void clmCastActors
( mclx** mxpp /* is made stochastic and has loops added */
, mclx** clpp /* entries are set to self-value */
, mclx** el_to_clpp /* transpose of cl */
, mclx** el_on_clpp /* will be made stochastic */
, mclx** cl_on_clpp /* will be made stochastic */
, mclx** cl_on_elpp /* transpose of stochastic el_on_cl */
, double frac /* consider clusters in el_on_cl until frac
edge weight is covered */
)
{ mclxAdjustLoops(*mxpp, mclxLoopCBmax, NULL)
; mclxMakeStochastic(*mxpp)
; *el_to_clpp = mclxTranspose(*clpp)
/* el_to_cl not stochastic? */
; *el_on_clpp = mclxCompose(*el_to_clpp, *mxpp, 0, 1)
; mclxMakeStochastic(*el_on_clpp)
; *cl_on_clpp = mclxCompose(*el_on_clpp, *clpp, 0, 1)
; mclxMakeStochastic(*cl_on_clpp)
; set_cl_to_projection(*clpp, *el_on_clpp)
; prune_el_on_cl(*el_to_clpp, *el_on_clpp, frac, 10)
; *cl_on_elpp = mclxTranspose(*el_on_clpp)
; }
static int test_cycle
( const mclx* mx
, dim n_limit
)
{ mclv* starts = run_through(mx), *starts2
; if (starts->n_ivps)
{ dim i
; if (n_limit)
{ mclx* mxt = mclxTranspose(mx)
; starts2 = run_through(mxt)
; mclxFree(&mxt)
; mclvBinary(starts, starts2, starts, fltMultiply)
; mcxErr
(me, "cycles detected (%u nodes)", (unsigned) starts->n_ivps)
; if (starts->n_ivps)
{ fprintf(stdout, "%lu", (ulong) starts->ivps[0].idx)
; for (i=1; i<MCX_MIN(starts->n_ivps, n_limit); i++)
fprintf(stdout, " %lu", (ulong) starts->ivps[i].idx)
; fputc('\n', stdout)
; }
else
mcxErr(me, "strange, no nodes selected")
; }
else
mcxErr(me, "cycles detected")
; return 1
; }
mcxTell(me, "no cycles detected")
; return 0
; }
void test_for_cycles
( mclx* mx
)
{ mclx* tp = mclxTranspose(mx)
; mclv* fwd = mclxColSizes(mx, MCL_VECTOR_COMPLETE)
; mclv* bwd = mclxColSizes(tp, MCL_VECTOR_COMPLETE)
; dim i, n_cycle = 0
; for (i=0;i<bwd->n_ivps;i++)
{ ofs level_up = fire_node(mx, i, NULL)
; ofs level_dn = fire_node(tp, i, NULL)
; if (level_up < 0 || level_dn < 0)
fprintf(stderr, " [%lu cycle]", (ulong) i)
, n_cycle++
; }
if (n_cycle)
fputc('\n', stderr)
; mclvFree(&bwd)
; mclvFree(&fwd)
; mclxFree(&tp)
; fprintf
( stderr
, "file with %lu edges has %d cycles\n"
, (ulong) mclxNrofEntries(mx)
, (int) n_cycle
)
; exit(n_cycle ? 1 : 0)
; }
mclMatrix* mclInterpret
( mclMatrix* dag
)
{ mclv* v_attr = mclvCopy(NULL, dag->dom_cols)
; mclx* m_attr = NULL, *m_cls = NULL, *m_clst = NULL
; dim d
; mclvMakeCharacteristic(v_attr)
; for (d=0;d<N_COLS(dag);d++)
{ mclv* col = dag->cols+d
; if (mclvGetIvp(col, col->vid, NULL)) /* deemed attractor */
mclvInsertIdx(v_attr, col->vid, 2.0)
; }
mclvSelectGqBar(v_attr, 1.5)
; m_attr = mclxSub(dag, v_attr, v_attr)
; mclxAddTranspose(m_attr, 1.0)
