static mcxstatus cttyArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_IMX
: mcxIOnewName(xfmx_g, val)
; break
;
case MY_OPT_ABC
: xfabc_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_OUT
: out_g = val
; break
;
case MY_OPT_INCLUDE_ENDS
: include_ends_g = TRUE
; break
;
case MY_OPT_LIST_NODES
: break
;
case MY_OPT_littleG
: i_group = atoi(val)
; break
;
case MY_OPT_G
: n_group_G = atoi(val)
; break
;
case MY_OPT_T
: n_thread_l = (unsigned) atoi(val)
; break
;
case MY_OPT_MOD
: mod_up = TRUE
; break
;
default
: mcxExit(1)
;
; }
return STATUS_OK
; }
static mcxstatus qInit
( void
)
{ mode_get = 0
; n_limit = 0
; xfout_g = mcxIOnew("-", "w")
; xftab_g = NULL
; vary_z = 0
; divide_g = 3
; vary_a = 0
; vary_s = 0
; vary_n = 1
; xfmx_g = mcxIOnew("-", "r")
; xfcl_g = NULL
; n_thread_g = 1
; mode_vary = 0
; transpose= FALSE
; knnexact_g = TRUE
; doclcf_g = FALSE
; weefreemen = FALSE
; output_table = FALSE
; user_imx = FALSE
; weight_scale = 0.0
; transform = NULL
; transform_spec = NULL
; return STATUS_OK
; }
static mcxstatus qInit
( void
)
{ mode_get = 0
; n_limit = 0
; xfout_g = mcxIOnew("-", "w")
; xftab_g = NULL
; tab_g = NULL
; vary_z = 0
; divide_g = 3
; vary_a = 0
; vary_s = 0
; vary_n = 1
; xfmx_g = mcxIOnew("-", "r")
; xfabc_g = NULL
; xfcl_g = NULL
; n_thread_l = 1
; mode_vary = 0
; transpose= FALSE
; rebase_g = TRUE
#define COMPUTE_CLCF 1
#define COMPUTE_EFF 2
; compute_flags = 0
; weefreemen = FALSE
#define OUTPUT_TABLE 1
#define OUTPUT_KEY 2
; output_flags = OUTPUT_KEY
; user_imx = FALSE
; weight_scale = 0.0
; transform = NULL
; transform_spec = NULL
; return STATUS_OK
; }
static mcxstatus erdosArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_IMX
: xfmx_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_PATH
: path_g = val
; break
;
case MY_OPT_STEP
: step_g = val
; break
;
case MY_OPT_OUT
: out_g = val
; break
;
case MY_OPT_ABC
: xfabc_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_ISUNDIRECTED
: input_status = 'u'
; break
;
case MY_OPT_ISDIRECTED
: input_status = 'd'
; break
;
case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_QUERY
: mcxIOnewName(xq_g, val)
; break
;
default
: mcxExit(1)
;
; }
return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ mclx* mx_score, *mx_start, *mx_end
; mcxIO* xfs, *xfl, *xfr
; dim i, j
; if (argc != 4)
mcxDie(1, me, "need score start end matrices")
; xfs = mcxIOnew(argv[1], "r")
; xfl = mcxIOnew(argv[2], "r")
; xfr = mcxIOnew(argv[3], "r")
; mx_score = mclxRead(xfs, EXIT_ON_FAIL)
; mx_start = mclxRead(xfl, EXIT_ON_FAIL)
; mx_end = mclxRead(xfr, EXIT_ON_FAIL)
; fprintf
( stdout
, "%10s%10s%10s%10s%10s%10s%10s%10s%10s%10s%10s%10s\n"
, "vid1"
, "vid2"
, "diff1"
, "diff2"
, "meet"
, "score"
, "mean"
, "csn"
, "euclid"
, "frac"
, "re1"
, "re2"
)
; for (i=0;i< N_COLS(mx_score);i++)
{ for (j=0;j<N_COLS(mx_score);j++)
{ double s
; s =
get_score
( mx_score->cols+i
, mx_score->cols+j
, mx_start->cols+i
, mx_start->cols+j
, mx_end->cols+i
, mx_end->cols+j
)
; }
}
return 0
; }
static mcxstatus alterInit
( void
)
{ xfmx_g = mcxIOnew("-", "r")
; xfabc_g = NULL
; xftab_g = NULL
; xfout_g = mcxIOnew("-", "w")
; transform = NULL
; transform_spec = NULL
; tab_g = NULL
; canonical_g = 0
; return STATUS_OK
; }
static mcxstatus allInit
( void
)
