nysol-take 3.0.0
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- checksums.yaml +7 -0
- data/bin/mbiclique.rb +317 -0
- data/bin/mbipolish.rb +362 -0
- data/bin/mccomp.rb +235 -0
- data/bin/mclique.rb +295 -0
- data/bin/mclique2g.rb +105 -0
- data/bin/mcliqueInfo.rb +203 -0
- data/bin/mfriends.rb +202 -0
- data/bin/mgdiff.rb +252 -0
- data/bin/mhifriend.rb +456 -0
- data/bin/mhipolish.rb +465 -0
- data/bin/mitemset.rb +168 -0
- data/bin/mpal.rb +410 -0
- data/bin/mpolishing.rb +399 -0
- data/bin/msequence.rb +165 -0
- data/bin/mtra2g.rb +476 -0
- data/bin/mtra2gc.rb +360 -0
- data/ext/grhfilrun/extconf.rb +12 -0
- data/ext/grhfilrun/grhfilrun.c +85 -0
- data/ext/grhfilrun/src/_sspc.c +358 -0
- data/ext/grhfilrun/src/aheap.c +545 -0
- data/ext/grhfilrun/src/aheap.h +251 -0
- data/ext/grhfilrun/src/base.c +92 -0
- data/ext/grhfilrun/src/base.h +59 -0
- data/ext/grhfilrun/src/fstar.c +497 -0
- data/ext/grhfilrun/src/fstar.h +80 -0
- data/ext/grhfilrun/src/grhfil.c +214 -0
- data/ext/grhfilrun/src/itemset.c +713 -0
- data/ext/grhfilrun/src/itemset.h +170 -0
- data/ext/grhfilrun/src/problem.c +415 -0
- data/ext/grhfilrun/src/problem.h +179 -0
- data/ext/grhfilrun/src/queue.c +533 -0
- data/ext/grhfilrun/src/queue.h +182 -0
- data/ext/grhfilrun/src/sample.c +19 -0
- data/ext/grhfilrun/src/sspc.c +597 -0
- data/ext/grhfilrun/src/sspc2.c +491 -0
- data/ext/grhfilrun/src/stdlib2.c +1482 -0
- data/ext/grhfilrun/src/stdlib2.h +892 -0
- data/ext/grhfilrun/src/trsact.c +817 -0
- data/ext/grhfilrun/src/trsact.h +160 -0
- data/ext/grhfilrun/src/vec.c +745 -0
- data/ext/grhfilrun/src/vec.h +172 -0
- data/ext/lcmrun/extconf.rb +20 -0
- data/ext/lcmrun/lcmrun.cpp +99 -0
- data/ext/lcmrun/src/aheap.c +216 -0
- data/ext/lcmrun/src/aheap.h +111 -0
- data/ext/lcmrun/src/base.c +92 -0
- data/ext/lcmrun/src/base.h +59 -0
- data/ext/lcmrun/src/itemset.c +496 -0
- data/ext/lcmrun/src/itemset.h +157 -0
- data/ext/lcmrun/src/lcm.c +427 -0
- data/ext/lcmrun/src/problem.c +349 -0
- data/ext/lcmrun/src/problem.h +177 -0
- data/ext/lcmrun/src/queue.c +528 -0
- data/ext/lcmrun/src/queue.h +176 -0
- data/ext/lcmrun/src/sgraph.c +359 -0
- data/ext/lcmrun/src/sgraph.h +173 -0
- data/ext/lcmrun/src/stdlib2.c +1282 -0
- data/ext/lcmrun/src/stdlib2.h +823 -0
- data/ext/lcmrun/src/trsact.c +747 -0
- data/ext/lcmrun/src/trsact.h +159 -0
- data/ext/lcmrun/src/vec.c +731 -0
- data/ext/lcmrun/src/vec.h +171 -0
- data/ext/lcmseq0run/extconf.rb +20 -0
- data/ext/lcmseq0run/lcmseq0run.cpp +59 -0
- data/ext/lcmseq0run/src/aheap.c +216 -0
- data/ext/lcmseq0run/src/aheap.h +111 -0
- data/ext/lcmseq0run/src/base.c +92 -0
- data/ext/lcmseq0run/src/base.h +59 -0
- data/ext/lcmseq0run/src/itemset.c +518 -0
- data/ext/lcmseq0run/src/itemset.h +157 -0
- data/ext/lcmseq0run/src/itemset_zero.c +522 -0
- data/ext/lcmseq0run/src/lcm_seq.c +446 -0
- data/ext/lcmseq0run/src/lcm_seq_zero.c +446 -0
- data/ext/lcmseq0run/src/problem.c +439 -0
- data/ext/lcmseq0run/src/problem.h +179 -0
- data/ext/lcmseq0run/src/problem_zero.c +439 -0
- data/ext/lcmseq0run/src/queue.c +533 -0
- data/ext/lcmseq0run/src/queue.h +182 -0
- data/ext/lcmseq0run/src/stdlib2.c +1350 -0
- data/ext/lcmseq0run/src/stdlib2.h +864 -0
- data/ext/lcmseq0run/src/trsact.c +747 -0
- data/ext/lcmseq0run/src/trsact.h +159 -0
- data/ext/lcmseq0run/src/vec.c +779 -0
- data/ext/lcmseq0run/src/vec.h +172 -0
- data/ext/lcmseqrun/extconf.rb +20 -0
