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
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/* itemset search input/output common routines
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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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/* routines for itemset mining */
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#ifndef _itemset_h_
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#define _itemset_h_
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#include"stdlib2.h"
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#include"queue.h"
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#define AHEAP_KEY_WEIGHT
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#include"aheap.h"
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typedef struct {
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// int a;
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QUEUE itemset; // current operating itemset
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QUEUE add; // for equisupport (hypercube decomposition)
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int ub, lb; // upper/lower bounds for the itemset size
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WEIGHT frq, pfrq, frq_ub, frq_lb; // upper/lower bounds for the frequency
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WEIGHT rposi_lb, rposi_ub, posi_lb, posi_ub, nega_ub, nega_lb; // upper/lower bounds for the sum of positive/negative weights
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WEIGHT setrule_lb; // frequency lower bound for set rule
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double ratio, prob, th; // confidence and independent probability of the current pattern
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double ratio_ub, ratio_lb, prob_ub, prob_lb; // upper/lower bounds for confidence and independent probability
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QUEUE_INT target; // target item for rule mining
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char *itemflag; // 1 if it is include in the pattern (and 2 if included in add)
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WEIGHT *item_frq; // frequency of each item
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WEIGHT total_weight; // total weight of the input database
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int len_ub, len_lb; // upper/lower bounds for the length of the pattern
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int gap_ub, gap_lb; // upper/lower bounds for the gaps in the pattern
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LONG *sc, *sc2; // #itemsets classified by the sizes / frequencies
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QUEUE_INT item_max, item_max_org; // (original) maximum item
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AHEAP topk, *itemtopk; // heap for topk mining. valid if topk->h is not NULL
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LONG itemtopk_end, itemtopk_item, itemtopk_item2; // the size of itemtopk heaps; specify topkheap to be used/the size of each in the initiaization
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char topk_sign, itemtopk_sign; // determine min/max (1, -1) for topk/itemtopk heaps
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QUEUE_INT **itemtopk_ary; // topk solutions for each item
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LONG topk_k, topk_frq; // counter for topk bucket and #remainings
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int flag, flag2; // flag for various functions
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PERM *perm; // permutation array for output itemset: item => original item
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FILE *fp; // file pointer to the output file
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char separator; // separator of items output
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int digits; // #decimals to be output, for non-natural numbers