{ xfmx_g = mcxIOnew("-", "r")
; xftab_g = NULL
; tab_g = NULL
; hsh_g = NULL
; xq_g = mcxIOnew("-", "r")
; xfabc_g = NULL
; debug_g = 0
; out_g = "-"
; path_g = NULL
; step_g = NULL
; input_status = 'x'
; return STATUS_OK
; }
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)
; }
static mcxstatus convertMain
( int argc_unused cpl__unused
, const char* argv[]
)
{ mclMatrix* mx
; mclxCat st
; xfin = mcxIOnew(argv[0], "r")
; xfout = mcxIOnew(argv[1], "w")
; mclxCatInit(&st)
; if (main_mode == 'l')
{ if (mclxCatRead(xfin, &st, catmax, NULL, NULL, 0))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
else if (main_mode == 'f')
{ int format
; mx = mclxRead(xfin, EXIT_ON_FAIL)
; format = mclxIOformat(xfin)
; if (!test_read)
{ mcxIOopen(xfout, EXIT_ON_FAIL)
; if (format == 'a')
mclxbWrite(mx, xfout, EXIT_ON_FAIL)
; else
mclxaWrite(mx, xfout, MCLXIO_VALUE_GETENV, EXIT_ON_FAIL)
; }
}
else
{ mcxbits bits
= main_mode == 'c'
? MCLX_REQUIRE_DOMTREE | MCLX_CATREAD_CLUSTERSTACK
: main_mode == 's'
? MCLX_REQUIRE_DOMSTACK | MCLX_CATREAD_CLUSTERTREE
: 0
; mcxIOopen(xfout, EXIT_ON_FAIL)
; if (mclxCatRead(xfin, &st, catmax, NULL, NULL, bits))
mcxDie(1, me, "failure is, if not an option, the result after all")
; mclxCatWrite(xfout, &st, MCLXIO_VALUE_NONE, EXIT_ON_FAIL)
; }
return 0
; }
static mcxstatus mateInit
( void
)
{ xfout = mcxIOnew("-", "w")
; legend = TRUE
; one2many = FALSE
; return STATUS_OK
; }
int main
( int argc
, const char* argv[]
)
{ int a = 0
; mcxTing* argtxt = mcxTingEmpty(NULL, 10)
; if (0)
mclxIOsetQMode("MCLXIOVERBOSITY", MCL_APP_VB_NO)
; opInitialize() /* symtable etc */
; globInitialize() /* hdltable etc */
; if (argc == 1)
{ mcxTing* ops = mcxTingEmpty(NULL, 20)
; mcxIO *xfin = mcxIOnew("-", "r")
; mcxIOopen(xfin, EXIT_ON_FAIL)
; fprintf
( stdout
, "At your service: "
"'[/<op>] help', '[/<str>] grep', 'ops', 'info', and 'quit'.\n"
)
; while (1)
{ int ok
; mcxTing* line = mcxTingEmpty(NULL, 30)
; fprintf(stdout, "> ")
; fflush(stdout)
; if (STATUS_OK != mcxIOreadLine(xfin, line, MCX_READLINE_BSC))
{ fprintf(stdout, "curtains!\n")
; mcxTingFree(&line)
; break
; }
mcxTingAppend(ops, line->str)
; mcxTingFree(&line)
; ok = zsDoSequence(ops->str)
; if (ok && (v_g & V_STACK))
zsList(0)
; mcxTingEmpty(ops, 20)
; }
}
else
{ for (a=1;a<argc;a++)
{ mcxTingWrite(argtxt, argv[a])
; if (!zgUser(argtxt->str))
mcxExit(1)
; }
}
mcxTingFree(&argtxt)
; return 0
; }
static mcxstatus collectArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_OUT
: out_g = val
; break
;
case MY_OPT_PASTE
: collect_g = 'p'
; break
;
case MY_OPT_NO_HEADER
: header_g = FALSE
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(val)
; break
;
case MY_OPT_MATRIX_MAX
: collect_g = 'm'
; fltop_g = fltMax
; break
;
case MY_OPT_MATRIX_ADD
: collect_g = 'm'
; break
;
case MY_OPT_2COLUMN
: collect_g = 'c'
; break
;
case MY_OPT_SUMMARY
: summary_g = 1
; break
;
default
: mcxExit(1)
;
}
; return STATUS_OK
; }
static mcxstatus adjustInit
( void
)
{ xfout = mcxIOnew("-", "w")
; xfcl = NULL
; xfmx = NULL
; lintl = 0
; lintk = 0
; fc = FALSE
; return STATUS_OK
; }
static mcxstatus alterArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_IMX
: mcxIOnewName(xfmx_g, val)
; break
;
case MY_OPT_ABC
: xfabc_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_O