- data/ext/lcmseqrun/lcmseqrun.cpp +101 -0
- data/ext/lcmseqrun/src/aheap.c +216 -0
- data/ext/lcmseqrun/src/aheap.h +111 -0
- data/ext/lcmseqrun/src/base.c +92 -0
- data/ext/lcmseqrun/src/base.h +59 -0
- data/ext/lcmseqrun/src/itemset.c +518 -0
- data/ext/lcmseqrun/src/itemset.h +157 -0
- data/ext/lcmseqrun/src/itemset_zero.c +522 -0
- data/ext/lcmseqrun/src/lcm_seq.c +447 -0
- data/ext/lcmseqrun/src/lcm_seq_zero.c +446 -0
- data/ext/lcmseqrun/src/problem.c +439 -0
- data/ext/lcmseqrun/src/problem.h +179 -0
- data/ext/lcmseqrun/src/problem_zero.c +439 -0
- data/ext/lcmseqrun/src/queue.c +533 -0
- data/ext/lcmseqrun/src/queue.h +182 -0
- data/ext/lcmseqrun/src/stdlib2.c +1350 -0
- data/ext/lcmseqrun/src/stdlib2.h +864 -0
- data/ext/lcmseqrun/src/trsact.c +747 -0
- data/ext/lcmseqrun/src/trsact.h +159 -0
- data/ext/lcmseqrun/src/vec.c +779 -0
- data/ext/lcmseqrun/src/vec.h +172 -0
- data/ext/lcmtransrun/extconf.rb +18 -0
- data/ext/lcmtransrun/lcmtransrun.cpp +264 -0
- data/ext/macerun/extconf.rb +20 -0
- data/ext/macerun/macerun.cpp +57 -0
- data/ext/macerun/src/aheap.c +217 -0
- data/ext/macerun/src/aheap.h +112 -0
- data/ext/macerun/src/itemset.c +491 -0
- data/ext/macerun/src/itemset.h +158 -0
- data/ext/macerun/src/mace.c +503 -0
- data/ext/macerun/src/problem.c +346 -0
- data/ext/macerun/src/problem.h +174 -0
- data/ext/macerun/src/queue.c +529 -0
- data/ext/macerun/src/queue.h +177 -0
- data/ext/macerun/src/sgraph.c +360 -0
- data/ext/macerun/src/sgraph.h +174 -0
- data/ext/macerun/src/stdlib2.c +993 -0
- data/ext/macerun/src/stdlib2.h +811 -0
- data/ext/macerun/src/vec.c +634 -0
- data/ext/macerun/src/vec.h +170 -0
- data/ext/sspcrun/extconf.rb +20 -0
- data/ext/sspcrun/src/_sspc.c +358 -0
- data/ext/sspcrun/src/aheap.c +545 -0
- data/ext/sspcrun/src/aheap.h +251 -0
- data/ext/sspcrun/src/base.c +92 -0
- data/ext/sspcrun/src/base.h +59 -0
- data/ext/sspcrun/src/fstar.c +496 -0
- data/ext/sspcrun/src/fstar.h +80 -0
- data/ext/sspcrun/src/grhfil.c +213 -0
- data/ext/sspcrun/src/itemset.c +713 -0
- data/ext/sspcrun/src/itemset.h +170 -0
- data/ext/sspcrun/src/problem.c +415 -0
- data/ext/sspcrun/src/problem.h +179 -0
- data/ext/sspcrun/src/queue.c +533 -0
- data/ext/sspcrun/src/queue.h +182 -0
- data/ext/sspcrun/src/sample.c +19 -0
- data/ext/sspcrun/src/sspc.c +598 -0
- data/ext/sspcrun/src/sspc2.c +491 -0
- data/ext/sspcrun/src/stdlib2.c +1482 -0
- data/ext/sspcrun/src/stdlib2.h +892 -0
- data/ext/sspcrun/src/trsact.c +817 -0
- data/ext/sspcrun/src/trsact.h +160 -0
- data/ext/sspcrun/src/vec.c +745 -0
- data/ext/sspcrun/src/vec.h +172 -0
- data/ext/sspcrun/sspcrun.cpp +54 -0
- data/lib/nysol/enumLcmEp.rb +338 -0
- data/lib/nysol/enumLcmEsp.rb +284 -0
- data/lib/nysol/enumLcmIs.rb +275 -0
- data/lib/nysol/enumLcmSeq.rb +143 -0
- data/lib/nysol/items.rb +201 -0
- data/lib/nysol/seqDB.rb +256 -0
- data/lib/nysol/take.rb +39 -0
- data/lib/nysol/taxonomy.rb +113 -0
- data/lib/nysol/traDB.rb +257 -0
- metadata +239 -0
@@ -0,0 +1,439 @@
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/* Common problem input/output routines /structure
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25/Nov/2007 by Takeaki Uno e-mail:uno@nii.jp,
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homepage: http://research.nii.ac.jp/~uno/index.html */
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/* This program is available for only academic use, basically.