; m_cls = clmUGraphComponents(m_attr, NULL) /* attractor systems as clusters */
; mclvCopy(m_cls->dom_rows, dag->dom_cols) /* add all nodes to this cluster matrix */
; m_clst = mclxTranspose(m_cls) /* nodes(columns) with zero neighbours need to be classified */
; mclgUnionvReset(dag) /* make mx->dom-rows characteristic */
; mclxFree(&m_cls)
; for (d=0;d<N_COLS(dag);d++)
{ mclv* closure, *clsids
; if (mclvGetIvp(v_attr, dag->cols[d].vid, NULL))
continue /* attractor already classified */
; closure = get_closure(dag, dag->cols+d) /* take all [neighbours of [neighbours of [..]]] */
; clsids = mclgUnionv(m_clst, closure, NULL, SCRATCH_READY, NULL)
; mclvAdd(m_clst->cols+d, clsids, m_clst->cols+d)
; mclvFree(&clsids)
; mclvFree(&closure)
; }
m_cls = mclxTranspose(m_clst)
; mclxFree(&m_attr)
; mclxFree(&m_clst)
; mclvFree(&v_attr)
; return m_cls
; }
static int calc_depth
( mclx* m_transient
)
{ mclx* m_inverse = mclxTranspose(m_transient)
;
dim c, depth = 0
;
if(0)puts("")
;
for (c=0; c<N_COLS(m_inverse); c++)
{ dim this_depth = 0
;
if (!m_inverse->cols[c].n_ivps) /* no incoming nodes */
{ mclv* next = mclxGetVector(m_transient, m_inverse->cols[c].vid, RETURN_ON_FAIL, NULL)
;
if (!next)
continue
;
mclgUnionvInitList(m_transient, next)
;
do
{ mclv* next2 = mclgUnionv(m_transient, next, NULL, SCRATCH_UPDATE, NULL)
;
if (0 && next->ivps)
fprintf(stdout, "chain %d ->\n", (int) m_inverse->cols[c].vid)
, mclvaDump(next, stdout, -1, " ", 0)
;
if (this_depth) /* otherwise starting vector in matrix */
mclvFree(&next)
;
next = next2
;
this_depth++
;
}
while (next->n_ivps)
;
mclvFree(&next) /* did loop at least once, so not the starting vector */
;
mclgUnionvReset(m_transient)
;
}
if (this_depth > depth)
depth = this_depth
;
}
mclxFree(&m_inverse)
;
return depth
;
}
void dump_dag
( mclx* mx
, mclTab* tab
)
{ mclx* mx = mclxTranspose(mx)
; dim i
; for (i=0;i<N_COLS(mx);i++)
{ mclv* v = mx->cols+i
; if (v->val < 1.5)
{ dump_label(tab, v->vid, 0)
; walk_dag(mx, v, 1)
; }
}
}
void mclgTFgraph
( mclx* mx
, pnum mode
, pval val
)
{ switch(mode)
{ case MCLG_TF_MAX: mclxMergeTranspose(mx, fltMax, 1.0)
; break ; case MCLG_TF_MIN: mclxMergeTranspose(mx, fltMin, 1.0)
; break ; case MCLG_TF_ADD: mclxMergeTranspose(mx, fltAdd, 1.0)
; break ; case MCLG_TF_SELFRM: mclxAdjustLoops(mx, mclxLoopCBremove, NULL)
; break ; case MCLG_TF_SELFMAX: mclxAdjustLoops(mx, mclxLoopCBmax, NULL)
; break ; case MCLG_TF_NORMSELF: mclxNormSelf(mx)
; break ; case MCLG_TF_MUL: mclxMergeTranspose(mx, fltMultiply, 1.0)
; break ; case MCLG_TF_ARCMAX: mclxMergeTranspose(mx, fltArcMax, 1.0)
; break ; case MCLG_TF_ARCMAXGQ: mclxMergeTranspose3(mx, fltArcMaxGQ, 1.0, val)
