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nauty/nauty-unbundle-cliquer.patch

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--- a/Makefile.am
+++ b/Makefile.am
@@ -166,11 +166,11 @@
AM_LDFLAGS =
LDADD =
-NAUTY_LDADD = $(top_builddir)/libnauty.la $(threadlib)
-NAUTYW0_LDADD = $(top_builddir)/libnautyW0.la $(threadlib)
-NAUTYW1_LDADD = $(top_builddir)/libnautyW1.la $(threadlib)
-NAUTYL1_LDADD = $(top_builddir)/libnautyL1.la $(threadlib)
-NAUTYS1_LDADD = $(top_builddir)/libnautyS1.la $(threadlib)
+NAUTY_LDADD = $(top_builddir)/libnauty.la -lcliquer $(threadlib)
+NAUTYW0_LDADD = $(top_builddir)/libnautyW0.la -lcliquer $(threadlib)
+NAUTYW1_LDADD = $(top_builddir)/libnautyW1.la -lcliquer $(threadlib)
+NAUTYL1_LDADD = $(top_builddir)/libnautyL1.la -lcliquer $(threadlib)
+NAUTYS1_LDADD = $(top_builddir)/libnautyS1.la -lcliquer $(threadlib)
AM_H2MFLAGS = \
--manual="Nauty Manual" \
@@ -449,7 +449,7 @@
libnautyL1_la_LD_VERSION_SCRIPT += -Wl,--version-script=$(top_builddir)/$(libnautyL1_la_MAP)
endif
-libnauty_la_LIBADD = $(threadlib)
+libnauty_la_LIBADD = -lcliquer $(threadlib)
libnauty_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnauty_la_LD_VERSION_SCRIPT)
libnauty_la_SOURCES = \
@@ -473,43 +473,43 @@
libnautyA1_la_DEPENDENCIES = $(libnautyA1_la_MAP)
libnautyA1_la_CPPFLAGS = $(nautyA1_flavour_CPPFLAGS)
-libnautyA1_la_LIBADD = $(threadlib)
+libnautyA1_la_LIBADD = -lcliquer $(threadlib)
libnautyA1_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyA1_la_LD_VERSION_SCRIPT)
libnautyA1_la_SOURCES =$(libnauty_la_SOURCES)
libnautyS0_la_DEPENDENCIES = $(libnautyS0_la_MAP)
libnautyS0_la_CPPFLAGS = $(nautyS0_flavour_CPPFLAGS)
-libnautyS0_la_LIBADD = $(threadlib)
+libnautyS0_la_LIBADD = -lcliquer $(threadlib)
libnautyS0_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyS0_la_LD_VERSION_SCRIPT)
libnautyS0_la_SOURCES =$(libnauty_la_SOURCES)
libnautyS1_la_DEPENDENCIES = $(libnautyS1_la_MAP)
libnautyS1_la_CPPFLAGS = $(nautyS1_flavour_CPPFLAGS)
-libnautyS1_la_LIBADD = $(threadlib)
+libnautyS1_la_LIBADD = -lcliquer $(threadlib)
libnautyS1_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyS1_la_LD_VERSION_SCRIPT)
libnautyS1_la_SOURCES =$(libnauty_la_SOURCES)
libnautyW0_la_DEPENDENCIES = $(libnautyW0_la_MAP)
libnautyW0_la_CPPFLAGS = $(nautyW0_flavour_CPPFLAGS)
-libnautyW0_la_LIBADD = $(threadlib)
+libnautyW0_la_LIBADD = -lcliquer $(threadlib)
libnautyW0_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyW0_la_LD_VERSION_SCRIPT)
libnautyW0_la_SOURCES =$(libnauty_la_SOURCES)
libnautyW1_la_DEPENDENCIES = $(libnautyW1_la_MAP)
libnautyW1_la_CPPFLAGS = $(nautyW1_flavour_CPPFLAGS)
-libnautyW1_la_LIBADD = $(threadlib)
+libnautyW1_la_LIBADD = -lcliquer $(threadlib)
libnautyW1_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyW1_la_LD_VERSION_SCRIPT)
libnautyW1_la_SOURCES =$(libnauty_la_SOURCES)
libnautyL0_la_DEPENDENCIES = $(libnautyL0_la_MAP)
libnautyL0_la_CPPFLAGS = $(nautyL0_flavour_CPPFLAGS)
-libnautyL0_la_LIBADD = $(threadlib)
+libnautyL0_la_LIBADD = -lcliquer $(threadlib)
libnautyL0_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyL0_la_LD_VERSION_SCRIPT)
libnautyL0_la_SOURCES =$(libnauty_la_SOURCES)
libnautyL1_la_DEPENDENCIES = $(libnautyL1_la_MAP)
libnautyL1_la_CPPFLAGS = $(nautyL1_flavour_CPPFLAGS)
-libnautyL1_la_LIBADD = $(threadlib)
+libnautyL1_la_LIBADD = -lcliquer $(threadlib)
libnautyL1_la_LDFLAGS = -version-info $(LIBNAUTY_LT_VERSION) $(libnautyL1_la_LD_VERSION_SCRIPT)
libnautyL1_la_SOURCES =$(libnauty_la_SOURCES)
@@ -540,17 +540,17 @@
nautestL_SOURCES = nauty.h naututil.h nautest.c
dreadtest_LDADD = $(NAUTY_LDADD)
-dreadtest1_LDADD = $(top_builddir)/libnautyA1.la $(threadlib)
-dreadtestS_LDADD = $(top_builddir)/libnautyS0.la $(threadlib)
-dreadtestS1_LDADD = $(top_builddir)/libnautyS1.la $(threadlib)
-dreadtestW_LDADD = $(top_builddir)/libnautyW0.la $(threadlib)
-dreadtestW1_LDADD = $(top_builddir)/libnautyW1.la $(threadlib)
-dreadtestL_LDADD = $(top_builddir)/libnautyL0.la $(threadlib)
-dreadtestL1_LDADD = $(top_builddir)/libnautyL1.la $(threadlib)
-dreadtest4K_LDADD = $(threadlib)
-nautestS_LDADD = $(top_builddir)/libnautyS0.la $(threadlib)
-nautestW_LDADD = $(top_builddir)/libnautyW0.la $(threadlib)
-nautestL_LDADD = $(top_builddir)/libnautyL0.la $(threadlib)
+dreadtest1_LDADD = $(top_builddir)/libnautyA1.la -lcliquer $(threadlib)
+dreadtestS_LDADD = $(top_builddir)/libnautyS0.la -lcliquer $(threadlib)
+dreadtestS1_LDADD = $(top_builddir)/libnautyS1.la -lcliquer $(threadlib)
+dreadtestW_LDADD = $(top_builddir)/libnautyW0.la -lcliquer $(threadlib)
+dreadtestW1_LDADD = $(top_builddir)/libnautyW1.la -lcliquer $(threadlib)
+dreadtestL_LDADD = $(top_builddir)/libnautyL0.la -lcliquer $(threadlib)
+dreadtestL1_LDADD = $(top_builddir)/libnautyL1.la -lcliquer $(threadlib)
+dreadtest4K_LDADD = -lcliquer $(threadlib)
+nautestS_LDADD = $(top_builddir)/libnautyS0.la -lcliquer $(threadlib)
+nautestW_LDADD = $(top_builddir)/libnautyW0.la -lcliquer $(threadlib)
+nautestL_LDADD = $(top_builddir)/libnautyL0.la -lcliquer $(threadlib)
CLEANFILES = \
$(man_MANS) \
--- a/nautycliquer.c
+++ b/nautycliquer.c
@@ -18,2573 +18,6 @@
#include "nautycliquer.h"
-/*
- * This file contains the clique searching routines.
- *
- * Copyright (C) 2002 Sampo Niskanen, Patric <20>sterg<72>rd.
- * Licensed under the GNU GPL, read the file LICENSE for details.
- * This version covered by nauty&Traces licence, see file COPYRIGHT.