: mcxIOnewName(xfout_g, val)
; break
;
case MY_OPT_CANONICAL
: canonical_g = atoi(val)
; break
;
case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(val)
; break
;
default
: mcxExit(1)
;
; }
return STATUS_OK
; }
static mcxstatus adjustArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_OUTPUT
: mcxIOnewName(xfout, val)
; break
;
case MY_OPT_IMX
: xfmx = mcxIOnew(val, "r")
; break
;
case MY_OPT_ICL
: xfcl = mcxIOnew(val, "r")
; break
;
case MY_OPT_LINT_L
: lintl = atoi(val)
; break
;
case MY_OPT_FORCE_CONNECTED
: fc = TRUE
; break
;
case MY_OPT_LINT_K
: lintk = atoi(val)
; break
;
default
: return STATUS_FAIL
;
}
return STATUS_OK
; }
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
; }
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
; }
static mcxstatus allInit
( void
)
{ xfmx_g = mcxIOnew("-", "r")
; xfabc_g = NULL
; xftab_g = NULL
; tab_g = NULL
; progress_g = 0
; rough = FALSE
; list_nodes = TRUE
; mod_up = FALSE
; n_group_G = 1
; i_group = 0
; n_thread_l = 0
; include_ends_g = FALSE
; out_g = "-"
; debug_g = 0
; return STATUS_OK
; }
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* 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 *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_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
; }
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
; }
mcxTingFree(&sa)
; mcxTingFree(&sb)
; mcxTingFree(&line)
; mclgSSPxyFree(&sspo)
; return mx
; }
static mcxstatus erdosMain
( int argc_unused cpl__unused
, const char* argv_unused[] cpl__unused
)
{ mclx* mx, *mxtp = NULL
; mcxIO* xfout = mcxIOnew(out_g, "w")
; mcxIO* xfpath = path_g ? mcxIOnew(path_g, "w") : NULL
; mcxIO* xfstep = step_g ? mcxIOnew(step_g, "w") : NULL
; mcxIOopen(xfout, EXIT_ON_FAIL)
; debug_g = mcx_debug_g
; mcxLogLevel =
MCX_LOG_AGGR | MCX_LOG_MODULE | MCX_LOG_IO | MCX_LOG_GAUGE | MCX_LOG_WARN
; mclx_app_init(stderr)
; if (xfabc_g)
{ if (xftab_g)
tab_g = mclTabRead(xftab_g, NULL, EXIT_ON_FAIL)
, streamer_g.tab_sym_in = tab_g
; mx
static mcxstatus qArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_IMX
: mcxIOnewName(xfmx_g, val)
; user_imx = TRUE
; break
;
case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_ICL
: xfcl_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(val)
; break
;
case MY_OPT_DIMENSION
: mode_get = 'd'
; break
;
case MY_OPT_TESTCYCLE
: mode_get = 'c'
; break
;
case MY_OPT_TESTCYCLE_N
: n_limit = atoi(val)
; mode_get = 'c'
; break
;
case MY_OPT_CLCF
: doclcf_g = TRUE
; break
;
case MY_OPT_KNNREDUCE
: knnexact_g = FALSE
; break
;
case MY_OPT_THREAD
: n_thread_g = atoi(val)
; break
;
case MY_OPT_NODE
: mode_get = 'n'
; break
;
case MY_OPT_FOUT
: mcxIOnewName(xfout_g, val)
; break
;
case MY_OPT_WEIGHT_SCALE
: weight_scale = atof(val)
; break
;
case MY_OPT_OUTPUT_TABLE
: output_table = TRUE
; break
;
case MY_OPT_MYTH
: weefreemen = TRUE
; break
;
case MY_OPT_EDGEWEIGHTS
: mode_get = 'e'
; break
;
case MY_OPT_EDGEWEIGHTS_HIST
: mode_get = 'H'
; if (4 != sscanf(val, "%d,%d,%d,%d", &vary_a, &vary_z, &vary_s, &vary_n))
mcxDie(1, me, "failed to parse argument as integers start,end,step,norm")
; break
;
case MY_OPT_EDGEWEIGHTS_SORTED
: mode_get = 'E'
; break
;
case MY_OPT_DIVIDE
: divide_g = atoi(val)
; break
;
case MY_OPT_VARY_CORRELATION
: vary_a = 4
; vary_z = 20