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int progress;
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LONG iters, iters2, iters3; //iterations
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LONG solutions, solutions2; // number of solutions output
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LONG outputs, outputs2; // #calls of ITEMSET_output_itemse3t or ITEMSET_solusion
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LONG max_solutions; // maximum solutions to be output
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void *X; // pointer to the original data
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int dir; // direction flag for AGRAPH & SGRAPH
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int multi_core; // number of processors
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LONG *multi_iters, *multi_iters2, *multi_iters3; //iterations
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LONG *multi_solutions, *multi_solutions2; // number of solutions output
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LONG *multi_outputs, *multi_outputs2; // #calls of ITEMSET_output_itemset or ITEMSET_solusion
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FILE2 *multi_fp; // output file2 pointer for multi-core mode
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WEIGHT *set_weight; // the frequency of each prefix of current itemset
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QUEUE **set_occ; // the occurrence of each prefix of current itemset
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IHEAP minh, maxh; // for 2D LAMP mode
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LONG *patn; // cardinarity of each patten group
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#ifdef MULTI_CORE
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pthread_spinlock_t lock_counter; // couneter locker for jump counter
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pthread_spinlock_t lock_sc; // couneter locker for score counter
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pthread_spinlock_t lock_output; // couneter locker for #output
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#endif
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} ITEMSET;
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/* parameters for ITEMSET.flag */
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#define ITEMSET_ITERS2 4 // output #iters2
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#define ITEMSET_PRE_FREQ 8 // output frequency preceding to each itemset
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#define ITEMSET_FREQ 16 // output frequency following to each itemset
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#define ITEMSET_ALL 32 // concat all combinations of "add" to each itemset
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#define ITEMSET_TRSACT_ID 64 // output transaction ID's in occurrences
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#define ITEMSET_OUTPUT_EDGE 128 // output itemset as edge set (refer AGRAPH)
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#define ITEMSET_IGNORE_BOUND 256 // ignore constraint for frequency
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#define ITEMSET_RM_DUP_TRSACT 512 // remove duplicated transaction ID's
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#define ITEMSET_MULTI_OCC_PRINT 1024 //print each component of occ
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// TRSACT_ID+MULTI_OCC_PRINT means print first two components of occ
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#define ITEMSET_NOT_ITEMSET 2048 // do not print itemset to the output file
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#define ITEMSET_RULE_SUPP 4096 // output confidence and item frquency by abusolute value
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#define ITEMSET_OUTPUT_POSINEGA 8192 // output negative/positive frequencies