- */
-
-/*
-#include <stdio.h>
-#include <stdlib.h>
-#include <limits.h>
-#include <unistd.h>
-#include <sys/time.h>
-#include <sys/times.h>
-
-#include "cliquer.h"
-*/
-
-
-/* Default cliquer options; no TLS_ATTR on this one */
-static clique_options clique_default_options_struct = {
- reorder_by_default, NULL, clique_print_time, NULL, NULL, NULL, NULL, 0
-};
-clique_options *clique_default_options=&clique_default_options_struct;
-
-
-/* Calculate d/q, rounding result upwards/downwards. */
-#define DIV_UP(d,q) (((d)+(q)-1)/(q))
-#define DIV_DOWN(d,q) ((int)((d)/(q)))
-
-
-/* Global variables used: */
-/* These must be saved and restored in re-entrance. */
-static TLS_ATTR int *clique_size; /* c[i] == max. clique size in {0,1,...,i-1} */
-static TLS_ATTR set_t current_clique; /* Current clique being searched. */
-static TLS_ATTR set_t best_clique; /* Largest/heaviest clique found so far. */
-#if 0
-static struct tms cputimer; /* Timer for opts->time_function() */
-static struct timeval realtimer; /* Timer for opts->time_function() */
-#endif
-static TLS_ATTR int clique_list_count=0; /* No. of cliques in opts->clique_list[] */
-static TLS_ATTR int weight_multiplier=1; /* Weights multiplied by this when passing
- * to time_function(). */
-
-/* List cache (contains memory blocks of size g->n * sizeof(int)) */
-static TLS_ATTR int **temp_list=NULL;
-static TLS_ATTR int temp_count=0;
-
-
-/*
- * Macros for re-entrance. ENTRANCE_SAVE() must be called immediately
- * after variable definitions, ENTRANCE_RESTORE() restores global
- * variables to original values. entrance_level should be increased
- * and decreased accordingly.
- */
-static int entrance_level=0; /* How many levels for entrance have occurred? */
-
-#define ENTRANCE_SAVE() \
-int *old_clique_size = clique_size; \
-set_t old_current_clique = current_clique; \
-set_t old_best_clique = best_clique; \
-int old_clique_list_count = clique_list_count; \
-int old_weight_multiplier = weight_multiplier; \
-int **old_temp_list = temp_list; \
-int old_temp_count = temp_count;
-/*
-struct tms old_cputimer; \
-struct timeval old_realtimer; \
-memcpy(&old_cputimer,&cputimer,sizeof(struct tms)); \
-memcpy(&old_realtimer,&realtimer,sizeof(struct timeval))
-*/
-
-#define ENTRANCE_RESTORE() \
-clique_size = old_clique_size; \
-current_clique = old_current_clique; \
-best_clique = old_best_clique; \
-clique_list_count = old_clique_list_count; \
-weight_multiplier = old_weight_multiplier; \
-temp_list = old_temp_list;
-/*
-temp_count = old_temp_count; \
-memcpy(&cputimer,&old_cputimer,sizeof(struct tms)); \
-memcpy(&realtimer,&old_realtimer,sizeof(struct timeval));
-temp_count = old_temp_count;
-*/
-
-
-/* Number of clock ticks per second (as returned by sysconf(_SC_CLK_TCK)) */
-static int clocks_per_sec=0;
-
-
-
-/* Recursion and helper functions */
-static boolean sub_unweighted_single(int *table, int size, int min_size,
- graph_t *g);
-static int sub_unweighted_all(int *table, int size, int min_size, int max_size,
- boolean maximal, graph_t *g,
- clique_options *opts);
-static int sub_weighted_all(int *table, int size, int weight,
- int current_weight, int prune_low, int prune_high,
- int min_weight, int max_weight, boolean maximal,
- graph_t *g, clique_options *opts);
-
-
-static boolean store_clique(set_t clique, graph_t *g, clique_options *opts);
-static boolean is_maximal(set_t clique, graph_t *g);
-static boolean false_function(set_t clique,graph_t *g,clique_options *opts);
-
-/***** Unweighted searches *****/
-/*
- * Unweighted searches are done separately from weighted searches because
- * some effective pruning methods can be used when the vertex weights
- * are all 1. Single and all clique finding routines are separated,
- * because the single clique finding routine can store the found clique
- * while it is returning from the recursion, thus requiring no implicit
- * storing of the current clique. When searching for all cliques the
- * current clique must be stored.
- */
-
-
-/*
- * unweighted_clique_search_single()
- *
- * Searches for a single clique of size min_size. Stores maximum clique
- * sizes into clique_size[].
- *
- * table - the order of the vertices in g to use
- * min_size - minimum size of clique to search for. If min_size==0,
- * searches for a maximum clique.
- * g - the graph
- * opts - time printing options
- *
- * opts->time_function is called after each base-level recursion, if
- * non-NULL. (NOT IN THIS VERSION)
- *
- * Returns the size of the clique found, or 0 if min_size>0 and a clique
- * of that size was not found (or if time_function aborted the search).
- * The largest clique found is stored in current_clique.
- *
- * Note: Does NOT use opts->user_function of opts->clique_list.
- */
-static int unweighted_clique_search_single(int *table, int min_size,
- graph_t *g, clique_options *opts) {
-#if 0
- struct tms tms;
- struct timeval timeval;
-#endif
- int i,j;
- int v,w;
- int *newtable;
- int newsize;
-
- v=table[0];
- clique_size[v]=1;
- set_empty(current_clique);
- SET_ADD_ELEMENT(current_clique,v);
- if (min_size==1)
- return 1;
-
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
- for (i=1; i < g->n; i++) {
- w=v;
- v=table[i];
-
- newsize=0;
- for (j=0; j<i; j++) {
- if (GRAPH_IS_EDGE(g, v, table[j])) {
- newtable[newsize]=table[j];
- newsize++;
- }
- }
-
- if (sub_unweighted_single(newtable,newsize,clique_size[w],g)) {
- SET_ADD_ELEMENT(current_clique,v);
- clique_size[v]=clique_size[w]+1;
- } else {
- clique_size[v]=clique_size[w];
- }
-
-#if 0
- if (opts && opts->time_function) {
- gettimeofday(&timeval,NULL);
- times(&tms);
- if (!opts->time_function(entrance_level,
- i+1,g->n,clique_size[v] *
- weight_multiplier,
- (double)(tms.tms_utime-
- cputimer.tms_utime)/
- clocks_per_sec,
- timeval.tv_sec-
- realtimer.tv_sec+
- (double)(timeval.tv_usec-
- realtimer.tv_usec)/
- 1000000,opts)) {
- temp_list[temp_count++]=newtable;
- return 0;
- }
- }
-#endif
-
- if (min_size) {
- if (clique_size[v]>=min_size) {
- temp_list[temp_count++]=newtable;
- return clique_size[v];
- }
- if (clique_size[v]+g->n-i-1 < min_size) {
- temp_list[temp_count++]=newtable;
- return 0;
- }
- }
- }
-
- temp_list[temp_count++]=newtable;
-
- if (min_size)
- return 0;
- return clique_size[v];
-}
-
-/*
- * sub_unweighted_single()
- *
- * Recursion function for searching for a single clique of size min_size.
- *
- * table - subset of the vertices in graph
- * size - size of table
- * min_size - size of clique to look for within the subgraph
- * (decreased with every recursion)
- * g - the graph
- *
- * Returns TRUE if a clique of size min_size is found, FALSE otherwise.
- * If a clique of size min_size is found, it is stored in current_clique.
- *
- * clique_size[] for all values in table must be defined and correct,
- * otherwise inaccurate results may occur.
- */
-static boolean sub_unweighted_single(int *table, int size, int min_size,
- graph_t *g) {
- int i;
- int v;
- int *newtable;
- int *p1, *p2;
-
- /* Zero or one vertices needed anymore. */
- if (min_size <= 1) {
- if (size>0 && min_size==1) {
- set_empty(current_clique);
- SET_ADD_ELEMENT(current_clique,table[0]);
- return TRUE;
- }
- if (min_size==0) {
- set_empty(current_clique);
- return TRUE;
- }
- return FALSE;
- }
- if (size < min_size)
- return FALSE;
-
- /* Dynamic memory allocation with cache */
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- for (i = size-1; i >= 0; i--) {
- v = table[i];
-
- if (clique_size[v] < min_size)
- break;
- /* This is faster when compiling with gcc than placing
- * this in the for-loop condition. */
- if (i+1 < min_size)
- break;
-
- /* Very ugly code, but works faster than "for (i=...)" */
- p1 = newtable;
- for (p2=table; p2 < table+i; p2++) {
- int w = *p2;
- if (GRAPH_IS_EDGE(g, v, w)) {
- *p1 = w;
- p1++;
- }
- }
-
- /* Avoid unneccessary loops (next size == p1-newtable) */
- if (p1-newtable < min_size-1)
- continue;
- /* Now p1-newtable >= min_size-1 >= 2-1 == 1, so we can use
- * p1-newtable-1 safely. */
- if (clique_size[newtable[p1-newtable-1]] < min_size-1)
- continue;
-
- if (sub_unweighted_single(newtable,p1-newtable,
- min_size-1,g)) {
- /* Clique found. */
- SET_ADD_ELEMENT(current_clique,v);
- temp_list[temp_count++]=newtable;
- return TRUE;
- }
- }
- temp_list[temp_count++]=newtable;
- return FALSE;
-}
-
-
-/*
- * unweighted_clique_search_all()
- *
- * Searches for all cliques with size at least min_size and at most
- * max_size. Stores the cliques as opts declares.
