void caml_mcl_initialize(void)
{
if (caml_mcl_initialized)
return;
srandom(mcxSeed(315));
mclx_app_init(NULL);
caml_mcl_initialized = 1;
}
int main
( int argc
, const char* argv[]
)
{ const char* fn_input = argc > 1 ? argv[1] : ""
; mclAlgParam* mlp = NULL
; const char* me = "mcl"
; mcxstatus status = STATUS_OK
; srandom(mcxSeed(315))
; signal(SIGALRM, mclSigCatch)
; if (signal(SIGUSR1, mcxLogSig) == SIG_ERR)
mcxErr(me, "cannot catch SIGUSR1!")
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclx_app_init(stderr)
; if (argc < 2)
{ mcxTell
( me
, "usage: mcl <-|file name> [options],"
" do 'mcl -h' or 'man mcl' for help"
)
; mcxExit(0)
; }
status
= mclAlgInterface
(&mlp, (char**) (argv+2), argc-2, fn_input, NULL, ALG_DO_IO)
; if (status == ALG_INIT_DONE)
return 0
; else if (status)
mcxDie(STATUS_FAIL, me, "no tango")
; if ((status = mclAlgorithm(mlp)) == STATUS_FAIL)
mcxDie(STATUS_FAIL, me, "failed")
; if (mlp->n_assimilated)
mcxLog(MCX_LOG_MODULE, me, "%lu nodes will assimilate", (ulong) mlp->n_assimilated)
; if (mlp->mx_start)
mcxLog(MCX_LOG_MODULE, me, "cached matrix with %lu columns", (ulong) N_COLS(mlp->mx_start))
; mclAlgParamFree(&mlp, TRUE)
; helpful_reminder()
; return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ mcxDispBundle bundle
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; mclx_app_init(stderr)
; bundle.disp_argc = argc
; bundle.disp_argv = argv
; bundle.disp_name = "clm"
; bundle.disp_syntax = clm_syntax
; bundle.disp_shared = clmSharedOptions
; bundle.n_disp_shared = sizeof(clmSharedOptions) / sizeof(mcxOptAnchor) -1;
; bundle.disp_version = app_report_version
; bundle.disp_table = clm_dir
; bundle.shared_handler= sharedArgHandle
; return mcxDispatch(&bundle)
; }
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
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO *xfin = mcxIOnew("-", "r")
; mcxIO *xfout = mcxIOnew("-", "w")
; mclMatrix *mx = NULL
; mclx* cmapx = NULL, *rmapx = NULL
; const char* me = "mcxmap"
; long cshift = 0
; long rshift = 0
; long cmul = 1
; long rmul = 1
; mcxIO* xf_cannc = NULL
; mcxIO* xf_cannr = NULL
; mcxstatus status = STATUS_OK
; mcxbool invert = FALSE
; mcxbool invertr = FALSE
; mcxbool invertc = FALSE
; mcxIO* xf_map_c = NULL, *xf_map_r = NULL, *xf_map = NULL, *xf_tab = NULL
; mcxOption* opts, *opt
; mcxstatus parseStatus = STATUS_OK
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; mclx_app_init(stderr)
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)
; if (!opts)
exit(0)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 0, 0, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_IMX
: mcxIOnewName(xfin, opt->val)
; break
;
case MY_OPT_OUT
: mcxIOnewName(xfout, opt->val)
; break
;
case MY_OPT_MUL
: cmul = atol(opt->val)
; rmul = cmul
; break
;
case MY_OPT_CMUL
: cmul = atol(opt->val)
; break
;
case MY_OPT_RMUL
: rmul = atol(opt->val)
; break
;
case MY_OPT_SHIFT
: cshift = atol(opt->val)
; rshift = atol(opt->val)
; break
;
case MY_OPT_CSHIFT
: cshift = atol(opt->val)
; break
;
case MY_OPT_RSHIFT
: rshift = atol(opt->val)
; break
;
case MY_OPT_MAP
: xf_map = mcxIOnew(opt->val, "r")
; invert = FALSE
; break
;
case MY_OPT_CMAP
: invertc = FALSE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAP
: invertr = FALSE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAPI
: invert = TRUE
; xf_map = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_CMAPI
: invertc = TRUE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAPI
: invertr = TRUE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAKE_MAP
: xf_cannc = mcxIOnew(opt->val, "w")
; xf_cannr = xf_cannc
; break
;
case MY_OPT_MAKE_MAPC
: xf_cannc = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_MAKE_MAPR
: xf_cannr = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_TAB
: xf_tab = mcxIOnew(opt->val, "r")
; break
;
}
}