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#define ITEMSET_MULTI_OUTPUT 16384 // for multi-core mode
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#define ITEMSET_USE_ORG 32768 // use item_max_org to the size of use
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#define ITEMSET_ITEMFRQ 65536 // allocate item_frq
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#define ITEMSET_ADD 131072 // allocate add
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#define ITEMSET_RULE_FRQ 262144
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#define ITEMSET_RULE_INFRQ 524288
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#define ITEMSET_RULE_RFRQ 1048576
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#define ITEMSET_RULE_RINFRQ 2097152
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#define ITEMSET_RFRQ 4194304
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#define ITEMSET_RINFRQ 8388608
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#define ITEMSET_POSI_RATIO 16777216
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#define ITEMSET_SET_RULE 134217728
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#define ITEMSET_APPEND 268435456 // append the output to the fiile
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#define ITEMSET_RULE_ADD 536870912 // append items in add to the solution, for rule output
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#define ITEMSET_SC2 1073741824 // count #items classified by frequencies
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#define ITEMSET_LAMP 256 // LAMP mode
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#define ITEMSET_LAMP2 512 // 2D LAMP mode
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//#define ITEMSET_RULE (ITEMSET_RULE_FRQ + ITEMSET_RULE_INFRQ + ITEMSET_RULE_RFRQ + ITEMSET_RULE_RINFRQ + ITEMSET_RFRQ + ITEMSET_RINFRQ + ITEMSET_SET_RULE) // for check any rule is true
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#define ITEMSET_RULE (ITEMSET_RULE_FRQ + ITEMSET_RULE_INFRQ + ITEMSET_RULE_RFRQ + ITEMSET_RULE_RINFRQ + ITEMSET_SET_RULE) // for check any rule is true
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#ifndef ITEMSET_INTERVAL
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#define ITEMSET_INTERVAL 500000
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#endif
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/* Output information about ITEMSET structure. flag&1: print frequency constraint */
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void ITEMSET_print (ITEMSET *II, int flag);
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/* topk.end>0 => initialize heap for topk mining */
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/* all pointers will be set to 0, but not for */
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/* if topK mining, set topk.end to "K" */
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void ITEMSET_init (ITEMSET *I);
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void ITEMSET_alloc (ITEMSET *I, char *fname, PERM *perm, QUEUE_INT item_max, size_t item_max_org);
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void ITEMSET_end (ITEMSET *I);
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/* sum the counters computed by each thread */
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void ITEMSET_merge_counters (ITEMSET *I);
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/*******************************************************************/
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/* output at the termination of the algorithm */
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/* print #of itemsets of size k, for each k */
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/*******************************************************************/
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void ITEMSET_last_output (ITEMSET *I);
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/* output frequency, coverage */
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void ITEMSET_output_frequency (ITEMSET *I, int core_id);