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Anyone can modify this program, but he/she has to write down
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the change of the modification on the top of the source code.
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Neither contact nor appointment to Takeaki Uno is needed.
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If one wants to re-distribute this code, please
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refer the newest code, and show the link to homepage of
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Takeaki Uno, to notify the news about the codes for the users. */
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/***************************************************/
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#ifndef _problem_c_
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#define _problem_c_
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#include"problem.h"
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#include"stdlib2.c"
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#include"queue.c"
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#include"itemset.c"
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void PROBLEM_error (){
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ERROR_MES = "command explanation";
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EXIT;
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}
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/*************************************************************************/
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/* PROBLEM and ITEMSET initialization */
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/*************************************************************************/
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void PROBLEM_init (PROBLEM *P){
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P->start_time = clock();
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RAND_INIT;
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//ERROR_MES = NULL;
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org2__ = __load_from_memory__ = __load_from_memory_org__;
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#endif
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P->problem = P->problem2 = 0;
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P->prog = 0;
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P->prog2 = 0;
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P->input_fname = P->input_fname2 = P->output_fname = P->output_fname2 = NULL;
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P->workdir = P->workdir2 = NULL;
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P->weight_fname = P->header_fname = P->table_fname = P->sc_fname = NULL;
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P->position_fname = P->position2_fname = NULL;
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P->outperm_fname = NULL;
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P->root = 0;
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P->dir = P->edge_dir = 0;
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P->th = P->th2 = P->th3 = 0;
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P->ratio = P->ratio2 = 0;
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P->num = P->siz = P->dim = P->len = P->width = P->height = 0;
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P->rows = 0;
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P->clms = 0;
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P->gap_ub = INTHUGE;
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P->gap_lb = 0;
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P->xmax = P->ymax = P->pxmax = P->pymax = 0;
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P->tmax = P->tmin = 0;
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P->cost = P->cost2 = 0;
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ITEMSET_init (&P->II);
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ITEMSET_init (&P->II2);
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P->vf = P->dep = NULL;
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P->ff = INIT_QUEUE;
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P->shift = NULL;
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P->occ_w = P->occ_pw = P->occ_w2 = P->occ_pw2 = NULL;
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P->buf = P->buf_org = NULL;
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P->buf_end = 0;
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P->itemjump = P->itemcand = P->vecjump = P->veccand = INIT_QUEUE; // for delivery
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P->itemchr = P->vecchr = NULL;
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P->OQ = P->OQ2 = P->VQ = P->VQ2 = NULL; // for delivery
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P->itemary = NULL;
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P->itemmark = P->itemflag = P->vecmark = P->vecflag = NULL; // mark for vector
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P->occ_t = P->vecary = NULL;
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P->oo = INIT_QUEUE;