; vary_s = 1
; vary_n = 20
; weight_scale = 100
; mode_vary = 'c'
; break
;
case MY_OPT_VARY_KNN
: if (4 != sscanf(val, "%d,%d,%d,%d", &vary_a, &vary_z, &vary_s, &vary_n))
mcxDie(1, me, "failed to parse argument as integers start,end,step,norm")
; mode_vary = 'k'
; break
;
case MY_OPT_VARY_THRESHOLD
: if (4 != sscanf(val, "%u,%u,%u,%u", &vary_a, &vary_z, &vary_s, &vary_n))
mcxDie(1, me, "failed to parse argument as integers start,end,step,norm")
; mode_vary = 't'
; break
;
default
: mcxExit(1)
;
; }
if (mode_vary && 1000 * vary_s < vary_z - vary_a)
mcxDie(1, me, "argument leads to more than one thousand steps")
; if (!vary_n)
mcxDie(1, me, "need nonzero scaling factor (last component)")
; 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
; }
static mcxstatus qArgHandle
( int optid
, const char* val
)
{ switch(optid)
{ case MY_OPT_IMX
: mcxIOnewName(xfmx_g, val)
; user_imx = TRUE
; break
;
case MY_OPT_ABC
: xfabc_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_TAB
: xftab_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_ICL
: xfcl_g = mcxIOnew(val, "r")
; break
;
case MY_OPT_TRANSFORM
: transform_spec = mcxTingNew(val)
; break
;
case MY_OPT_DIMENSION
: mode_get = 'd'
; break
;
case MY_OPT_TESTMETRIC
: mode_get = 'm'
; break
;
case MY_OPT_TESTCYCLE
: mode_get = 'c'
; break
;
case MY_OPT_TESTCYCLE_N
: n_limit = atoi(val)
; mode_get = 'c'
; break
;
case MY_OPT_INFO
: compute_flags |= COMPUTE_EFF
; break
;
case MY_OPT_CLCF
: compute_flags |= COMPUTE_CLCF
; break
;
case MY_OPT_REDUCE
: rebase_g = FALSE
; break
;
case MY_OPT_THREAD
: n_thread_l = atoi(val)
; break
;
case MY_OPT_NODE
: mode_get = 'n'
; break
;
case MY_OPT_FOUT
: mcxIOnewName(xfout_g, val)
; break
;
case MY_OPT_WEIGHT_SCALE
: weight_scale = atof(val)
; break
;
case MY_OPT_OUTPUT_NOLEGEND
: output_flags ^= OUTPUT_KEY
; break
;
case MY_OPT_OUTPUT_TABLE
: output_flags |= OUTPUT_TABLE
; break
;
case MY_OPT_SCALEFREE
: weefreemen = TRUE
; break
;
case MY_OPT_EDGEWEIGHTS
: mode_get = 'e'
; break
;
case MY_OPT_EDGEWEIGHTS_HIST
: mode_get = 'H'
; if (4 != sscanf(val, "%d,%d,%d,%d", &vary_a, &vary_z, &vary_s, &vary_n))
mcxDie(1, me, "failed to parse argument as integers start,end,step,norm")
; break
;
case MY_OPT_EDGEWEIGHTS_SORTED
: mode_get = 'E'
; break
;
case MY_OPT_DIVIDE
: divide_g = atoi(val)
; break
;
case MY_OPT_VARY_CORRELATION
: vary_a = 4
; vary_z = 20
; vary_s = 1
; vary_n = 20
; weight_scale = 100
; mode_vary = 'c'
; break
;
case MY_OPT_VARY_CEIL
: case MY_OPT_VARY_KNN
: case MY_OPT_VARY_N
: case MY_OPT_VARY_THRESHOLD
: if (4 != sscanf(val, "%d,%d,%d,%d", &vary_a, &vary_z, &vary_s, &vary_n))
mcxDie(1, me, "failed to parse argument as integers start,end,step,norm")
; mode_vary
= optid == MY_OPT_VARY_THRESHOLD
? 't'
: optid == MY_OPT_VARY_KNN
? 'k'
: optid == MY_OPT_VARY_CEIL
? 'n'
: optid == MY_OPT_VARY_N
? 'l'
: 'X'
; break
;
default
: mcxExit(1)
;
; }
if (mode_vary && 1000 * vary_s < vary_z - vary_a)
mcxDie(1, me, "argument leads to more than one thousand steps")
; if (!vary_n)
mcxDie(1, me, "need nonzero scaling factor (last component)")
; 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
;
}
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
; }
static mcxstatus meetInit
( void
)
{ xfout = mcxIOnew("-", "w")
; return STATUS_OK
; }