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/* output an itemset to the output file */
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void ITEMSET_output_itemset (ITEMSET *I, QUEUE *occ, int core_id);
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/* output itemsets with adding all combination of "add"
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at the first call, i has to be "add->t" */
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void ITEMSET_solution (ITEMSET *I, QUEUE *occ, int core_id);
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/*************************************************************************/
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/* ourput a rule */
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/*************************************************************************/
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void ITEMSET_output_rule (ITEMSET *I, QUEUE *occ, double p1, double p2, size_t item, int core_id);
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/*************************************************************************/
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/* check all rules for a pair of itemset and item */
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/*************************************************************************/
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void ITEMSET_check_rule (ITEMSET *I, WEIGHT *w, QUEUE *occ, size_t item, int core_id);
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/*************************************************************************/
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/* check all rules for an itemset and all items */
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/*************************************************************************/
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void ITEMSET_check_all_rule (ITEMSET *I, WEIGHT *w, QUEUE *occ, QUEUE *jump, WEIGHT total, int core_id);
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#endif
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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
|
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_c_
|
15
|
+
#define _problem_c_
|
16
|
+
|
17
|
+
#include"problem.h"
|
18
|
+
|
19
|
+
#include"stdlib2.c"
|
20
|
+
#include"queue.c"
|
21
|
+
#include"itemset.c"
|
22
|
+
|
23
|
+
void PROBLEM_error (){
|
24
|
+
ERROR_MES = "command explanation";
|
25
|
+
EXIT;
|
26
|
+
}
|
27
|
+
|
28
|
+
/*************************************************************************/
|
29
|
+
/* PROBLEM and ITEMSET initialization */
|
30
|
+
/*************************************************************************/
|
31
|
+
void PROBLEM_init (PROBLEM *P){
|
32
|
+
P->start_time = clock();
|
33
|
+
RAND_INIT;
|
34
|
+
//ERROR_MES = NULL;
|
35
|
+
|
36
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
37
|
+
__load_from_memory_org2__ = __load_from_memory__ = __load_from_memory_org__;
|
38
|
+
#endif
|
39
|
+
|
40
|
+
P->problem = P->problem2 = 0;
|
41
|
+
P->prog = 0;
|
42
|
+
P->prog2 = 0;
|
43
|
+
P->input_fname = P->input_fname2 = P->output_fname = P->output_fname2 = NULL;
|
44
|
+
P->workdir = P->workdir2 = NULL;
|
45
|
+
P->weight_fname = P->header_fname = P->table_fname = P->sc_fname = NULL;
|
46
|
+
P->position_fname = P->position2_fname = NULL;
|
47
|
+
P->outperm_fname = NULL;
|
48
|
+
|
49
|
+
P->root = 0;
|
50
|
+
P->dir = P->edge_dir = 0;
|
51
|
+
P->th = P->th2 = P->th3 = 0;
|
52
|
+
P->ratio = P->ratio2 = 0;
|
53
|
+
P->num = P->siz = P->dim = P->len = P->width = P->height = 0;
|
54
|
+
P->rows = 0;
|
55
|
+
P->clms = 0;
|
56
|
+
P->gap_ub = INTHUGE;
|
57
|
+
P->gap_lb = 0;
|
58
|
+
P->xmax = P->ymax = P->pxmax = P->pymax = 0;
|
59
|
+
P->tmax = P->tmin = 0;
|
60
|
+
P->cost = P->cost2 = 0;
|
61
|
+
|
62
|
+
ITEMSET_init (&P->II);
|
63
|
+
ITEMSET_init (&P->II2);
|
64
|
+
|
65
|
+
P->vf = P->dep = NULL;
|
66
|
+
P->ff = INIT_QUEUE;
|
67
|
+
|
68
|
+
P->shift = NULL;
