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)
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO* xf1, *xf2
; mclx* mx1, *mx2
; mcxbits modes = 0
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclx_app_init(stdout)
; if (argc < 4)
mcxUsage(stdout, me, usagelines)
, mcxExit(0)
; modes = atoi(argv[1])
; xf1 = mcxIOnew(argv[2], "r")
; xf2 = mcxIOnew(argv[3], "r")
; mx1 = mclxRead(xf1, EXIT_ON_FAIL)
; mx2 = mclxRead(xf2, EXIT_ON_FAIL)
; pairwise_setops(mx1, mx2, modes)
; if (modes & MMM_DUMPMX)
{ mcxIO* xo = mcxIOnew("out.mmm", "w")
; mclxWrite(mx1, xo, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
mclxFree(&mx1)
; mclxFree(&mx2)
; mcxIOfree(&xf1)
; mcxIOfree(&xf2)
; return 0
; }
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)
; }
}
void mcxIOfree_v
( void* xfpp
)
{ mcxIOfree((mcxIO**) xfpp)
; }
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* 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
; }
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
; }