- *
- * table - the order of the vertices in g to search
- * start - first index where the subgraph table[0], ..., table[start]
- * might include a requested kind of clique
- * min_size - minimum size of clique to search for. min_size > 0 !
- * max_size - maximum size of clique to search for. If no upper limit
- * is desired, use eg. INT_MAX
- * maximal - requires cliques to be maximal
- * g - the graph
- * opts - time printing and clique storage options
- *
- * Cliques found are stored as defined by opts->user_function and
- * opts->clique_list. opts->time_function is called after each
- * base-level recursion, if non-NULL.
- *
- * clique_size[] must be defined and correct for all values of
- * table[0], ..., table[start-1].
- *
- * Returns the number of cliques stored (not neccessarily number of cliques
- * in graph, if user/time_function aborts).
- */
-static int unweighted_clique_search_all(int *table, int start,
- int min_size, int max_size,
- boolean maximal, graph_t *g,
- clique_options *opts) {
-#if 0
- struct timeval timeval;
- struct tms tms;
-#endif
- int i,j;
- int v;
- int *newtable;
- int newsize;
- int count=0;
-
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- clique_list_count=0;
- set_empty(current_clique);
- for (i=start; i < g->n; i++) {
- v=table[i];
- clique_size[v]=min_size; /* Do not prune here. */
-
- newsize=0;
- for (j=0; j<i; j++) {
- if (GRAPH_IS_EDGE(g,v,table[j])) {
- newtable[newsize]=table[j];
- newsize++;
- }
- }
-
- SET_ADD_ELEMENT(current_clique,v);
- j=sub_unweighted_all(newtable,newsize,min_size-1,max_size-1,
- maximal,g,opts);
- SET_DEL_ELEMENT(current_clique,v);
- if (j<0) {
- /* Abort. */
- count-=j;
- break;
- }
- count+=j;
-
-#if 0
- if (opts->time_function) {
- gettimeofday(&timeval,NULL);
- times(&tms);
- if (!opts->time_function(entrance_level,
- i+1,g->n,min_size *
- weight_multiplier,
- (double)(tms.tms_utime-
- cputimer.tms_utime)/
- clocks_per_sec,
- timeval.tv_sec-
- realtimer.tv_sec+
- (double)(timeval.tv_usec-
- realtimer.tv_usec)/
- 1000000,opts)) {
- /* Abort. */
- break;
- }
- }
-#endif
- }
- temp_list[temp_count++]=newtable;
- return count;
-}
-
-/*
- * sub_unweighted_all()
- *
- * Recursion function for searching for all cliques of given size.
- *
- * table - subset of vertices of graph g
- * size - size of table
- * min_size - minimum size of cliques to search for (decreased with
- * every recursion)
- * max_size - maximum size of cliques to search for (decreased with
- * every recursion). If no upper limit is desired, use
- * eg. INT_MAX
- * maximal - require cliques to be maximal (passed through)
- * g - the graph
- * opts - storage options
- *
- * All cliques of suitable size found are stored according to opts.
- *
- * Returns the number of cliques found. If user_function returns FALSE,
- * then the number of cliques is returned negative.
- *
- * Uses current_clique to store the currently-being-searched clique.
- * clique_size[] for all values in table must be defined and correct,
- * otherwise inaccurate results may occur.
- */
-static int sub_unweighted_all(int *table, int size, int min_size, int max_size,
- boolean maximal, graph_t *g,
- clique_options *opts) {
- int i;
- int v;
- int n;
- int *newtable;
- int *p1, *p2;
- int count=0; /* Amount of cliques found */
-
- if (min_size <= 0) {
- if ((!maximal) || is_maximal(current_clique,g)) {
- /* We've found one. Store it. */
- count++;
- if (!store_clique(current_clique,g,opts)) {
- return -count;
- }
- }
- if (max_size <= 0) {
- /* If we add another element, size will be too big. */
- return count;
- }
- }
-
- if (size < min_size) {
- return count;
- }
-
- /* Dynamic memory allocation with cache */
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- for (i=size-1; i>=0; i--) {
- v = table[i];
- if (clique_size[v] < min_size) {
- break;
- }
- if (i+1 < min_size) {
- break;
- }
-
- /* Very ugly code, but works faster than "for (i=...)" */
- p1 = newtable;
- for (p2=table; p2 < table+i; p2++) {
- int w = *p2;
- if (GRAPH_IS_EDGE(g, v, w)) {
- *p1 = w;
- p1++;
- }
- }
-
- /* Avoid unneccessary loops (next size == p1-newtable) */
- if (p1-newtable < min_size-1) {
- continue;
- }
-
- SET_ADD_ELEMENT(current_clique,v);
- n=sub_unweighted_all(newtable,p1-newtable,
- min_size-1,max_size-1,maximal,g,opts);
- SET_DEL_ELEMENT(current_clique,v);
- if (n < 0) {
- /* Abort. */
- count -= n;
- count = -count;
- break;
- }
- count+=n;
- }
- temp_list[temp_count++]=newtable;
- return count;
-}
-
-
-
-
-/***** Weighted clique searches *****/
-/*
- * Weighted clique searches can use the same recursive routine, because
- * in both cases (single/all) they have to search through all potential
- * permutations searching for heavier cliques.
- */
-
-
-/*
- * weighted_clique_search_single()
- *
- * Searches for a single clique of weight at least min_weight, and at
- * most max_weight. Stores maximum clique sizes into clique_size[]
- * (or min_weight-1, whichever is smaller).
- *
- * table - the order of the vertices in g to use
- * min_weight - minimum weight of clique to search for. If min_weight==0,
- * then searches for a maximum weight clique
- * max_weight - maximum weight of clique to search for. If no upper limit
- * is desired, use eg. INT_MAX
- * g - the graph
- * opts - time printing options
- *
- * opts->time_function is called after each base-level recursion, if
- * non-NULL.
- *
- * Returns 0 if a clique of requested weight was not found (also if
- * time_function requested an abort), otherwise returns >= 1.
- * If min_weight==0 (search for maximum-weight clique), then the return
- * value is the weight of the clique found. The found clique is stored
- * in best_clique.
- *
- * Note: Does NOT use opts->user_function of opts->clique_list.
- */
-static int weighted_clique_search_single(int *table, int min_weight,
- int max_weight, graph_t *g,
- clique_options *opts) {
-#if 0
- struct timeval timeval;
- struct tms tms;
-#endif
- int i,j;
- int v;
- int *newtable;
- int newsize;
- int newweight;
- int search_weight;
- int min_w;
- clique_options localopts;
-
- if (min_weight==0)
- min_w=INT_MAX;
- else
- min_w=min_weight;
-
-
- if (min_weight==1) {
- /* min_weight==1 may cause trouble in the routine, and
- * it's trivial to check as it's own case.