|
69
|
+
P->occ_w = P->occ_pw = P->occ_w2 = P->occ_pw2 = NULL;
|
70
|
+
P->buf = P->buf_org = NULL;
|
71
|
+
P->buf_end = 0;
|
72
|
+
|
73
|
+
P->itemjump = P->itemcand = P->vecjump = P->veccand = INIT_QUEUE; // for delivery
|
74
|
+
P->itemchr = P->vecchr = NULL;
|
75
|
+
P->OQ = P->OQ2 = P->VQ = P->VQ2 = NULL; // for delivery
|
76
|
+
P->itemary = NULL;
|
77
|
+
P->itemmark = P->itemflag = P->vecmark = P->vecflag = NULL; // mark for vector
|
78
|
+
P->occ_t = P->vecary = NULL;
|
79
|
+
P->oo = INIT_QUEUE;
|
80
|
+
P->vecw = NULL;
|
81
|
+
|
82
|
+
P->pat = NULL;
|
83
|
+
P->plen = P->perr = 0;
|
84
|
+
|
85
|
+
#ifdef _base_h_
|
86
|
+
P->B = INIT_BASE;
|
87
|
+
#endif
|
88
|
+
|
89
|
+
#ifdef _alist_h_
|
90
|
+
P->occ = INIT_MALIST;
|
91
|
+
P->itemlist = INIT_ALIST;
|
92
|
+
P->veclist = INIT_ALIST;
|
93
|
+
#endif
|
94
|
+
|
95
|
+
#ifdef _trsact_h_
|
96
|
+
TRSACT_init (&P->TT);
|
97
|
+
TRSACT_init (&P->TT2);
|
98
|
+
#endif
|
99
|
+
#ifdef _sgraph_h_
|
100
|
+
P->SG = INIT_SGRAPH;
|
101
|
+
P->SG2 = INIT_SGRAPH;
|
102
|
+
#endif
|
103
|
+
#ifdef _agraph_h_
|
104
|
+
P->AG = INIT_AGRAPH;
|
105
|
+
P->AG2 = INIT_AGRAPH;
|
106
|
+
#endif
|
107
|
+
#ifdef _seq_h_
|
108
|
+
SEQ_init (&P->SS);
|
109
|
+
SEQ_init (&P->SS2);
|
110
|
+
#endif
|
111
|
+
#ifdef _pos_h_
|
112
|
+
POS_init (&P->PS);
|
113
|
+
POS_init (&P->PS2);
|
114
|
+
P->PS.S = &P->SS;
|
115
|
+
P->PS2.S = &P->SS2;
|
116
|
+
P->PS.I = &P->II;
|
117
|
+
P->PS2.I = &P->II;
|
118
|
+
#endif
|
119
|
+
#ifdef _fstar_h_
|
120
|
+
P->FS = INIT_FSTAR;
|
121
|
+
P->FS2 = INIT_FSTAR;
|
122
|
+
#endif
|
123
|
+
|
124
|
+
#ifdef _vec_h_
|
125
|
+
P->MM = INIT_MAT;
|
126
|
+
P->MM2 = INIT_MAT;
|
127
|
+
P->SM = INIT_SMAT;
|
128
|
+
P->SM2 = INIT_SMAT;
|
129
|
+
P->FF = INIT_SETFAMILY;
|
130
|
+
P->FF2 = INIT_SETFAMILY;
|
131
|
+
#endif
|
132
|
+
|
133
|
+
#ifdef _barray_h_
|
134
|
+
P->BA = INIT_BARRAY;
|
135
|
+
P->BA2 = INIT_BARRAY;
|
136
|
+
#endif
|
137
|
+
}
|
138
|
+
|
139
|
+
/*************************************************************************/
|
140
|
+
/* PROBLEM load */
|
141
|
+
/*************************************************************************/
|
142
|
+
void PROBLEM_load (PROBLEM *P){
|
143
|
+
int f=0;
|
144
|
+
ITEMSET *II = &P->II;
|
145
|
+
/******************************/
|
146
|
+
#ifdef _trsact_h_
|
147
|
+
if ( P->TT.fname ){ TRSACT_load (&P->TT); if (ERROR_MES) goto ERR; }
|
148
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
149
|
+
__load_from_memory_org__ = __load_from_memory__;
|
150
|
+
#endif
|
151
|
+
if ( P->TT2.fname ){ TRSACT_load (&P->TT2); if (ERROR_MES) goto ERR; }
|
152
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
153
|
+
__load_from_memory_org__ = __load_from_memory__;
|
154
|
+
#endif
|
155
|
+
#endif
|
156
|
+
|
157
|
+
#ifdef _sgraph_h_
|
158
|
+
if ( P->SG.fname ){ SGRAPH_load (&P->SG); if (ERROR_MES) goto ERR; }
|
159
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
160
|
+
__load_from_memory_org__ = __load_from_memory__;
|
161
|
+
#endif
|
162
|
+
if ( P->SG2.fname ){ SGRAPH_load (&P->SG); if (ERROR_MES) goto ERR; }
|
163
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
164
|
+
__load_from_memory_org__ = __load_from_memory__;
|
165
|
+
#endif
|
166
|
+
#endif
|
167
|
+
|
168
|
+
#ifdef _agraph_h_
|
169
|
+
if ( P->AG.fname ){ AGRAPH_load (&P->AG); if (ERROR_MES) goto ERR;}
|
170
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
171
|
+
__load_from_memory_org__ = __load_from_memory__;
|
172
|
+
#endif
|
173
|
+
if ( P->AG2.fname ){ AGRAPH_load (&P->AG2); if (ERROR_MES) goto ERR; }
|
174
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
175
|
+
__load_from_memory_org__ = __load_from_memory__;
|
176
|
+
#endif
|
177
|
+
#endif
|
178
|
+
|
179
|
+
#ifdef _fstar_h_
|
180
|
+
if ( P->FS.fname ){ FSTAR_load (&P->FS); if (ERROR_MES) goto ERR; }
|
181
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
182
|
+
__load_from_memory_org__ = __load_from_memory__;
|
183
|
+
#endif
|
184
|
+
if ( P->FS2.fname ){ FSTAR_load (&P->FS2); if (ERROR_MES) goto ERR; }
|
185