; break ; case MCLG_TF_ARCMAXGT: mclxMergeTranspose3(mx, fltArcMaxGT, 1.0, val)
; break ; case MCLG_TF_ARCMAXLQ: mclxMergeTranspose3(mx, fltArcMaxLQ, 1.0, val)
; break ; case MCLG_TF_ARCMAXLT: mclxMergeTranspose3(mx, fltArcMaxLT, 1.0, val)
; break ; case MCLG_TF_ARCMINGQ: mclxMergeTranspose3(mx, fltArcMinGQ, 1.0, val)
; break ; case MCLG_TF_ARCMINGT: mclxMergeTranspose3(mx, fltArcMinGT, 1.0, val)
; break ; case MCLG_TF_ARCMINLQ: mclxMergeTranspose3(mx, fltArcMinLQ, 1.0, val)
; break ; case MCLG_TF_ARCMINLT: mclxMergeTranspose3(mx, fltArcMinLT, 1.0, val)
; break ; case MCLG_TF_ARCDIFFGQ: mclxMergeTranspose3(mx, fltArcDiffGQ, 1.0, val)
; break ; case MCLG_TF_ARCDIFFGT: mclxMergeTranspose3(mx, fltArcDiffGT, 1.0, val)
; break ; case MCLG_TF_ARCDIFFLQ: mclxMergeTranspose3(mx, fltArcDiffLQ, 1.0, val)
; break ; case MCLG_TF_ARCDIFFLT: mclxMergeTranspose3(mx, fltArcDiffLT, 1.0, val)
; break ; case MCLG_TF_ARCSUB: mclxMergeTranspose(mx, fltSubtract, 1.0)
; break ; case MCLG_TF_TUG: mclxPerturb(mx, val, MCLX_PERTURB_SYMMETRIC)
; break ; case MCLG_TF_TRANSPOSE: { mclx* tp = mclxTranspose(mx); mclxTransplant(mx, &tp); }
; break ; case MCLG_TF_SHRUG: mclxPerturb(mx, val, MCLX_PERTURB_SYMMETRIC | MCLX_PERTURB_RAND)
; break ; case MCLG_TF_ILS: mclxILS(mx)
; break ; case MCLG_TF_TOPN: mclxKNNdispatch(mx, val+0.5, mclx_n_thread_g, 0)
; break ; case MCLG_TF_KNN: mclxKNNdispatch(mx, val+0.5, mclx_n_thread_g, 1)
; break ; case MCLG_TF_MCL: tf_do_mcl(mx, val, FALSE)
; break ; case MCLG_TF_ARC_MCL: tf_do_mcl(mx, val, TRUE)
; break ; case MCLG_TF_THREAD: mclx_n_thread_g = val + 0.5
; break ; case MCLG_TF_CEILNB: { mclv* cv = mclgCeilNB(mx, val+0.5, NULL, NULL, NULL); mclvFree(&cv); }
; break ; case MCLG_TF_STEP: mclg_tf_step(mx, val+0.5)
; break ; case MCLG_TF_QT: mclxQuantiles(mx, val)
; break ; case MCLG_TF_SSQ: tf_ssq(mx, val)
; break ; case MCLG_TF_SHUFFLE: mcxErr("mclgTFgraph", "shuffle not yet done (lift from mcxrand)")
; break ; default: mcxErr("mclgTFgraph", "unknown mode")
; break
; }
}
static mclx* get_coarse
( const mclx* mxbase
, mclx* clprev
, mcxbool add_transpose
)
{ mclx* blockc = mclxBlocksC(mxbase, clprev)
; mclx* clprevtp = mclxTranspose(clprev)
; mclx *p1 = NULL /* p_roduct */
; mclx* mx_coarse= NULL
; mclxMakeStochastic(clprev)
/****************** <EXPERIMENTAL CRAP> ************************************/
; if (hdp_g)
mclxUnary(clprev, fltxPower, &hdp_g)
/* parameter: use mxbase rather than blockc */
; if (getenv("MCLCM_BLOCK_STOCHASTIC")) /* this works very badly! */
mclxMakeStochastic(blockc)
; else if (getenv("MCLCM_BASE_UNSCALE") && start_col_sums_g)
{ dim i
; for (i=0;i<N_COLS(blockc);i++)
{ double f = start_col_sums_g->ivps[i].val