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P->vecw = NULL;
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P->pat = NULL;
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P->plen = P->perr = 0;
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#ifdef _base_h_
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P->B = INIT_BASE;
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#endif
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#ifdef _alist_h_
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P->occ = INIT_MALIST;
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P->itemlist = INIT_ALIST;
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P->veclist = INIT_ALIST;
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#endif
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#ifdef _trsact_h_
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TRSACT_init (&P->TT);
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TRSACT_init (&P->TT2);
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#endif
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#ifdef _sgraph_h_
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P->SG = INIT_SGRAPH;
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P->SG2 = INIT_SGRAPH;
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#endif
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#ifdef _agraph_h_
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P->AG = INIT_AGRAPH;
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P->AG2 = INIT_AGRAPH;
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#endif
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#ifdef _seq_h_
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SEQ_init (&P->SS);
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SEQ_init (&P->SS2);
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#endif
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#ifdef _pos_h_
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POS_init (&P->PS);
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POS_init (&P->PS2);
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P->PS.S = &P->SS;
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P->PS2.S = &P->SS2;
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P->PS.I = &P->II;
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P->PS2.I = &P->II;
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#endif
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#ifdef _fstar_h_
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P->FS = INIT_FSTAR;
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P->FS2 = INIT_FSTAR;
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#endif
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#ifdef _vec_h_
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P->MM = INIT_MAT;
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P->MM2 = INIT_MAT;
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P->SM = INIT_SMAT;
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P->SM2 = INIT_SMAT;
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P->FF = INIT_SETFAMILY;
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P->FF2 = INIT_SETFAMILY;
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#endif
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#ifdef _barray_h_
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P->BA = INIT_BARRAY;
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P->BA2 = INIT_BARRAY;
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#endif
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}
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/*************************************************************************/
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/* PROBLEM load */
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/*************************************************************************/
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void PROBLEM_load (PROBLEM *P){
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int f=0;
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ITEMSET *II = &P->II;
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/******************************/
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#ifdef _trsact_h_
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if ( P->TT.fname ){ TRSACT_load (&P->TT); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->TT2.fname ){ TRSACT_load (&P->TT2); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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#endif
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#ifdef _sgraph_h_
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if ( P->SG.fname ){ SGRAPH_load (&P->SG); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->SG2.fname ){ SGRAPH_load (&P->SG); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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#endif
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#ifdef _agraph_h_
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if ( P->AG.fname ){ AGRAPH_load (&P->AG); if (ERROR_MES) goto ERR;}
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->AG2.fname ){ AGRAPH_load (&P->AG2); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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#endif