- * We write nothing to clique_size[]. */
- for (i=0; i < g->n; i++) {
- if (g->weights[table[i]] <= max_weight) {
- set_empty(best_clique);
- SET_ADD_ELEMENT(best_clique,table[i]);
- return g->weights[table[i]];
- }
- }
- return 0;
- }
-
- localopts.time_function=NULL;
- localopts.reorder_function=NULL;
- localopts.reorder_map=NULL;
- localopts.user_function=false_function;
- localopts.user_data=NULL;
- localopts.clique_list=&best_clique;
- localopts.clique_list_length=1;
- clique_list_count=0;
-
- v=table[0];
- set_empty(best_clique);
- SET_ADD_ELEMENT(best_clique,v);
- search_weight=g->weights[v];
- if (min_weight && (search_weight >= min_weight)) {
- if (search_weight <= max_weight) {
- /* Found suitable clique. */
- return search_weight;
- }
- search_weight=min_weight-1;
- }
- clique_size[v]=search_weight;
- set_empty(current_clique);
-
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- for (i = 1; i < g->n; i++) {
- v=table[i];
-
- newsize=0;
- newweight=0;
- for (j=0; j<i; j++) {
- if (GRAPH_IS_EDGE(g,v,table[j])) {
- newweight += g->weights[table[j]];
- newtable[newsize]=table[j];
- newsize++;
- }
- }
-
-
- SET_ADD_ELEMENT(current_clique,v);
- search_weight=sub_weighted_all(newtable,newsize,newweight,
- g->weights[v],search_weight,
- clique_size[table[i-1]] +
- g->weights[v],
- min_w,max_weight,FALSE,
- g,&localopts);
- SET_DEL_ELEMENT(current_clique,v);
- if (search_weight < 0) {
- break;
- }
-
- clique_size[v]=search_weight;
-
-#if 0
- if (opts->time_function) {
- gettimeofday(&timeval,NULL);
- times(&tms);
- if (!opts->time_function(entrance_level,
- i+1,g->n,clique_size[v] *
- weight_multiplier,
- (double)(tms.tms_utime-
- cputimer.tms_utime)/
- clocks_per_sec,
- timeval.tv_sec-
- realtimer.tv_sec+
- (double)(timeval.tv_usec-
- realtimer.tv_usec)/
- 1000000,opts)) {
- set_free(current_clique);
- current_clique=NULL;
- break;
- }
- }
-#endif
- }
- temp_list[temp_count++]=newtable;
- if (min_weight && (search_weight > 0)) {
- /* Requested clique has not been found. */
- return 0;
- }
- return clique_size[table[i-1]];
-}
-
-
-/*
- * weighted_clique_search_all()
- *
- * Searches for all cliques with weight at least min_weight and at most
- * max_weight. Stores the cliques as opts declares.
- *
- * table - the order of the vertices in g to search
- * start - first index where the subgraph table[0], ..., table[start]
- * might include a requested kind of clique
- * min_weight - minimum weight of clique to search for. min_weight > 0 !
- * max_weight - maximum weight of clique to search for. If no upper limit
- * is desired, use eg. INT_MAX
- * maximal - search only for maximal cliques
- * g - the graph
- * opts - time printing and clique storage options
- *
- * Cliques found are stored as defined by opts->user_function and
- * opts->clique_list. opts->time_function is called after each
- * base-level recursion, if non-NULL.
- *
- * clique_size[] must be defined and correct for all values of
- * table[0], ..., table[start-1].
- *
- * Returns the number of cliques stored (not neccessarily number of cliques
- * in graph, if user/time_function aborts).
- */
-static int weighted_clique_search_all(int *table, int start,
- int min_weight, int max_weight,
- boolean maximal, graph_t *g,
- clique_options *opts) {
-#if 0
- struct timeval timeval;
- struct tms tms;
-#endif
- int i,j;
- int v;
- int *newtable;
- int newsize;
- int newweight;
-
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- clique_list_count=0;
- set_empty(current_clique);
- for (i=start; i < g->n; i++) {
- v=table[i];
- clique_size[v]=min_weight; /* Do not prune here. */
-
- newsize=0;
- newweight=0;
- for (j=0; j<i; j++) {
- if (GRAPH_IS_EDGE(g,v,table[j])) {
- newtable[newsize]=table[j];
- newweight+=g->weights[table[j]];
- newsize++;
- }
- }
-
- SET_ADD_ELEMENT(current_clique,v);
- j=sub_weighted_all(newtable,newsize,newweight,
- g->weights[v],min_weight-1,INT_MAX,
- min_weight,max_weight,maximal,g,opts);
- SET_DEL_ELEMENT(current_clique,v);
-
- if (j<0) {
- /* Abort. */
- break;
- }
-
-#if 0
- if (opts->time_function) {
- gettimeofday(&timeval,NULL);
- times(&tms);
- if (!opts->time_function(entrance_level,
- i+1,g->n,clique_size[v] *
- weight_multiplier,
- (double)(tms.tms_utime-
- cputimer.tms_utime)/
- clocks_per_sec,
- timeval.tv_sec-
- realtimer.tv_sec+
- (double)(timeval.tv_usec-
- realtimer.tv_usec)/
- 1000000,opts)) {
- set_free(current_clique);
- current_clique=NULL;
- break;
- }
- }
-#endif
- }
- temp_list[temp_count++]=newtable;
-
- return clique_list_count;
-}
-
-/*
- * sub_weighted_all()
- *
- * Recursion function for searching for all cliques of given weight.
- *
- * table - subset of vertices of graph g
- * size - size of table
- * weight - total weight of vertices in table
- * current_weight - weight of clique found so far
- * prune_low - ignore all cliques with weight less or equal to this value
- * (often heaviest clique found so far) (passed through)
- * prune_high - maximum weight possible for clique in this subgraph
- * (passed through)
- * min_size - minimum weight of cliques to search for (passed through)
- * Must be greater than 0.
- * max_size - maximum weight of cliques to search for (passed through)
- * If no upper limit is desired, use eg. INT_MAX
- * maximal - search only for maximal cliques
- * g - the graph
- * opts - storage options
- *
- * All cliques of suitable weight found are stored according to opts.
- *
- * Returns weight of heaviest clique found (prune_low if a heavier clique
- * hasn't been found); if a clique with weight at least min_size is found
- * then min_size-1 is returned. If clique storage failed, -1 is returned.
- *
- * The largest clique found smaller than max_weight is stored in
- * best_clique, if non-NULL.
- *
- * Uses current_clique to store the currently-being-searched clique.
- * clique_size[] for all values in table must be defined and correct,
- * otherwise inaccurate results may occur.
- *
- * To search for a single maximum clique, use min_weight==max_weight==INT_MAX,
- * with best_clique non-NULL. To search for a single given-weight clique,
- * use opts->clique_list and opts->user_function=false_function. When
- * searching for all cliques, min_weight should be given the minimum weight
- * desired.
- */
-static int sub_weighted_all(int *table, int size, int weight,
- int current_weight, int prune_low, int prune_high,
- int min_weight, int max_weight, boolean maximal,
- graph_t *g, clique_options *opts) {
- int i;
- int v,w;
- int *newtable;
- int *p1, *p2;
- int newweight;
-
- if (current_weight >= min_weight) {
- if ((current_weight <= max_weight) &&
- ((!maximal) || is_maximal(current_clique,g))) {
- /* We've found one. Store it. */
- if (!store_clique(current_clique,g,opts)) {
- return -1;
- }
- }
- if (current_weight >= max_weight) {
- /* Clique too heavy. */
- return min_weight-1;
- }
- }
- if (size <= 0) {
- /* current_weight < min_weight, prune_low < min_weight,
- * so return value is always < min_weight. */
- if (current_weight>prune_low) {
- if (best_clique)
- set_copy(best_clique,current_clique);
- if (current_weight < min_weight)
- return current_weight;
- else
- return min_weight-1;
- } else {
- return prune_low;
- }
- }
-
- /* Dynamic memory allocation with cache */
- if (temp_count) {
- temp_count--;
- newtable=temp_list[temp_count];
- } else {
- newtable=malloc(g->n * sizeof(int));
- }
-
- for (i = size-1; i >= 0; i--) {
- v = table[i];
- if (current_weight+clique_size[v] <= prune_low) {
- /* Dealing with subset without heavy enough clique. */
- break;
- }
- if (current_weight+weight <= prune_low) {
- /* Even if all elements are added, won't do. */
- break;
- }
-
- /* Very ugly code, but works faster than "for (i=...)" */
- p1 = newtable;
- newweight = 0;
- for (p2=table; p2 < table+i; p2++) {
- w = *p2;
- if (GRAPH_IS_EDGE(g, v, w)) {
- *p1 = w;
- newweight += g->weights[w];
- p1++;
- }
- }
-
- w=g->weights[v];
- weight-=w;
- /* Avoid a few unneccessary loops */
- if (current_weight+w+newweight <= prune_low) {
- continue;
- }
-
- SET_ADD_ELEMENT(current_clique,v);
- prune_low=sub_weighted_all(newtable,p1-newtable,
- newweight,
- current_weight+w,
- prune_low,prune_high,
- min_weight,max_weight,maximal,
- g,opts);
- SET_DEL_ELEMENT(current_clique,v);
- if ((prune_low<0) || (prune_low>=prune_high)) {
- /* Impossible to find larger clique. */
- break;
- }
- }
- temp_list[temp_count++]=newtable;
- return prune_low;
-}
-
-
-
-
-/***** Helper functions *****/
-
-
-/*
- * store_clique()
- *
- * Stores a clique according to given user options.