; mclvUnary(blockc->cols+i, fltxMul, &f)
; }
; }
/****************** </EXPERIMENTAL> *****************************************/
p1 = mclxCompose(blockc, clprev, 0)
;if (0)
{mcxIO* t = mcxIOnew("-", "w")
;mclxWrite(blockc, t, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
;
}
; mclxFree(&blockc)
; mx_coarse = mclxCompose(clprevtp, p1, 0)
; if (add_transpose)
mclxAddTranspose(mx_coarse, 0.0)
; mclxAdjustLoops(mx_coarse, mclxLoopCBremove, NULL)
; mclxFree(&p1)
; mclxFree(&clprevtp)
; mclxMakeCharacteristic(clprev)
; return mx_coarse
; }
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)
; }
}
int main
( int argc
, const char* argv[]
)
{ mcxIO *xfin = mcxIOnew("-", "r")
; mcxIO *xfout = mcxIOnew("-", "w")
; mclMatrix *mx = NULL
; mclx* cmapx = NULL, *rmapx = NULL
; const char* me = "mcxmap"
; long cshift = 0
; long rshift = 0
; long cmul = 1
; long rmul = 1
; mcxIO* xf_cannc = NULL
; mcxIO* xf_cannr = NULL
; mcxstatus status = STATUS_OK
; mcxbool invert = FALSE
; mcxbool invertr = FALSE
; mcxbool invertc = FALSE
; mcxIO* xf_map_c = NULL, *xf_map_r = NULL, *xf_map = NULL, *xf_tab = NULL
; mcxOption* opts, *opt
; mcxstatus parseStatus = STATUS_OK
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; mclx_app_init(stderr)
; mcxOptAnchorSortById(options, sizeof(options)/sizeof(mcxOptAnchor) -1)
; opts = mcxOptParse(options, (char**) argv, argc, 1, 0, &parseStatus)
; if (!opts)
exit(0)
; for (opt=opts;opt->anch;opt++)
{ mcxOptAnchor* anch = opt->anch
; switch(anch->id)
{ case MY_OPT_HELP
: case MY_OPT_APROPOS
: mcxOptApropos(stdout, me, syntax, 0, 0, options)
; return 0
;
case MY_OPT_VERSION
: app_report_version(me)
; return 0
;
case MY_OPT_IMX
: mcxIOnewName(xfin, opt->val)
; break
;
case MY_OPT_OUT
: mcxIOnewName(xfout, opt->val)
; break
;
case MY_OPT_MUL
: cmul = atol(opt->val)
; rmul = cmul
; break
;
case MY_OPT_CMUL
: cmul = atol(opt->val)
; break
;
case MY_OPT_RMUL
: rmul = atol(opt->val)
; break
;
case MY_OPT_SHIFT
: cshift = atol(opt->val)
; rshift = atol(opt->val)
; break
;
case MY_OPT_CSHIFT
: cshift = atol(opt->val)
; break
;
case MY_OPT_RSHIFT
: rshift = atol(opt->val)
; break
;
case MY_OPT_MAP
: xf_map = mcxIOnew(opt->val, "r")
; invert = FALSE
; break
;
case MY_OPT_CMAP
: invertc = FALSE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAP
: invertr = FALSE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAPI
: invert = TRUE
; xf_map = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_CMAPI
: invertc = TRUE
; xf_map_c = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_RMAPI
: invertr = TRUE
; xf_map_r = mcxIOnew(opt->val, "r")
; break
;
case MY_OPT_MAKE_MAP