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#ifdef _fstar_h_
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if ( P->FS.fname ){ FSTAR_load (&P->FS); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->FS2.fname ){ FSTAR_load (&P->FS2); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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#endif
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#ifdef _vec_h_
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if ( P->MM.fname ){ MAT_load (&P->MM); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->MM2.fname ){ MAT_load (&P->MM2); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
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if ( P->SM.fname ){ SMAT_load (&P->SM); if (ERROR_MES) goto ERR; }
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#ifdef _FILE2_LOAD_FROM_MEMORY_
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__load_from_memory_org__ = __load_from_memory__;
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#endif
|
203
|
+
if ( P->SM2.fname ){ SMAT_load (&P->SM2); if (ERROR_MES) goto ERR; }
|
204
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
205
|
+
__load_from_memory_org__ = __load_from_memory__;
|
206
|
+
#endif
|
207
|
+
if ( P->FF.fname ){ SETFAMILY_load (&P->FF); if (ERROR_MES) goto ERR; }
|
208
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
209
|
+
__load_from_memory_org__ = __load_from_memory__;
|
210
|
+
#endif
|
211
|
+
if ( P->FF2.fname ){ SETFAMILY_load (&P->FF2); if (ERROR_MES) goto ERR; }
|
212
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
213
|
+
__load_from_memory_org__ = __load_from_memory__;
|
214
|
+
#endif
|
215
|
+
if ( P->FF.wfname ){ SETFAMILY_load_weight (&P->FF); if (ERROR_MES) goto ERR; }
|
216
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
217
|
+
__load_from_memory_org__ = __load_from_memory__;
|
218
|
+
#endif
|
219
|
+
if ( P->FF2.wfname ){ SETFAMILY_load_weight (&P->FF2); if (ERROR_MES) goto ERR; }
|
220
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
221
|
+
__load_from_memory_org__ = __load_from_memory__;
|
222
|
+
#endif
|
223
|
+
if ( P->FF.cwfname ){ SETFAMILY_load_column_weight (&P->FF); if (ERROR_MES) goto ERR; }
|
224
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
225
|
+
__load_from_memory_org__ = __load_from_memory__;
|
226
|
+
#endif
|
227
|
+
if ( P->FF2.cwfname ){ SETFAMILY_load_column_weight (&P->FF2); if (ERROR_MES) goto ERR; }
|
228
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
229
|
+
__load_from_memory_org__ = __load_from_memory__;
|
230
|
+
#endif
|
231
|
+
if ( P->FF.rwfname ){ SETFAMILY_load_row_weight (&P->FF); if (ERROR_MES) goto ERR; }
|
232
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
233
|
+
__load_from_memory_org__ = __load_from_memory__;
|
234
|
+
#endif
|
235
|
+
if ( P->FF2.rwfname ){ SETFAMILY_load_row_weight (&P->FF2); if (ERROR_MES) goto ERR; }
|
236
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
237
|
+
__load_from_memory_org__ = __load_from_memory__;
|
238
|
+
#endif
|
239
|
+
#endif
|
240
|
+
|
241
|
+
#ifdef _seq_h_
|
242
|
+
if ( P->SS.fname ){ SEQ_load (&P->SS); if (ERROR_MES) goto ERR; }
|
243
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
244
|
+
__load_from_memory_org__ = __load_from_memory__;
|
245
|
+
#endif
|
246
|
+
if ( P->SS2.fname ){ SEQ_load (&P->SS2); if (ERROR_MES) goto ERR; }
|
247
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
248
|
+
__load_from_memory_org__ = __load_from_memory__;
|
249
|
+
#endif
|
250
|
+
#endif
|
251
|
+
|
252
|
+
#ifdef _barray_h_
|
253
|
+
if ( P->BA.fname ){ BARRAY_load (&P->BA); if (ERROR_MES) goto ERR; }
|
254
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
255
|
+
__load_from_memory_org__ = __load_from_memory__;
|
256
|
+
#endif
|
257
|
+
if ( P->BA2.fname ){ BARRAY_load (&P->BA2); if (ERROR_MES) goto ERR; }
|
258
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
259
|
+
__load_from_memory_org__ = __load_from_memory__;
|
260
|
+
#endif
|
261
|
+
#endif
|
262
|
+
|
263
|
+
if (P->input_fname){ f=1; print_mes (II, " input: %s", P->input_fname); }
|
264
|
+
if (P->weight_fname){ f=1; print_mes (II, " weight: %s", P->weight_fname); }
|
265
|
+
if (P->output_fname){ f=1; print_mes (II, " output to: %s",P->output_fname); }
|
266
|
+
if ( f ) print_mes (II, "\n");
|
267
|
+
|
268
|
+
/******************************/
|
269
|
+
|
270
|
+
if ( !ERROR_MES ) return;
|
271
|
+
ERR:;
|
272
|
+
PROBLEM_end (P);
|
273
|
+
EXIT;
|
274
|
+
}
|
275
|
+
|
276
|
+
/* termination of problem */
|
277
|
+
void PROBLEM_end (PROBLEM *P){
|
278
|
+
ITEMSET *II = &P->II;
|
279
|
+
|
280
|
+
#ifdef _trsact_h_
|
281
|
+
TRSACT_end (&P->TT);
|
282
|
+
TRSACT_end (&P->TT2);
|
283
|
+
#endif
|
284
|
+
#ifdef _sgraph_h_
|
285
|
+
SGRAPH_end (&P->SG);
|
286
|
+
SGRAPH_end (&P->SG2);
|
287
|
+
#endif
|
288
|
+
#ifdef _agraph_h_
|
289
|
+
AGRAPH_end (&P->AG);
|
290
|
+
AGRAPH_end (&P->AG2);
|
291
|
+
#endif
|
292
|
+
#ifdef _seq_h_
|
293
|
+
SEQ_end (&P->SS);
|
294
|
+
SEQ_end (&P->SS2);
|
295
|
+
#endif
|
296
|
+
#ifdef _fstar_h_
|
297
|
+
FSTAR_end (&P->FS);
|
298
|
+
FSTAR_end (&P->FS2);
|
299
|
+
#endif
|
300
|
+
#ifdef _vec_h_
|
301
|
+
MAT_end (&P->MM);
|
302
|
+
MAT_end (&P->MM2);
|
303
|
+
SMAT_end (&P->SM);
|
304
|
+
SMAT_end (&P->SM2);
|