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
186
|
+
__load_from_memory_org__ = __load_from_memory__;
|
187
|
+
#endif
|
188
|
+
#endif
|
189
|
+
|
190
|
+
#ifdef _vec_h_
|
191
|
+
if ( P->MM.fname ){ MAT_load (&P->MM); if (ERROR_MES) goto ERR; }
|
192
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
193
|
+
__load_from_memory_org__ = __load_from_memory__;
|
194
|
+
#endif
|
195
|
+
if ( P->MM2.fname ){ MAT_load (&P->MM2); if (ERROR_MES) goto ERR; }
|
196
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
197
|
+
__load_from_memory_org__ = __load_from_memory__;
|
198
|
+
#endif
|
199
|
+
if ( P->SM.fname ){ SMAT_load (&P->SM); if (ERROR_MES) goto ERR; }
|
200
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
201
|
+
__load_from_memory_org__ = __load_from_memory__;
|
202
|
+
#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
|
+
#endif
|
216
|
+
|
217
|
+
#ifdef _seq_h_
|
218
|
+
if ( P->SS.fname ){ SEQ_load (&P->SS); if (ERROR_MES) goto ERR; }
|
219
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
220
|
+
__load_from_memory_org__ = __load_from_memory__;
|
221
|
+
#endif
|
222
|
+
if ( P->SS2.fname ){ SEQ_load (&P->SS2); if (ERROR_MES) goto ERR; }
|
223
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
224
|
+
__load_from_memory_org__ = __load_from_memory__;
|
225
|
+
#endif
|
226
|
+
#endif
|
227
|
+
|
228
|
+
#ifdef _barray_h_
|
229
|
+
if ( P->BA.fname ){ BARRAY_load (&P->BA); if (ERROR_MES) goto ERR; }
|
230
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
231
|
+
__load_from_memory_org__ = __load_from_memory__;
|
232
|
+
#endif
|
233
|
+
if ( P->BA2.fname ){ BARRAY_load (&P->BA2); if (ERROR_MES) goto ERR; }
|
234
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
235
|
+
__load_from_memory_org__ = __load_from_memory__;
|
236
|
+
#endif
|
237
|
+
#endif
|
238
|
+
|
239
|
+
if (P->input_fname){ f=1; print_mes (II, " input: %s", P->input_fname); }
|
240
|
+
if (P->weight_fname){ f=1; print_mes (II, " weight: %s", P->weight_fname); }
|
241
|
+
if (P->output_fname){ f=1; print_mes (II, " output to: %s",P->output_fname); }
|
242
|
+
if ( f ) print_mes (II, "\n");
|
243
|
+
|
244
|
+
/******************************/
|
245
|
+
|
246
|
+
if ( !ERROR_MES ) return;
|
247
|
+
ERR:;
|
248
|
+
PROBLEM_end (P);
|
249
|
+
EXIT;
|
250
|
+
}
|
251
|
+
|
252
|
+
/* termination of problem */
|
253
|
+
void PROBLEM_end (PROBLEM *P){
|
254
|
+
ITEMSET *II = &P->II;
|
255
|
+
|
256
|
+
#ifdef _trsact_h_
|
257
|
+
TRSACT_end (&P->TT);
|
258
|
+
TRSACT_end (&P->TT2);
|
259
|
+
#endif
|
260
|
+
#ifdef _sgraph_h_
|
261
|
+
SGRAPH_end (&P->SG);
|
262
|
+
SGRAPH_end (&P->SG2);
|
263
|
+
#endif
|
264
|
+
#ifdef _agraph_h_
|
265
|
+
AGRAPH_end (&P->AG);
|
266
|
+
AGRAPH_end (&P->AG2);
|
267
|
+
#endif
|
268
|
+
#ifdef _seq_h_
|
269
|
+
SEQ_end (&P->SS);
|
270
|
+
SEQ_end (&P->SS2);
|
271
|
+
#endif
|
272
|
+
#ifdef _fstar_h_
|
273
|
+
FSTAR_end (&P->FS);
|
274
|
+
FSTAR_end (&P->FS2);
|
275
|
+
#endif
|
276
|
+
#ifdef _vec_h_
|
277
|
+
MAT_end (&P->MM);
|
278
|
+
MAT_end (&P->MM2);
|
279
|
+
SMAT_end (&P->SM);
|
280
|
+
SMAT_end (&P->SM2);
|
281
|
+
SETFAMILY_end (&P->FF);
|
282
|
+
SETFAMILY_end (&P->FF2);
|
283
|
+
#endif
|
284
|
+
#ifdef _pos_h_
|
285
|
+
POS_end (&P->PS);
|
286
|
+
POS_end (&P->PS2);
|
287
|
+
#endif
|
288
|
+
#ifdef _barray_h_
|
289
|
+
BARRAY_end (&P->BA);
|
290
|
+
BARRAY_end (&P->BA2);
|
291
|
+
#endif
|
292
|
+
|
293
|
+
/******************************/
|
294
|
+
|
295
|
+
mfree (P->vf, P->dep);
|
296
|
+
QUEUE_end (&P->ff);
|
297
|
+
|
298
|
+
ITEMSET_end (II);
|
299
|
+
ITEMSET_end (&P->II2);
|
300
|
+
|
301
|
+
if ( P->occ_pw2 != P->occ_pw && P->occ_pw2 != P->occ_w2 ) free2 (P->occ_pw2);
|
302
|
+
if ( P->occ_w2 != P->occ_w ) free2 (P->occ_w2);
|
303
|
+
if ( P->occ_pw != P->occ_w ) free2 (P->occ_pw);
|
304
|
+
mfree (P->shift, P->occ_t, P->occ_w);
|
305
|
+
|
306
|
+
if ( P->OQ ) free2 (P->OQ[0].v);
|
307
|
+
if ( P->OQ2 ) free2 (P->OQ2[0].v);
|
308
|
+
if ( P->VQ ) free2 (P->VQ[0].v);
|
309
|
+
if ( P->VQ2 ) free2 (P->VQ2[0].v);
|
310
|
+
mfree (P->OQ, P->OQ2, P->VQ, P->VQ2, P->itemchr, P->vecchr);