: xf_cannc = mcxIOnew(opt->val, "w")
; xf_cannr = xf_cannc
; break
;
case MY_OPT_MAKE_MAPC
: xf_cannc = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_MAKE_MAPR
: xf_cannr = mcxIOnew(opt->val, "w")
; break
;
case MY_OPT_TAB
: xf_tab = mcxIOnew(opt->val, "r")
; break
;
}
}
/* little special case. restructure when it grows */
if (xf_tab)
{ mclTab* tab1, *tab2
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; }
else
mcxDie(1, me, "-tab option requires -map option")
; tab1 = mclTabRead(xf_tab, NULL, EXIT_ON_FAIL)
; if ((tab2 = mclTabMap(tab1, cmapx)))
mclTabWrite(tab2, xfout, NULL, EXIT_ON_FAIL)
; else
mcxDie(1, me, "map file error (subsumption/bijection)")
; return 0
; }
mx = mclxRead(xfin, EXIT_ON_FAIL)
; if (xf_map)
{ mcxIOopen(xf_map, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map, EXIT_ON_FAIL)
; rmapx = cmapx
; }
else
{ if (xf_map_c)
{ mcxIOopen(xf_map_c, EXIT_ON_FAIL)
; cmapx = mclxRead(xf_map_c, EXIT_ON_FAIL)
; }
else if (cshift || cmul > 1)
cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvMap(NULL, cmul, cshift, mx->dom_cols)
)
; else if (xf_cannc) /* fixme slightly flaky interface */
{ cmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_cols)
, mclvCanonical(NULL, mx->dom_cols->n_ivps, 1.0)
)
; mclxWrite(cmapx, xf_cannc, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; }
if (xf_map_r)
{ mcxIOopen(xf_map_r, EXIT_ON_FAIL)
; rmapx = mclxRead(xf_map_r, EXIT_ON_FAIL)
; }
else if (rshift || rmul > 1)
rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvMap(NULL, rmul, rshift, mx->dom_rows)
)
; else if (xf_cannr)
{ rmapx
= mclxMakeMap
( mclvCopy(NULL, mx->dom_rows)
, mclvCanonical(NULL, mx->dom_rows->n_ivps, 1.0)
)
; if (xf_cannr != xf_cannc)
mclxWrite(rmapx, xf_cannr, MCLXIO_VALUE_GETENV, RETURN_ON_FAIL)
; else if (!mclxIsGraph(mx))
mcxErr(me, "row map not written but matrix is not a graph")
; }
}
if (invert && cmapx && cmapx == rmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = rmapx = cmapxi
; }
else
{ if ((invert || invertr) && rmapx)
{ mclx* rmapxi = mclxTranspose(rmapx)
; mclxFree(&rmapx)
; rmapx = rmapxi
; }
if ((invert || invertc) && cmapx)
{ mclx* cmapxi = mclxTranspose(cmapx)
; mclxFree(&cmapx)
; cmapx = cmapxi
; }
}
; status = STATUS_FAIL
; do
{ if (cmapx && mclxMapCols(mx, cmapx))
break
; if (rmapx && mclxMapRows(mx, rmapx))
break
; status = STATUS_OK
; }
while (0)
; if (status)
{ mcxErr(me, "error, nothing written")
; return 1
; }
mclxWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; return 0
; }
static mcxstatus mateMain
( int argc_unused cpl__unused
, const char* argv[]
)
{ mcxIO* xfx, *xfy
; mclx* mx, *my, *meet, *teem, *myt
; dim x, y