305
|
+
SETFAMILY_end (&P->FF);
|
306
|
+
SETFAMILY_end (&P->FF2);
|
307
|
+
#endif
|
308
|
+
#ifdef _pos_h_
|
309
|
+
POS_end (&P->PS);
|
310
|
+
POS_end (&P->PS2);
|
311
|
+
#endif
|
312
|
+
#ifdef _barray_h_
|
313
|
+
BARRAY_end (&P->BA);
|
314
|
+
BARRAY_end (&P->BA2);
|
315
|
+
#endif
|
316
|
+
|
317
|
+
/******************************/
|
318
|
+
|
319
|
+
mfree (P->vf, P->dep);
|
320
|
+
QUEUE_end (&P->ff);
|
321
|
+
|
322
|
+
ITEMSET_end (II);
|
323
|
+
ITEMSET_end (&P->II2);
|
324
|
+
|
325
|
+
if ( P->occ_pw2 != P->occ_pw && P->occ_pw2 != P->occ_w2 ) free2 (P->occ_pw2);
|
326
|
+
if ( P->occ_w2 != P->occ_w ) free2 (P->occ_w2);
|
327
|
+
if ( P->occ_pw != P->occ_w ) free2 (P->occ_pw);
|
328
|
+
mfree (P->shift, P->occ_t, P->occ_w);
|
329
|
+
|
330
|
+
if ( P->OQ ) free2 (P->OQ[0].v);
|
331
|
+
if ( P->OQ2 ) free2 (P->OQ2[0].v);
|
332
|
+
if ( P->VQ ) free2 (P->VQ[0].v);
|
333
|
+
if ( P->VQ2 ) free2 (P->VQ2[0].v);
|
334
|
+
mfree (P->OQ, P->OQ2, P->VQ, P->VQ2, P->itemchr, P->vecchr);
|
335
|
+
|
336
|
+
mfree (P->itemary, P->itemflag, P->itemmark, P->vecary, P->vecflag, P->vecmark, P->vecw);
|
337
|
+
QUEUE_end (&P->itemcand);
|
338
|
+
QUEUE_end (&P->itemjump);
|
339
|
+
|
340
|
+
QUEUE_end (&P->veccand);
|
341
|
+
QUEUE_end (&P->vecjump);
|
342
|
+
QUEUE_end (&P->oo);
|
343
|
+
|
344
|
+
free2 (P->buf_org);
|
345
|
+
|
346
|
+
#ifdef _alist_h_
|
347
|
+
MALIST_end (&P->occ);
|
348
|
+
ALIST_end (&P->itemlist);
|
349
|
+
ALIST_end (&P->veclist);
|
350
|
+
#endif
|
351
|
+
|
352
|
+
#ifdef _undo_h_
|
353
|
+
ALISTundo_end ();
|
354
|
+
#endif
|
355
|
+
|
356
|
+
P->end_time = clock();
|
357
|
+
if ( print_time_flag )
|
358
|
+
print_mes (II, "computation_time= %3f\n", ((double)(P->end_time-P->start_time))/CLOCKS_PER_SEC);
|
359
|
+
|
360
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
361
|
+
__load_from_memory_org__ = __load_from_memory_org2__;
|
362
|
+
__write_to_memory__ = __write_to_memory_org__;
|
363
|
+
#endif
|
364
|
+
|
365
|
+
PROBLEM_init (P);
|
366
|
+
}
|
367
|
+
|
368
|
+
/* allocate arrays and structures */
|
369
|
+
void PROBLEM_alloc (PROBLEM *P, QUEUE_ID siz, QUEUE_ID siz2, size_t siz3, PERM *perm, int f){
|
370
|
+
PERM *p;
|
371
|
+
#ifdef _alist_h_
|
372
|
+
ALIST_ID i=0;
|
373
|
+
#endif
|
374
|
+
int j;
|
375
|
+
|
376
|
+
if ( f&PROBLEM_SHIFT ) calloc2 (P->shift, siz+2, goto ERR);
|
377
|
+
if ( f&PROBLEM_OCC_T ) calloc2 (P->occ_t, siz+2, goto ERR);
|
378
|
+
if ( f&(PROBLEM_OCC_W+PROBLEM_OCC_PW) ) calloc2 (P->occ_w, siz+2, goto ERR);
|
379
|
+
if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw, siz+2, goto ERR);
|
380
|
+
else P->occ_pw = P->occ_w;
|
381
|
+
if ( f&PROBLEM_OCC_W2 ){
|
382
|
+
calloc2 (P->occ_w2, siz+2, goto ERR);
|
383
|
+
if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw2, siz+2, goto ERR);
|
384
|
+
else P->occ_pw2 = P->occ_w2;
|
385
|
+
} else { P->occ_w2 = P->occ_w; P->occ_pw2 = P->occ_pw; }
|
386
|
+
|
387
|
+
if ( f&PROBLEM_ITEMFLAG ) calloc2 (P->itemflag, siz+2, goto ERR);
|
388
|
+
if ( f&PROBLEM_ITEMMARK ) calloc2 (P->itemmark, siz+2, goto ERR);
|
389
|
+
if ( f&PROBLEM_ITEMARY ) calloc2(P->itemary, siz+2, goto ERR);
|
390
|
+
if ( f&PROBLEM_ITEMCHR ) calloc2(P->itemchr, siz+2, goto ERR);
|
391
|
+
if ( f&PROBLEM_ITEMJUMP ) QUEUE_alloc (&P->itemjump, siz+2);
|
392
|
+
if ( f&PROBLEM_ITEMCAND ) QUEUE_alloc (&P->itemcand, siz+2);
|
393
|
+
|
394
|
+
if ( f&PROBLEM_VECFLAG ) calloc2 (P->vecflag, siz2+2, goto ERR);
|
395
|
+
if ( f&PROBLEM_VECMARK ) calloc2 (P->vecmark, siz2+2, goto ERR);
|
396
|
+
if ( f&PROBLEM_VECARY ) calloc2 (P->vecary, siz2+2, goto ERR);
|
397
|
+
if ( f&PROBLEM_VECCHR ) calloc2 (P->vecchr, siz2+2, goto ERR);
|
398
|
+
if ( f&PROBLEM_VECJUMP ) QUEUE_alloc (&P->vecjump, siz2+2);
|
399
|
+
if ( f&PROBLEM_VECCAND ) QUEUE_alloc (&P->veccand, siz2+2);
|
400
|
+
if ( f&PROBLEM_VECW ) calloc2 (P->vecw, siz2+2, goto ERR);
|
401
|
+
|
402
|
+
#ifdef _alist_h_
|
403
|
+
if ( f&PROBLEM_ITEMLIST ) ALIST_alloc (&P->itemlist, siz+2);
|
404
|
+
if ( f&PROBLEM_VECLIST ) ALIST_alloc (&P->veclist, siz2+2);
|
405
|
+
|
406
|
+
if ( f&PROBLEM_OCC3 ){
|
407
|
+
MALIST_alloc (&P->occ, siz, siz2+2); // element=>
|
408
|
+
if ( ERROR_MES ) goto ERR;
|
409
|
+
if ( f&PROBLEM_OCC2 ){
|
410
|
+
FLOOP (i, 0, siz) MALIST_ins_tail (&P->occ, (f&PROBLEM_OCC1)?siz2: 0, i, 0);
|
411
|
+
}
|
412
|
+
}
|
413
|
+
#endif
|
414
|
+
|
415
|
+
// set outperm
|
416
|
+
if ( P->outperm_fname ){
|
417
|
+
ARY_LOAD (p, int, j, P->outperm_fname, 1, EXIT);
|
418
|
+
if ( perm ){
|
419
|
+
FLOOP (j, 0, siz) perm[j] = p[perm[j]];
|
420
|
+
free2 (p);
|
421
|
+
} else perm = p;
|
422
|
+
}
|
423
|
+
ITEMSET_alloc (&P->II, P->output_fname, perm, siz, siz3);
|
424
|
+
if ( P->II.target<siz && P->II.perm )
|
425
|
+
FLOOP (j, 0, P->II.item_max){ if ( P->II.target == P->II.perm[j] ){ P->II.target = j; break; } }
|
426
|
+
|
427
|
+
#ifdef _undo_h_
|
428
|
+
ALISTundo_init ();
|
429
|
+
#endif
|
430
|
+
|
431
|
+
return;
|
432
|
+
ERR:;
|
433
|
+
PROBLEM_end (P);
|
434
|
+
EXIT;
|
435
|
+
}
|
436
|
+
|
437
|
+
#endif
|
438
|
+
|
439
|
+
|
@@ -0,0 +1,179 @@
|
|
1
|
+
/* Common problem input/output routines /structure
|
2
|
+
25/Nov/2007 by Takeaki Uno e-mail:uno@nii.jp,
|
3
|
+
homepage: http://research.nii.ac.jp/~uno/index.html */
|
4
|
+
/* This program is available for only academic use, basically.