/* little special case. restructure when it grows */
if (xf_tab)
{ mclTab* tab1, *tab2
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; }
else
mcxDie(1, me, "-tab option requires -map option")
; tab1 = mclTabRead(xf_tab, NULL, EXIT_ON_FAIL)
; if ((tab2 = mclTabMap(tab1, cmapx)))
mclTabWrite(tab2, xfout, NULL, EXIT_ON_FAIL)
; else
mcxDie(1, me, "map file error (subsumption/bijection)")
; return 0
; }
mx = mclxRead(xfin, EXIT_ON_FAIL)
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; rmapx = cmapx
; }
else
{ if (xf_map_c)
{ mcxIOopen(xf_map_c, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map_c, EXIT_ON_FAIL)
; }
else if (cshift || cmul > 1)
cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvMap(NULL, cmul, cshift, mx->dom_cols)
)
; else if (xf_cannc) /* fixme slightly flaky interface */
{ cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvCanonical(NULL, mx->dom_cols->n_ivps, 1.0)
)
; mclxWrite(cmapx, xf_cannc, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
if (xf_map_r)
{ mcxIOopen(xf_map_r, EXIT_ON_FAIL)
; rmapx = mclxRead(xf_map_r, EXIT_ON_FAIL)
; }
else if (rshift || rmul > 1)
rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvMap(NULL, rmul, rshift, mx->dom_rows)
)
; else if (xf_cannr)
{ rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvCanonical(NULL, mx->dom_rows->n_ivps, 1.0)
)
; if (xf_cannr != xf_cannc)
mclxWrite(rmapx, xf_cannr, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; else if (!mclxIsGraph(mx))
mcxErr(me, "row map not written but matrix is not a graph")
; }
}
if (invert && cmapx && cmapx == rmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = rmapx = cmapxi
; }
else
{ if ((invert || invertr) && rmapx)
{ mclx* rmapxi = mclxTranspose(rmapx)
; mclxFree(&rmapx)
; rmapx = rmapxi
; }
if ((invert || invertc) && cmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = cmapxi
; }
}
; status = STATUS_FAIL
; do
{ if (cmapx && mclxMapCols(mx, cmapx))
break
; if (rmapx && mclxMapRows(mx, rmapx))
break
; status = STATUS_OK
; }
while (0)
; if (status)
{ mcxErr(me, "error, nothing written")
; return 1
; }
mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; return 0
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO *xf_cl = NULL, *xf_mx = NULL
;
mclx *cl = NULL, *elcl = NULL
;
int a = 1
;
dim i
;
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)
;
while(a < argc)
{ if (!strcmp(argv[a], "-icl"))
{ if (a++ + 1 < argc)
xf_cl = mcxIOnew(argv[a], "r")
;
else goto arg_missing
;
}
else if (!strcmp(argv[a], "-h"))
{ help
:
mcxUsage(stdout, me, usagelines)
;
mcxExit(STATUS_FAIL)
;
}
else if (!strcmp(argv[a], "--version"))
{ app_report_version(me)
;
exit(0)
;
}
else if (!strcmp(argv[a], "-imx"))
{ if (a++ + 1 < argc)
xf_mx = mcxIOnew(argv[a], "r")
;
else goto arg_missing
;
}
else if (!strcmp(argv[a], "-h"))
{ goto help
;
}
else if (0)
{ arg_missing:
;
mcxErr
( me
, "flag <%s> needs argument; see help (-h)"
, argv[argc-1]
)
;
mcxExit(1)
;
}
else
{ mcxErr
( me
, "unrecognized flag <%s>; see help (-h)"
, argv[a]
)
;
mcxExit(1)
;
}
a++
;
}
if (!xf_cl)
mcxErr(me, "need cluster file")
, mcxExit(1)
;
cl = mclxRead(xf_cl, EXIT_ON_FAIL)
;
elcl = mclxTranspose(cl)
;
for (i=0; i<N_COLS(elcl); i++)
{ mclv* vec = elcl->cols+i
;
if (vec->n_ivps > 1)
fprintf(stdout, "%ld\n", (long) vec->vid)
;
}
return 0
;
}
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* xfmx = mcxIOnew("-", "r"), *xfout = mcxIOnew("-", "w")
; mclx* mx = NULL
; mclv* mx_diag = NULL
; mcxstatus parseStatus = STATUS_OK
; mcxOption* opts, *opt
; dim N_edge = 0
; dim* offsets
; dim template_n_nodes = 0
; mcxbool plus = FALSE
; double e_min = 1.0
; double e_max = 0.0
; double skew = 0.0
; double radius = 0.0
; double n_sdev = 0.5
; double n_range = 2.0
; double g_radius = 0.0
; double g_mean = 0.0
; double g_sdev = 0.0
; double g_min = 1.0
; double g_max = 0.0