|
311
|
+
|
312
|
+
mfree (P->itemary, P->itemflag, P->itemmark, P->vecary, P->vecflag, P->vecmark, P->vecw);
|
313
|
+
QUEUE_end (&P->itemcand);
|
314
|
+
QUEUE_end (&P->itemjump);
|
315
|
+
|
316
|
+
QUEUE_end (&P->veccand);
|
317
|
+
QUEUE_end (&P->vecjump);
|
318
|
+
QUEUE_end (&P->oo);
|
319
|
+
|
320
|
+
free2 (P->buf_org);
|
321
|
+
|
322
|
+
#ifdef _alist_h_
|
323
|
+
MALIST_end (&P->occ);
|
324
|
+
ALIST_end (&P->itemlist);
|
325
|
+
ALIST_end (&P->veclist);
|
326
|
+
#endif
|
327
|
+
|
328
|
+
#ifdef _undo_h_
|
329
|
+
ALISTundo_end ();
|
330
|
+
#endif
|
331
|
+
|
332
|
+
P->end_time = clock();
|
333
|
+
if ( print_time_flag )
|
334
|
+
print_mes (II, "computation_time= %3f\n", ((double)(P->end_time-P->start_time))/CLOCKS_PER_SEC);
|
335
|
+
|
336
|
+
#ifdef _FILE2_LOAD_FROM_MEMORY_
|
337
|
+
__load_from_memory_org__ = __load_from_memory_org2__;
|
338
|
+
__write_to_memory__ = __write_to_memory_org__;
|
339
|
+
#endif
|
340
|
+
|
341
|
+
PROBLEM_init (P);
|
342
|
+
}
|
343
|
+
|
344
|
+
/* allocate arrays and structures */
|
345
|
+
void PROBLEM_alloc (PROBLEM *P, QUEUE_ID siz, QUEUE_ID siz2, size_t siz3, PERM *perm, int f){
|
346
|
+
PERM *p;
|
347
|
+
#ifdef _alist_h_
|
348
|
+
ALIST_ID i=0;
|
349
|
+
#endif
|
350
|
+
int j;
|
351
|
+
|
352
|
+
if ( f&PROBLEM_SHIFT ) calloc2 (P->shift, siz+2, goto ERR);
|
353
|
+
if ( f&PROBLEM_OCC_T ) calloc2 (P->occ_t, siz+2, goto ERR);
|
354
|
+
if ( f&(PROBLEM_OCC_W+PROBLEM_OCC_PW) ) calloc2 (P->occ_w, siz+2, goto ERR);
|
355
|
+
if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw, siz+2, goto ERR);
|
356
|
+
else P->occ_pw = P->occ_w;
|
357
|
+
if ( f&PROBLEM_OCC_W2 ){
|
358
|
+
calloc2 (P->occ_w2, siz+2, goto ERR);
|
359
|
+
if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw2, siz+2, goto ERR);
|
360
|
+
else P->occ_pw2 = P->occ_w2;
|
361
|
+
} else { P->occ_w2 = P->occ_w; P->occ_pw2 = P->occ_pw; }
|
362
|
+
|
363
|
+
if ( f&PROBLEM_ITEMFLAG ) calloc2 (P->itemflag, siz+2, goto ERR);
|
364
|
+
if ( f&PROBLEM_ITEMMARK ) calloc2 (P->itemmark, siz+2, goto ERR);
|
365
|
+
if ( f&PROBLEM_ITEMARY ) calloc2(P->itemary, siz+2, goto ERR);
|
366
|
+
if ( f&PROBLEM_ITEMCHR ) calloc2(P->itemchr, siz+2, goto ERR);
|
367
|
+
if ( f&PROBLEM_ITEMJUMP ) QUEUE_alloc (&P->itemjump, siz+2);
|
368
|
+
if ( f&PROBLEM_ITEMCAND ) QUEUE_alloc (&P->itemcand, siz+2);
|
369
|
+
|
370
|
+
if ( f&PROBLEM_VECFLAG ) calloc2 (P->vecflag, siz2+2, goto ERR);
|
371
|
+
if ( f&PROBLEM_VECMARK ) calloc2 (P->vecmark, siz2+2, goto ERR);
|
372
|
+
if ( f&PROBLEM_VECARY ) calloc2 (P->vecary, siz2+2, goto ERR);
|
373
|
+
if ( f&PROBLEM_VECCHR ) calloc2 (P->vecchr, siz2+2, goto ERR);
|
374
|
+
if ( f&PROBLEM_VECJUMP ) QUEUE_alloc (&P->vecjump, siz2+2);
|
375
|
+
if ( f&PROBLEM_VECCAND ) QUEUE_alloc (&P->veccand, siz2+2);
|
376
|
+
if ( f&PROBLEM_VECW ) calloc2 (P->vecw, siz2+2, goto ERR);
|
377
|
+
|
378
|
+
#ifdef _alist_h_
|
379
|
+
if ( f&PROBLEM_ITEMLIST ) ALIST_alloc (&P->itemlist, siz+2);
|
380
|
+
if ( f&PROBLEM_VECLIST ) ALIST_alloc (&P->veclist, siz2+2);
|
381
|
+
|
382
|
+
if ( f&PROBLEM_OCC3 ){
|
383
|
+
MALIST_alloc (&P->occ, siz, siz2+2); // element=>
|
384
|
+
if ( ERROR_MES ) goto ERR;
|
385
|
+
if ( f&PROBLEM_OCC2 ){
|
386
|
+
FLOOP (i, 0, siz) MALIST_ins_tail (&P->occ, (f&PROBLEM_OCC1)?siz2: 0, i, 0);
|
387
|
+
}
|
388
|
+
}
|
389
|
+
#endif
|
390
|
+
|
391
|
+
// set outperm
|
392
|
+
if ( P->outperm_fname ){
|
393
|
+
ARY_LOAD (p, int, j, P->outperm_fname, 1, EXIT);
|
394
|
+
if ( perm ){
|
395
|
+
FLOOP (j, 0, siz) perm[j] = p[perm[j]];
|
396
|
+
free2 (p);
|
397
|
+
} else perm = p;
|
398
|
+
}
|
399
|
+
ITEMSET_alloc (&P->II, P->output_fname, perm, siz, siz3);
|
400
|
+
if ( P->II.target<siz && P->II.perm )
|
401
|
+
FLOOP (j, 0, P->II.item_max){ if ( P->II.target == P->II.perm[j] ){ P->II.target = j; break; } }
|
402
|
+
|
403
|
+
#ifdef _undo_h_
|
404
|
+
ALISTundo_init ();
|
405
|
+
#endif
|
406
|
+
|
407
|
+
return;
|
408
|
+
ERR:;
|
409
|
+
PROBLEM_end (P);
|
410
|
+
EXIT;
|
411
|
+
}
|
412
|
+
|
413
|
+
#endif
|
414
|
+
|
415
|
+
|