog
( MCX_LOG_AGGR
, me
, "distance %lu|%lu"
, (ulong) dist_curr_adj, (ulong) dist_adj_curr
)
; mclvAdd(ls_adjusted, nid_affected, ls_adjusted)
; if (cl_curr != cl)
mclxFree(&cl_curr)
; cl_curr = cl_adj
; sum_adjusted += n_adjusted
; mclvFree(&cid_affected)
; mclvFree(&nid_affected)
; }
if (cl_curr != cl) /* fixme free logic */
{ mclxColumnsRealign(cl_curr, mclvSizeRevCmp)
; *cl_adjustedpp = cl_curr
; *ls_adjustedpp = ls_adjusted
; clmSJDistance
(cl, cl_curr, NULL, NULL, &dist_curr_adj, &dist_adj_curr)
; if (sjd_left)
*sjd_left = dist_curr_adj
, *sjd_right = dist_adj_curr
; }
else
{ if (sjd_left)
*sjd_left = 0
, *sjd_right = 0
; mclvFree(&ls_adjusted)
; }
mcxLog
( MCX_LOG_AGGR
, me
, "total adjusted %lu, final distance %lu|%lu"
, (ulong) sum_adjusted
, (ulong) dist_curr_adj
, (ulong) dist_adj_curr
)
; mclxColumnsRealign(cl, mclvSizeRevCmp)
; return sum_adjusted
; }