- *
- * clique - the clique to store
- * opts - storage options
- *
- * Returns FALSE if opts->user_function() returned FALSE; otherwise
- * returns TRUE.
- */
-static boolean store_clique(set_t clique, graph_t *g, clique_options *opts) {
-
- clique_list_count++;
-
- /* clique_list[] */
- if (opts->clique_list) {
- /*
- * This has been a major source of bugs:
- * Has clique_list_count been set to 0 before calling
- * the recursions?
- */
- if (clique_list_count <= 0) {
- fprintf(stderr,"CLIQUER INTERNAL ERROR: "
- "clique_list_count has negative value!\n");
- fprintf(stderr,"Please report as a bug.\n");
- abort();
- }
- if (clique_list_count <= opts->clique_list_length)
- opts->clique_list[clique_list_count-1] =
- set_duplicate(clique);
- }
-
- /* user_function() */
- if (opts->user_function) {
- if (!opts->user_function(clique,g,opts)) {
- /* User function requested abort. */
- return FALSE;
- }
- }
-
- return TRUE;
-}
-
-/*
- * maximalize_clique()
- *
- * Adds greedily all possible vertices in g to set s to make it a maximal
- * clique.
- *
- * s - clique of vertices to make maximal
- * g - graph
- *
- * Note: Not very optimized (uses a simple O(n^2) routine), but is called
- * at maximum once per clique_xxx() call, so it shouldn't matter.
- */
-static void maximalize_clique(set_t s,graph_t *g) {
- int i,j;
- boolean add;
-
- for (i=0; i < g->n; i++) {
- add=TRUE;
- for (j=0; j < g->n; j++) {
- if (SET_CONTAINS_FAST(s,j) && !GRAPH_IS_EDGE(g,i,j)) {
- add=FALSE;
- break;
- }
- }
- if (add) {
- SET_ADD_ELEMENT(s,i);
- }
- }
- return;
-}
-
-
-/*
- * is_maximal()
- *
- * Check whether a clique is maximal or not.
- *
- * clique - set of vertices in clique
- * g - graph
- *
- * Returns TRUE is clique is a maximal clique of g, otherwise FALSE.
- */
-static boolean is_maximal(set_t clique, graph_t *g) {
- int i,j;
- int *table;
- int len;
- boolean addable;
-
- if (temp_count) {
- temp_count--;
- table=temp_list[temp_count];
- } else {
- table=malloc(g->n * sizeof(int));
- }
-
- len=0;
- for (i=0; i < g->n; i++)
- if (SET_CONTAINS_FAST(clique,i))
- table[len++]=i;
-
- for (i=0; i < g->n; i++) {
- addable=TRUE;
- for (j=0; j<len; j++) {
- if (!GRAPH_IS_EDGE(g,i,table[j])) {
- addable=FALSE;
- break;
- }
- }
- if (addable) {
- temp_list[temp_count++]=table;
- return FALSE;
- }
- }
- temp_list[temp_count++]=table;
- return TRUE;
-}
-
-
-/*
- * false_function()
- *
- * Returns FALSE. Can be used as user_function.
- */
-static boolean false_function(set_t clique,graph_t *g,clique_options *opts) {
- return FALSE;
-}
-
-
-
-
-/***** API-functions *****/
-
-/*
- * clique_unweighted_max_weight()
- *
- * Returns the size of the maximum (sized) clique in g (or 0 if search
- * was aborted).
- *
- * g - the graph
- * opts - time printing options
- *
- * Note: As we don't have an algorithm faster than actually finding
- * a maximum clique, we use clique_unweighted_find_single().
- * This incurs only very small overhead.
- */
-int clique_unweighted_max_weight(graph_t *g, clique_options *opts) {
- set_t s;
- int size;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
-
- s=clique_unweighted_find_single(g,0,0,FALSE,opts);
- if (s==NULL) {
- /* Search was aborted. */
- return 0;
- }
- size=set_size(s);
- set_free(s);
- return size;
-}
-
-
-/*
- * clique_unweighted_find_single()
- *
- * Returns a clique with size at least min_size and at most max_size.
- *
- * g - the graph
- * min_size - minimum size of clique to search for. If min_size==0,
- * searches for maximum clique.
- * max_size - maximum size of clique to search for. If max_size==0, no
- * upper limit is used. If min_size==0, this must also be 0.
- * maximal - require returned clique to be maximal
- * opts - time printing options
- *
- * Returns the set of vertices forming the clique, or NULL if a clique
- * of requested size/maximality does not exist in the graph (or if
- * opts->time_function() requests abort).
- *
- * The returned clique is newly allocated and can be freed by set_free().
- *
- * Note: Does NOT use opts->user_function() or opts->clique_list[].
- */
-set_t clique_unweighted_find_single(graph_t *g,int min_size,int max_size,
- boolean maximal, clique_options *opts) {
- int i;
- int *table;
- set_t s;
-
- ENTRANCE_SAVE();
- entrance_level++;
-
- if (opts==NULL)
- opts=clique_default_options;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
- ASSERT(min_size>=0);
- ASSERT(max_size>=0);
- ASSERT((max_size==0) || (min_size <= max_size));
- ASSERT(!((min_size==0) && (max_size>0)));
- ASSERT((opts->reorder_function==NULL) || (opts->reorder_map==NULL));
-
- if ((max_size>0) && (min_size>max_size)) {
- /* state was not changed */
- entrance_level--;
- return NULL;
- }
-
-#if 0
- if (clocks_per_sec==0)
- clocks_per_sec=sysconf(_SC_CLK_TCK);
- ASSERT(clocks_per_sec>0);
-#endif
-
- /* Dynamic allocation */
- current_clique=set_new(g->n);
- clique_size=malloc(g->n * sizeof(int));
- /* table allocated later */
- temp_list=malloc((g->n+2)*sizeof(int *));
- temp_count=0;
-
-#if 0
- /* "start clock" */
- gettimeofday(&realtimer,NULL);
- times(&cputimer);
-#endif
-
- /* reorder */
- if (opts->reorder_function) {
- table=opts->reorder_function(g,FALSE);
- } else if (opts->reorder_map) {
- table=reorder_duplicate(opts->reorder_map,g->n);
- } else {
- table=reorder_ident(g->n);
- }
- ASSERT(reorder_is_bijection(table,g->n));
-
-
- if (unweighted_clique_search_single(table,min_size,g,opts)==0) {
- set_free(current_clique);
- current_clique=NULL;
- goto cleanreturn;
- }
- if (maximal && (min_size>0)) {
- maximalize_clique(current_clique,g);
-
- if ((max_size > 0) && (set_size(current_clique) > max_size)) {
- clique_options localopts;
-
- s = set_new(g->n);
- localopts.time_function = opts->time_function;
- localopts.output = opts->output;
- localopts.user_function = false_function;
- localopts.clique_list = &s;
- localopts.clique_list_length = 1;
-
- for (i=0; i < g->n-1; i++)
- if (clique_size[table[i]]>=min_size)
- break;
- if (unweighted_clique_search_all(table,i,min_size,
- max_size,maximal,
- g,&localopts)) {
- set_free(current_clique);
- current_clique=s;
- } else {
- set_free(current_clique);
- current_clique=NULL;
- }
- }
- }
-
- cleanreturn:
- s=current_clique;
-
- /* Free resources */
- for (i=0; i < temp_count; i++)
- free(temp_list[i]);
- free(temp_list);
- free(table);
- free(clique_size);
-
- ENTRANCE_RESTORE();
- entrance_level--;
-
- return s;
-}
-
-
-/*
- * clique_unweighted_find_all()
- *
- * Find all cliques with size at least min_size and at most max_size.
- *
- * g - the graph
- * min_size - minimum size of cliques to search for. If min_size==0,
- * searches for maximum cliques.