|
5
|
+
Anyone can modify this program, but he/she has to write down
|
6
|
+
the change of the modification on the top of the source code.
|
7
|
+
Neither contact nor appointment to Takeaki Uno is needed.
|
8
|
+
If one wants to re-distribute this code, please
|
9
|
+
refer the newest code, and show the link to homepage of
|
10
|
+
Takeaki Uno, to notify the news about the codes for the users. */
|
11
|
+
|
12
|
+
/***************************************************/
|
13
|
+
|
14
|
+
#ifndef _problem_h_
|
15
|
+
#define _problem_h_
|
16
|
+
|
17
|
+
#include"stdlib2.h"
|
18
|
+
#include"queue.h"
|
19
|
+
#include"itemset.h"
|
20
|
+
|
21
|
+
#define PROBLEM_FREQSET 1
|
22
|
+
#define PROBLEM_MAXIMAL 2
|
23
|
+
#define PROBLEM_CLOSED 4
|
24
|
+
#define PROBLEM_EX_MAXIMAL 8
|
25
|
+
#define PROBLEM_EX_CLOSED 16
|
26
|
+
#define PROBLEM_MINIMAL 32
|
27
|
+
#define PROBLEM_DOC 64
|
28
|
+
|
29
|
+
/***** parameters for PROBLEM initialization, given to flag *****/
|
30
|
+
|
31
|
+
#define PROBLEM_PRINT_DENSE 4 // print density threshold
|
32
|
+
#define PROBLEM_PRINT_SHRINK 8 // print properties of shrinked database
|
33
|
+
#define PROBLEM_PRINT_FRQ 16 // print density threshold
|
34
|
+
#define PROBLEM_NORMALIZE 32 // print density threshold
|
35
|
+
|
36
|
+
#define PROBLEM_ITEMARY 128 // alloc itemary
|
37
|
+
#define PROBLEM_ITEMJUMP 256 // alloc itemjump
|
38
|
+
#define PROBLEM_ITEMFLAG 512 // alloc itemflag
|
39
|
+
#define PROBLEM_ITEMMARK 1024 // alloc itemmark
|
40
|
+
#define PROBLEM_ITEMCAND 2048 // alloc itemcand
|
41
|
+
#define PROBLEM_VECARY 4096 // alloc itemary
|
42
|
+
#define PROBLEM_VECJUMP 8192 // alloc vecjump
|
43
|
+
#define PROBLEM_VECFLAG 16384 // alloc vecflag
|
44
|
+
#define PROBLEM_VECMARK 32768 // alloc vecmark
|
45
|
+
#define PROBLEM_VECCAND 65536 // alloc veccand
|
46
|
+
#define PROBLEM_ITEMCHR 131072 //alloc itemchr
|
47
|
+
#define PROBLEM_VECCHR 262144 //alloc vecchr
|
48
|
+
//4194304
|
49
|
+
#define PROBLEM_OCC_T 524288 // alloc occ_t
|
50
|
+
#define PROBLEM_SHIFT 1048576 // allocate shift
|
51
|
+
#define PROBLEM_OCC_W 2097152 // weight/positive-weight sum for items
|
52
|
+
#define PROBLEM_OCC_PW 4194304 // weight/positive-weight sum for items
|
53
|
+
#define PROBLEM_OCC_W2 8388608 // weight/positive-weight sum for items
|
54
|
+
#define PROBLEM_ITEMLIST 16777216 // alist for items
|
55
|
+
#define PROBLEM_VECLIST 33554432 // alist for vecs
|
56
|
+
#define PROBLEM_VECW 67108864 // weight array for vecs
|
57
|
+
|
58
|
+
#define PROBLEM_OCC1 16 // alloc occ
|
59
|
+
#define PROBLEM_OCC2 32 // alloc occ and ins all to list 0
|
60
|
+
#define PROBLEM_OCC3 48 // alloc occ and ins all to list "siz"
|
61
|
+
|
62
|
+
typedef struct {
|
63
|
+
clock_t start_time, end_time;
|
64
|
+
int problem, problem2;
|
65
|
+
LONG prog;
|
66
|
+
int prog2;
|
67
|
+
double dense;
|
68
|
+
char *input_fname, *input_fname2;
|
69
|
+
char *output_fname, *output_fname2;
|
70
|
+
char *workdir, *workdir2;
|
71
|
+
|
72
|
+
char *weight_fname;
|
73
|
+
char *table_fname, *table2_fname;
|