; mcxIOopen(xfout, EXIT_ON_FAIL)
; xfx = mcxIOnew(argv[0], "r")
; mx = mclxRead(xfx, EXIT_ON_FAIL)
; mcxIOclose(xfx)
; xfy = mcxIOnew(argv[1], "r")
; my = mclxRead(xfy, EXIT_ON_FAIL)
; myt = mclxTranspose(my)
; if (!MCLD_EQUAL(mx->dom_rows, my->dom_rows))
mcxDie(1, me, "domains are not equal")
; meet= mclxCompose(myt, mx, 0, 0) /* fixme thread interface */
; teem= mclxTranspose(meet)
; if (legend)
fprintf
( xfout->fp
, "%-10s %6s %6s %6s %6s %6s %6s %6s\n"
, "overlap"
, "x-idx"
, "y-idx"
, "meet"
, "xdiff"
, "ydiff"
, "x-size"
, "y-size"
)
; for (x=0;x<N_COLS(meet);x++)
{ mclv* xvec = meet->cols+x
; long X = xvec->vid
; long xsize = mx->cols[x].n_ivps
; if (one2many && xvec->n_ivps < 2)
continue
; for (y=0;y<N_COLS(teem);y++)
{ mclv* yvec = teem->cols+y
; long Y = yvec->vid
; long ysize = my->cols[y].n_ivps
; double twinfac
; long meetsize
; mclp* ivp = mclvGetIvp(yvec, X, NULL)
; if (!ivp)
continue
/*
* meet size, left diff, right diff, right size.
*/
; meetsize = ivp->val
; if (!xsize && !ysize) /* paranoia */
continue
; twinfac = 2 * meetsize / ( (double) (xsize + ysize) )
; if (xfout)
fprintf
( xfout->fp
, "%-10.3f %6ld %6ld %6ld %6ld %6ld %6ld %6ld\n"
, twinfac
, X
, Y
, meetsize
, xsize - meetsize
, ysize - meetsize
, xsize
, ysize
)
; }
}
return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ mcxIO *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
;
}
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
; }
void get_attr
( mclx* mx
, mclTab* tab
, mcxIO* xfattr
)
{ mclx* tp = mclxTranspose(mx)
; mclx* G = mclxAdd(mx, tp)
; mclv* fwd = mclxColSizes(mx, MCL_VECTOR_COMPLETE)
; mclv* bwd = mclxColSizes(tp, MCL_VECTOR_COMPLETE)
; mclx* cc = clmComponents(G, NULL)
; mclx* node2cc = mclxTranspose(cc)
; dim i, n_cycle = 0
; fprintf(xfattr->fp, "node\tup\tdown\tnparent\tnchild\tndag\n")
; for (i=0;i<bwd->n_ivps;i++)
{ mclv* seenpp1 = NULL, *seenpp2 = NULL
; ofs level_up = fire_node(mx, i, &seenpp1)
; ofs level_dn = fire_node(tp, i, &seenpp2)
; ofs ccidx = node2cc->cols[i].ivps[0].idx
; dim ccsize = cc->cols[ccidx].n_ivps
; mclvFree(&seenpp1)
; mclvFree(&seenpp2)
; if ((i+1) % 500 == 0)
fputc('.', stderr)
; if (tab)
{ const char* label = mclTabGet(tab, mx->cols[i].vid, NULL)
; fputs(label, xfattr->fp)
; fputc('\t', xfattr->fp)
; }
else
fprintf
( xfattr->fp
, "%lu\t"
, (ulong) mx->cols[i].vid
)
; fprintf
( xfattr->fp
, "%ld\t%ld\t%lu\t%lu\t%lu\n"
, (long) level_up
, (long) level_dn
, (ulong) fwd->ivps[i].val
, (ulong) bwd->ivps[i].val
, (ulong) ccsize
)
; if (level_up < 0 || level_dn < 0)
fputc('.', stderr)
, n_cycle++
; }
if (n_cycle)
fputc('\n', stderr)
; mclvFree(&bwd)
; mclvFree(&fwd)
; mclxFree(&tp)
; }