- * max_size - maximum size of cliques to search for. If max_size==0, no
- * upper limit is used. If min_size==0, this must also be 0.
- * maximal - require cliques to be maximal cliques
- * opts - time printing and clique storage options
- *
- * Returns the number of cliques found. This can be less than the number
- * of cliques in the graph iff opts->time_function() or opts->user_function()
- * returns FALSE (request abort).
- *
- * The cliques found are stored in opts->clique_list[] and
- * opts->user_function() is called with them (if non-NULL). The cliques
- * stored in opts->clique_list[] are newly allocated, and can be freed
- * by set_free().
- */
-int clique_unweighted_find_all(graph_t *g, int min_size, int max_size,
- boolean maximal, clique_options *opts) {
- int i;
- int *table;
- int count;
-
- ENTRANCE_SAVE();
- entrance_level++;
-
- if (opts==NULL)
- opts=clique_default_options;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
- ASSERT(min_size>=0);
- ASSERT(max_size>=0);
- ASSERT((max_size==0) || (min_size <= max_size));
- ASSERT(!((min_size==0) && (max_size>0)));
- ASSERT((opts->reorder_function==NULL) || (opts->reorder_map==NULL));
-
- if ((max_size>0) && (min_size>max_size)) {
- /* state was not changed */
- entrance_level--;
- return 0;
- }
-
-#if 0
- if (clocks_per_sec==0)
- clocks_per_sec=sysconf(_SC_CLK_TCK);
- ASSERT(clocks_per_sec>0);
-#endif
-
- /* Dynamic allocation */
- current_clique=set_new(g->n);
- clique_size=malloc(g->n * sizeof(int));
- /* table allocated later */
- temp_list=malloc((g->n+2)*sizeof(int *));
- temp_count=0;
-
- clique_list_count=0;
- memset(clique_size,0,g->n * sizeof(int));
-
-#if 0
- /* "start clock" */
- gettimeofday(&realtimer,NULL);
- times(&cputimer);
-#endif
-
- /* reorder */
- if (opts->reorder_function) {
- table=opts->reorder_function(g,FALSE);
- } else if (opts->reorder_map) {
- table=reorder_duplicate(opts->reorder_map,g->n);
- } else {
- table=reorder_ident(g->n);
- }
- ASSERT(reorder_is_bijection(table,g->n));
-
-
- /* Search as normal until there is a chance to find a suitable
- * clique. */
- if (unweighted_clique_search_single(table,min_size,g,opts)==0) {
- count=0;
- goto cleanreturn;
- }
-
- if (min_size==0 && max_size==0) {
- min_size=max_size=clique_size[table[g->n-1]];
- maximal=FALSE; /* No need to test, since we're searching
- * for maximum cliques. */
- }
- if (max_size==0) {
- max_size=INT_MAX;
- }
-
- for (i=0; i < g->n-1; i++)
- if (clique_size[table[i]] >= min_size)
- break;
- count=unweighted_clique_search_all(table,i,min_size,max_size,
- maximal,g,opts);
-
- cleanreturn:
- /* Free resources */
- for (i=0; i<temp_count; i++)
- free(temp_list[i]);
- free(temp_list);
- free(table);
- free(clique_size);
- set_free(current_clique);
-
- ENTRANCE_RESTORE();
- entrance_level--;
-
- return count;
-}
-
-
-
-
-/*
- * clique_max_weight()
- *
- * Returns the weight of the maximum weight clique in the graph (or 0 if
- * the search was aborted).
- *
- * g - the graph
- * opts - time printing options
- *
- * Note: As we don't have an algorithm faster than actually finding
- * a maximum weight clique, we use clique_find_single().
- * This incurs only very small overhead.
- */
-int clique_max_weight(graph_t *g,clique_options *opts) {
- set_t s;
- int weight;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
-
- s=clique_find_single(g,0,0,FALSE,opts);
- if (s==NULL) {
- /* Search was aborted. */
- return 0;
- }
- weight=graph_subgraph_weight(g,s);
- set_free(s);
- return weight;
-}
-
-
-/*
- * clique_find_single()
- *
- * Returns a clique with weight at least min_weight and at most max_weight.
- *
- * g - the graph
- * min_weight - minimum weight of clique to search for. If min_weight==0,
- * searches for a maximum weight clique.
- * max_weight - maximum weight of clique to search for. If max_weight==0,
- * no upper limit is used. If min_weight==0, max_weight must
- * also be 0.
- * maximal - require returned clique to be maximal
- * opts - time printing options
- *
- * Returns the set of vertices forming the clique, or NULL if a clique
- * of requested weight/maximality does not exist in the graph (or if
- * opts->time_function() requests abort).
- *
- * The returned clique is newly allocated and can be freed by set_free().
- *
- * Note: Does NOT use opts->user_function() or opts->clique_list[].
- * Note: Automatically uses clique_unweighted_find_single if all vertex
- * weights are the same.
- */
-set_t clique_find_single(graph_t *g,int min_weight,int max_weight,
- boolean maximal, clique_options *opts) {
- int i;
- int *table;
- set_t s;
-
- ENTRANCE_SAVE();
- entrance_level++;
-
- if (opts==NULL)
- opts=clique_default_options;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
- ASSERT(min_weight>=0);
- ASSERT(max_weight>=0);
- ASSERT((max_weight==0) || (min_weight <= max_weight));
- ASSERT(!((min_weight==0) && (max_weight>0)));
- ASSERT((opts->reorder_function==NULL) || (opts->reorder_map==NULL));
-
- if ((max_weight>0) && (min_weight>max_weight)) {
- /* state was not changed */
- entrance_level--;
- return NULL;
- }
-
-#if 0
- if (clocks_per_sec==0)
- clocks_per_sec=sysconf(_SC_CLK_TCK);
- ASSERT(clocks_per_sec>0);
-#endif
-
- /* Check whether we can use unweighted routines. */
- if (!graph_weighted(g)) {
- min_weight=DIV_UP(min_weight,g->weights[0]);
- if (max_weight) {
- max_weight=DIV_DOWN(max_weight,g->weights[0]);
- if (max_weight < min_weight) {
- /* state was not changed */
- entrance_level--;
- return NULL;
- }
- }
-
- weight_multiplier = g->weights[0];
- entrance_level--;
- s=clique_unweighted_find_single(g,min_weight,max_weight,
- maximal,opts);
- ENTRANCE_RESTORE();
- return s;
- }
-
- /* Dynamic allocation */
- current_clique=set_new(g->n);
- best_clique=set_new(g->n);
- clique_size=malloc(g->n * sizeof(int));
- memset(clique_size, 0, g->n * sizeof(int));
- /* table allocated later */
- temp_list=malloc((g->n+2)*sizeof(int *));
- temp_count=0;
-
- clique_list_count=0;
-
-#if 0
- /* "start clock" */
- gettimeofday(&realtimer,NULL);
- times(&cputimer);
-#endif
-
- /* reorder */
- if (opts->reorder_function) {
- table=opts->reorder_function(g,TRUE);
- } else if (opts->reorder_map) {
- table=reorder_duplicate(opts->reorder_map,g->n);
- } else {
- table=reorder_ident(g->n);
- }
- ASSERT(reorder_is_bijection(table,g->n));
-
- if (max_weight==0)
- max_weight=INT_MAX;
-
- if (weighted_clique_search_single(table,min_weight,max_weight,
- g,opts)==0) {
- /* Requested clique has not been found. */
- set_free(best_clique);
- best_clique=NULL;
- goto cleanreturn;
- }
- if (maximal && (min_weight>0)) {
- maximalize_clique(best_clique,g);
- if (graph_subgraph_weight(g,best_clique) > max_weight) {
- clique_options localopts;
-
- localopts.time_function = opts->time_function;
- localopts.output = opts->output;
- localopts.user_function = false_function;
- localopts.clique_list = &best_clique;
- localopts.clique_list_length = 1;
-
- for (i=0; i < g->n-1; i++)
- if ((clique_size[table[i]] >= min_weight) ||
- (clique_size[table[i]] == 0))
- break;
- if (!weighted_clique_search_all(table,i,min_weight,
- max_weight,maximal,
- g,&localopts)) {
- set_free(best_clique);
- best_clique=NULL;
- }
- }
- }
-
- cleanreturn:
- s=best_clique;
-
- /* Free resources */
- for (i=0; i < temp_count; i++)
- free(temp_list[i]);
- free(temp_list);
- temp_list=NULL;
- temp_count=0;
- free(table);
- set_free(current_clique);
- current_clique=NULL;
- free(clique_size);
- clique_size=NULL;
-
- ENTRANCE_RESTORE();
- entrance_level--;
-
- return s;
-}
-
-
-
-
-
-/*
- * clique_find_all()
- *
- * Find all cliques with weight at least min_weight and at most max_weight.