74
|
+
char *outperm_fname, *outperm_fname2;
|
75
|
+
char *header_fname, *position_fname, *position2_fname, *sc_fname;
|
76
|
+
|
77
|
+
ITEMSET II, II2;
|
78
|
+
QUEUE ff; // for agraph search
|
79
|
+
int *vf, *dep; // for agraph search
|
80
|
+
|
81
|
+
int root, dir, edge_dir;
|
82
|
+
double th, th2, th3; // thresholds
|
83
|
+
double ratio, ratio2; // ratio
|
84
|
+
int num, siz, dim, len, width, height, gap_ub, gap_lb;
|
85
|
+
int xmax, ymax, pxmax, pymax;
|
86
|
+
int tmax, tmin;
|
87
|
+
QUEUE_INT clms;
|
88
|
+
VEC_ID rows;
|
89
|
+
WEIGHT cost, cost2;
|
90
|
+
|
91
|
+
QUEUE_ID **shift;
|
92
|
+
QUEUE itemjump, itemcand, vecjump, veccand, *OQ, *OQ2, *VQ, *VQ2; // for delivery
|
93
|
+
QUEUE_INT *itemary;
|
94
|
+
char *itemchr, *vecchr;
|
95
|
+
int *itemmark, *itemflag, *vecmark, *vecflag; // mark for vector
|
96
|
+
VEC_ID *vecary, *occ_t;
|
97
|
+
WEIGHT *occ_w, *occ_pw, *occ_w2, *occ_pw2, *vecw;
|
98
|
+
QUEUE oo;
|
99
|
+
QUEUE_INT *buf, *buf_org;
|
100
|
+
size_t buf_end;
|
101
|
+
|
102
|
+
char *pat; // pattern string
|
103
|
+
int plen, perr; // pattern length and #error allowed
|
104
|
+
|
105
|
+
#ifdef _base_h_
|
106
|
+
BASE B;
|
107
|
+
#endif
|
108
|
+
|
109
|
+
#ifdef _alist_h_
|
110
|
+
ALIST itemlist, veclist;
|
111
|
+
#endif
|
112
|
+
|
113
|
+
#ifdef _alist_h_
|
114
|
+
MALIST occ;
|
115
|
+
#endif
|
116
|
+
|
117
|
+
#ifdef _sgraph_h_
|
118
|
+
SGRAPH SG, SG2;
|
119
|
+
#endif
|
120
|
+
|
121
|
+
#ifdef _agraph_h_
|
122
|
+
AGRAPH AG, AG2;
|
123
|
+
#endif
|
124
|
+
|
125
|
+
#ifdef _trsact_h_
|
126
|
+
TRSACT TT, TT2;
|
127
|
+
#endif
|
128
|
+
|
129
|
+
#ifdef _seq_h_
|
130
|
+
SEQ SS, SS2;
|
131
|
+
#endif
|
132
|
+
#ifdef _pos_h_
|
133
|
+
POS PS, PS2;
|
134
|
+
#endif
|
135
|
+
|
136
|
+
#ifdef _fstar_h_
|
137
|
+
FSTAR FS, FS2;
|
138
|
+
#endif
|
139
|
+
|
140
|
+
#ifdef _vec_h_
|
141
|
+
MAT MM, MM2;
|
142
|
+
SMAT SM, SM2;
|
143
|
+
SETFAMILY FF, FF2;
|
144
|
+
#endif
|
145
|
+
|
146
|
+
#ifdef _barray_h_
|
147
|
+
BARRAY BA;
|
148
|
+
BARRAY BA2;
|
149
|
+
#endif
|
150
|
+
|
151
|
+
} PROBLEM;
|
152
|
+
|
153
|
+
|
154
|
+
/***** print filename information ****/
|
155
|
+
void PROBLEM_print (PROBLEM *P);
|
156
|
+
|
157
|
+
/***** print usage of the program *****/
|
158
|
+
void PROBLEM_error ();
|
159
|
+
|
160
|
+
/***** read parameters given by command line *****/
|
161
|
+
void PROBLEM_read_param (int argc, char *argv[], PROBLEM *P);
|
162
|
+
|
163
|
+
/***** PROBLEM and ITEMSET initialization *****/
|
164
|
+
/* all pointers are set to NULL, but don't touch filenames */
|
165
|
+
void PROBLEM_init (PROBLEM *P);
|
166
|
+
|
167
|
+
/***** PROBLEM initialization: load the files given by filenames ******/
|
168
|
+
void PROBLEM_load (PROBLEM *P);
|
169
|
+
|
170
|
+
/***** allocate memory according to flag *****/
|
171
|
+
void PROBLEM_alloc (PROBLEM *PP, QUEUE_ID siz, QUEUE_ID siz2, size_t siz3, PERM *p, int f);
|
172
|
+
|
173
|
+
/* termination of problem */
|
174
|
+
void PROBLEM_end (PROBLEM *PP);
|
175
|
+
|
176
|
+
|
177
|
+
#endif
|
178
|
+
|
179
|
+
|