; mcxbool do_gaussian = FALSE
; dim i = 0
; dim N_remove = 0
; dim N_add = 0
; dim N_shuffle = 0
; unsigned long random_ignore = 0
; srandom(mcxSeed(2308947))
; 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
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 20, MCX_OPT_DISPLAY_SKIP, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_SKEW
: skew = atof(opt->val)
; break
;
case MY_OPT_GEN
: template_n_nodes = atoi(opt->val)
; break
;
case MY_OPT_IMX
: mcxIOrenew(xfmx, opt->val, NULL)
; break
;
case MY_OPT_PLUS
: case MY_OPT_WB
: plus = TRUE
; break
;
case MY_OPT_OUT
: mcxIOrenew(xfout, opt->val, NULL)
; break
;
case MY_OPT_E_MAX
: if (!strcmp(opt->val, "copy"))
e_max = -DBL_MAX
; else
e_max = atof(opt->val)
; break
;
case MY_OPT_E_MIN
: e_min = atof(opt->val)
; break
;
case MY_OPT_G_MIN
: g_min = atof(opt->val)
; break
;
case MY_OPT_G_MAX
: g_max = atof(opt->val)
; break
;
case MY_OPT_G_SDEV
: g_sdev = atof(opt->val)
; break
;
case MY_OPT_G_MEAN
: g_mean = atof(opt->val)
; do_gaussian = TRUE
; break
;
case MY_OPT_G_RADIUS
: g_radius = atof(opt->val)
; break
;
case MY_OPT_N_RANGE
: n_range = atof(opt->val)
; break
;
case MY_OPT_N_SDEV
: n_sdev = atof(opt->val)
; break
;
case MY_OPT_N_RADIUS
: radius = atof(opt->val)
; break
;
case MY_OPT_SHUFFLE
: N_shuffle = atoi(opt->val)
; break
;
case MY_OPT_ADD
: N_add = atoi(opt->val)
; break
;
case MY_OPT_REMOVE
: N_remove = atoi(opt->val)
; break
; }
}
/* hitting y% in vi tells me the size of this block */
{ if (template_n_nodes)
mx = mclxAllocZero
( mclvCanonical(NULL, template_n_nodes, 1.0)
, mclvCanonical(NULL, template_n_nodes, 1.0)
)
; else
mx = mclxReadx
( xfmx
, EXIT_ON_FAIL
, MCLX_REQUIRE_GRAPH
)
; mx_diag = mclxDiagValues(mx, MCL_VECTOR_COMPLETE)
; if (N_shuffle)
mclxAdjustLoops(mx, mclxLoopCBremove, NULL)
; else
mclxSelectUpper(mx)
/* ^ apparently we always work on single arc representation (docme andsoon) */
; offsets = mcxAlloc(sizeof offsets[0] * N_COLS(mx), EXIT_ON_FAIL)
; N_edge = 0
; for (i=0;i<N_COLS(mx);i++)
{ offsets[i] = N_edge
; N_edge += mx->cols[i].n_ivps
; }
if (N_edge < N_remove)
{ mcxErr
( me
, "removal count %ld exceeds edge count %ld"
, (long) N_remove
, (long) N_edge
)
; N_remove = N_edge
; }
random_ignore = RAND_MAX - (N_edge ? RAND_MAX % N_edge : 0)
; if (RAND_MAX / 2 < N_edge)
mcxDie(1, me, "graph too large!")
; if (N_shuffle)
{ do_the_shuffle(mx, N_shuffle, offsets, N_edge, random_ignore)
; mx_readd_diagonal(mx, mx_diag)
; mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; exit(0)
; }
; if (N_remove)
{ dim n_remove = do_remove(mx, N_remove, offsets, N_edge, random_ignore)
/* Need to recompute N_edge and random_ignore.
* NOTE we work with *upper* matrix; this counts graph edges.
*/
; N_edge = mclxNrofEntries(mx) - n_remove
; random_ignore = RAND_MAX - (RAND_MAX % N_COLS(mx))
; }
if (g_mean)
{ if (!g_radius)
{ if (g_sdev)
g_radius = 2 * g_sdev
; mcxWarn(me, "set radius to %.5f\n", g_radius)
; }
}
; if (N_add)
N_edge += do_add
( mx
, N_add , N_edge
, do_gaussian ? &g_mean : NULL, g_radius , g_sdev , g_min , g_max
, skew
, e_min , e_max
)
; if (radius)
{ for (i=0;i<N_COLS(mx);i++)
{ mclp* ivp = mx->cols[i].ivps, *ivpmax = ivp + mx->cols[i].n_ivps
;if(DEBUG)fprintf(stderr, "here %d\n", (int) i)
; while (ivp < ivpmax)
{ double val = ivp->val
; double r = mcxNormalCut(n_range * n_sdev, n_sdev)
; double newval = val + radius * (r / (n_range * n_sdev))
; if (e_min < e_max && newval >= e_min && newval <= e_max)
; ivp->val = newval
; ivp++
; }
}
}
mclxUnary(mx, fltxCopy, NULL) /* remove zeroes */
; mclxAddTranspose(mx, 0.0)
; mx_readd_diagonal(mx, mx_diag)
; if (plus)
mclxbWrite(mx, xfout, RETURN_ON_FAIL)
; else
mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
return 0
; }
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
; }
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
; }