- *
- * g - the graph
- * min_weight - minimum weight of cliques to search for. If min_weight==0,
- * searches for maximum weight cliques.
- * max_weight - maximum weight of cliques to search for. If max_weight==0,
- * no upper limit is used. If min_weight==0, max_weight must
- * also be 0.
- * maximal - require cliques to be maximal cliques
- * opts - time printing and clique storage options
- *
- * Returns the number of cliques found. This can be less than the number
- * of cliques in the graph iff opts->time_function() or opts->user_function()
- * returns FALSE (request abort).
- *
- * The cliques found are stored in opts->clique_list[] and
- * opts->user_function() is called with them (if non-NULL). The cliques
- * stored in opts->clique_list[] are newly allocated, and can be freed
- * by set_free().
- *
- * Note: Automatically uses clique_unweighted_find_all if all vertex
- * weights are the same.
- */
-int clique_find_all(graph_t *g, int min_weight, int max_weight,
- boolean maximal, clique_options *opts) {
- int i,n;
- int *table;
-
- ENTRANCE_SAVE();
- entrance_level++;
-
- if (opts==NULL)
- opts=clique_default_options;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
- ASSERT(min_weight>=0);
- ASSERT(max_weight>=0);
- ASSERT((max_weight==0) || (min_weight <= max_weight));
- ASSERT(!((min_weight==0) && (max_weight>0)));
- ASSERT((opts->reorder_function==NULL) || (opts->reorder_map==NULL));
-
- if ((max_weight>0) && (min_weight>max_weight)) {
- /* state was not changed */
- entrance_level--;
- return 0;
- }
-
-#if 0
- if (clocks_per_sec==0)
- clocks_per_sec=sysconf(_SC_CLK_TCK);
- ASSERT(clocks_per_sec>0);
-#endif
-
- if (!graph_weighted(g)) {
- min_weight=DIV_UP(min_weight,g->weights[0]);
- if (max_weight) {
- max_weight=DIV_DOWN(max_weight,g->weights[0]);
- if (max_weight < min_weight) {
- /* state was not changed */
- entrance_level--;
- return 0;
- }
- }
-
- weight_multiplier = g->weights[0];
- entrance_level--;
- i=clique_unweighted_find_all(g,min_weight,max_weight,maximal,
- opts);
- ENTRANCE_RESTORE();
- return i;
- }
-
- /* Dynamic allocation */
- current_clique=set_new(g->n);
- best_clique=set_new(g->n);
- clique_size=malloc(g->n * sizeof(int));
- memset(clique_size, 0, g->n * sizeof(int));
- /* table allocated later */
- temp_list=malloc((g->n+2)*sizeof(int *));
- temp_count=0;
-
-#if 0
- /* "start clock" */
- gettimeofday(&realtimer,NULL);
- times(&cputimer);
-#endif
-
- /* reorder */
- if (opts->reorder_function) {
- table=opts->reorder_function(g,TRUE);
- } else if (opts->reorder_map) {
- table=reorder_duplicate(opts->reorder_map,g->n);
- } else {
- table=reorder_ident(g->n);
- }
- ASSERT(reorder_is_bijection(table,g->n));
-
- /* First phase */
- n=weighted_clique_search_single(table,min_weight,INT_MAX,g,opts);
- if (n==0) {
- /* Requested clique has not been found. */
- goto cleanreturn;
- }
-
- if (min_weight==0) {
- min_weight=n;
- max_weight=n;
- maximal=FALSE; /* They're maximum cliques already. */
- }
- if (max_weight==0)
- max_weight=INT_MAX;
-
- for (i=0; i < g->n; i++)
- if ((clique_size[table[i]] >= min_weight) ||
- (clique_size[table[i]] == 0))
- break;
-
- /* Second phase */
- n=weighted_clique_search_all(table,i,min_weight,max_weight,maximal,
- g,opts);
-
- cleanreturn:
- /* Free resources */
- for (i=0; i < temp_count; i++)
- free(temp_list[i]);
- free(temp_list);
- free(table);
- set_free(current_clique);
- set_free(best_clique);
- free(clique_size);
-
- ENTRANCE_RESTORE();
- entrance_level--;
-
- return n;
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-/*
- * clique_print_time()
- *
- * Reports current running information every 0.1 seconds or when values
- * change.
- *
- * level - re-entrance level
- * i - current recursion level
- * n - maximum recursion level
- * max - weight of heaviest clique found
- * cputime - CPU time used in algorithm so far
- * realtime - real time used in algorithm so far
- * opts - prints information to (FILE *)opts->output (or stdout if NULL)
- *
- * Returns always TRUE (ie. never requests abort).
- */
-boolean clique_print_time(int level, int i, int n, int max,
- double cputime, double realtime,
- clique_options *opts) {
- static float prev_time=100;
- static int prev_i=100;
- static int prev_max=100;
- static int prev_level=0;
- FILE *fp=opts->output;
- int j;
-
- if (fp==NULL)
- fp=stdout;
-
- if (ABS(prev_time-realtime)>0.1 || i==n || i<prev_i || max!=prev_max ||
- level!=prev_level) {
- for (j=1; j<level; j++)
- fprintf(fp," ");
- if (realtime-prev_time < 0.01 || i<=prev_i)
- fprintf(fp,"%3d/%d (max %2d) %2.2f s "
- "(0.00 s/round)\n",i,n,max,
- realtime);
- else
- fprintf(fp,"%3d/%d (max %2d) %2.2f s "
- "(%2.2f s/round)\n",
- i,n,max,realtime,
- (realtime-prev_time)/(i-prev_i));
- prev_time=realtime;
- prev_i=i;
- prev_max=max;
- prev_level=level;
- }
- return TRUE;
-}
-
-/*
- * clique_print_time_always()
- *
- * Reports current running information.
- *
- * level - re-entrance level
- * i - current recursion level
- * n - maximum recursion level
- * max - largest clique found
- * cputime - CPU time used in algorithm so far
- * realtime - real time used in algorithm so far
- * opts - prints information to (FILE *)opts->output (or stdout if NULL)
- *
- * Returns always TRUE (ie. never requests abort).
- */
-boolean clique_print_time_always(int level, int i, int n, int max,
- double cputime, double realtime,
- clique_options *opts) {
- static float prev_time=100;
- static int prev_i=100;
- FILE *fp=opts->output;
- int j;
-
- if (fp==NULL)
- fp=stdout;
-
- for (j=1; j<level; j++)
- fprintf(fp," ");
-
- if (realtime-prev_time < 0.01 || i<=prev_i)
- fprintf(fp,"%3d/%d (max %2d) %2.2f s (0.00 s/round)\n",
- i,n,max,realtime);
- else
- fprintf(fp,"%3d/%d (max %2d) %2.2f s (%2.2f s/round)\n",
- i,n,max,realtime,(realtime-prev_time)/(i-prev_i));
- prev_time=realtime;
- prev_i=i;
-
- return TRUE;
-}
-
-
-/*
- * This file contains the graph handling routines.
- *
- * Copyright (C) 2002 Sampo Niskanen, Patric <20>sterg<72>rd.
- * Licensed under the GNU GPL, read the file LICENSE for details.
- */
-
-/*
-#include <stdio.h>
-#include <ctype.h>
-#include <string.h>
-#include "graph.h"
-*/
-
-
-/*
- * graph_new()
- *
- * Returns a newly allocated graph with n vertices all with weight 1,
- * and no edges.
- */
-graph_t *graph_new(int n) {
- graph_t *g;
- int i;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(n>0);
-
- g=malloc(sizeof(graph_t));
- g->n=n;
- g->edges=malloc(g->n * sizeof(set_t));
- g->weights=malloc(g->n * sizeof(int));
- for (i=0; i < g->n; i++) {
- g->edges[i]=set_new(n);
- g->weights[i]=1;
- }
- return g;
-}
-
-/*
- * graph_free()
- *
- * Frees the memory associated with the graph g.
- */
-void graph_free(graph_t *g) {
- int i;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
- ASSERT(g!=NULL);
- ASSERT(g->n > 0);
-
- for (i=0; i < g->n; i++) {
- set_free(g->edges[i]);
- }
- free(g->weights);
- free(g->edges);
- free(g);
- return;
-}
-
-
-/*
- * graph_resize()
- *
- * Resizes graph g to given size. If size > g->n, the new vertices are
- * not connected to any others and their weights are set to 1.
- * If size < g->n, the last g->n - size vertices are removed.
- */
-void graph_resize(graph_t *g, int size) {
- int i;
-
- ASSERT(g!=NULL);
- ASSERT(g->n > 0);
- ASSERT(size > 0);
-
- if (g->n == size)
- return;
-
- /* Free/alloc extra edge-sets */
- for (i=size; i < g->n; i++)
- set_free(g->edges[i]);
- g->edges=realloc(g->edges, size * sizeof(set_t));
- for (i=g->n; i < size; i++)
- g->edges[i]=set_new(size);
-
- /* Resize original sets */
- for (i=0; i < MIN(g->n,size); i++) {
- g->edges[i]=set_resize(g->edges[i],size);
- }
-
- /* Weights */
- g->weights=realloc(g->weights,size * sizeof(int));
- for (i=g->n; i<size; i++)
- g->weights[i]=1;
-
- g->n=size;
- return;
-}
-
-/*
- * graph_crop()
- *
- * Resizes the graph so as to remove all highest-valued isolated vertices.
- */
-void graph_crop(graph_t *g) {
- int i;
-
- for (i=g->n-1; i>=1; i--)
- if (set_size(g->edges[i])>0)
- break;
- graph_resize(g,i+1);
- return;
-}
-
-
-/*
- * graph_weighted()
- *
- * Returns TRUE if all vertex weights of graph g are all the same.
- *
- * Note: Does NOT require weights to be 1.
- */
-boolean graph_weighted(graph_t *g) {
- int i,w;
-
- w=g->weights[0];
- for (i=1; i < g->n; i++)
- if (g->weights[i] != w)
- return TRUE;
- return FALSE;
-}
-
-/*
- * graph_edge_count()
- *
- * Returns the number of edges in graph g.
- */
-int graph_edge_count(graph_t *g) {
- int i;
- int count=0;
-
- for (i=0; i < g->n; i++) {
- count += set_size(g->edges[i]);
- }
- return count/2;
-}
-
-/*
- * graph_print()
- *
- * Prints a representation of the graph g to stdout (along with any errors
- * noticed). Mainly useful for debugging purposes and trivial output.
- *
- * The output consists of a first line describing the dimensions and then
- * one line per vertex containing the vertex number (numbered 0,...,n-1),
- * the vertex weight (if the graph is weighted), "->" and then a list
- * of all vertices it is adjacent to.
- */
-void graph_print(graph_t *g) {
- int i,j;
- int asymm=0;
- int refl=0;
- int nonpos=0;
- int extra=0;
- unsigned int weight=0;
- boolean weighted;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
-
- if (g==NULL) {
- printf(" WARNING: Graph pointer is NULL!\n");
- return;
- }
- if (g->n <= 0) {
- printf(" WARNING: Graph has %d vertices "
- "(should be positive)!\n",g->n);
- return;
- }
-
- weighted=graph_weighted(g);
-
- printf("%s graph has %d vertices, %d edges (density %.2f).\n",
- weighted?"Weighted":((g->weights[0]==1)?
- "Unweighted":"Semi-weighted"),
- g->n,graph_edge_count(g),
- (float)graph_edge_count(g)/((float)(g->n - 1)*(g->n)/2));
-
- for (i=0; i < g->n; i++) {
- printf("%2d",i);
- if (weighted) {
- printf(" w=%d",g->weights[i]);
- if (g->weights[i] <= 0) {
- printf("*NON-POSITIVE*");
- nonpos++;
- }
- }
- if (weight < INT_MAX)
- weight+=g->weights[i];
- printf(" ->");
- for (j=0; j < g->n; j++) {
- if (SET_CONTAINS_FAST(g->edges[i],j)) {
- printf(" %d",j);
- if (i==j) {
- printf("*REFLEXIVE*");
- refl++;
- }
- if (!SET_CONTAINS_FAST(g->edges[j],i)) {
- printf("*ASYMMERTIC*");
- asymm++;
- }
- }
- }
- for (j=g->n; j < SET_ARRAY_LENGTH(g->edges[i])*ELEMENTSIZE;
- j++) {
- if (SET_CONTAINS_FAST(g->edges[i],j)) {
- printf(" %d*NON-EXISTENT*",j);
- extra++;
- }
- }
- printf("\n");
- }
-
- if (asymm)
- printf(" WARNING: Graph contained %d asymmetric edges!\n",
- asymm);
- if (refl)
- printf(" WARNING: Graph contained %d reflexive edges!\n",
- refl);
- if (nonpos)
- printf(" WARNING: Graph contained %d non-positive vertex "
- "weights!\n",nonpos);
- if (extra)
- printf(" WARNING: Graph contained %d edges to "
- "non-existent vertices!\n",extra);
- if (weight>=INT_MAX)
- printf(" WARNING: Total graph weight >= INT_MAX!\n");
- return;
-}
-
-
-/*
- * graph_test()
- *
- * Tests graph g to be valid. Checks that g is non-NULL, the edges are
- * symmetric and anti-reflexive, and that all vertex weights are positive.
- * If output is non-NULL, prints a few lines telling the status of the graph
- * to file descriptor output.
- *
- * Returns TRUE if the graph is valid, FALSE otherwise.
- */
-boolean graph_test(graph_t *g,FILE *output) {
- int i,j;
- int edges=0;
- int asymm=0;
- int nonpos=0;
- int refl=0;
- int extra=0;
- unsigned int weight=0;
- boolean weighted;
-
- ASSERT((sizeof(setelement)*8)==ELEMENTSIZE);
-
- if (g==NULL) {
- if (output)
- fprintf(output," WARNING: Graph pointer is NULL!\n");
- return FALSE;
- }
-
- weighted=graph_weighted(g);
-
- for (i=0; i < g->n; i++) {
- if (g->edges[i]==NULL) {
- if (output)
- fprintf(output," WARNING: Graph edge set "
- "NULL!\n"
- " (further warning suppressed)\n");
- return FALSE;
- }
- if (SET_MAX_SIZE(g->edges[i]) < g->n) {
- if (output)
- fprintf(output," WARNING: Graph edge set "
- "too small!\n"
- " (further warnings suppressed)\n");
- return FALSE;
- }
- for (j=0; j < g->n; j++) {
- if (SET_CONTAINS_FAST(g->edges[i],j)) {
- edges++;
- if (i==j) {
- refl++;
- }
- if (!SET_CONTAINS_FAST(g->edges[j],i)) {
- asymm++;
- }
- }
- }
- for (j=g->n; j < SET_ARRAY_LENGTH(g->edges[i])*ELEMENTSIZE;
- j++) {
- if (SET_CONTAINS_FAST(g->edges[i],j))
- extra++;
- }
- if (g->weights[i] <= 0)
- nonpos++;
- if (weight<INT_MAX)
- weight += g->weights[i];
- }
-
- edges/=2; /* Each is counted twice. */
-
- if (output) {
- /* Semi-weighted means all weights are equal, but not 1. */
- fprintf(output,"%s graph has %d vertices, %d edges "
- "(density %.2f).\n",
- weighted?"Weighted":
- ((g->weights[0]==1)?"Unweighted":"Semi-weighted"),
- g->n,edges,(float)edges/((float)(g->n - 1)*(g->n)/2));
-
- if (asymm)
- fprintf(output," WARNING: Graph contained %d "
- "asymmetric edges!\n",asymm);
- if (refl)
- fprintf(output," WARNING: Graph contained %d "
- "reflexive edges!\n",refl);
- if (nonpos)
- fprintf(output," WARNING: Graph contained %d "
- "non-positive vertex weights!\n",nonpos);
- if (extra)
- fprintf(output," WARNING: Graph contained %d edges "
- "to non-existent vertices!\n",extra);
- if (weight>=INT_MAX)
- fprintf(output," WARNING: Total graph weight >= "
- "INT_MAX!\n");
- if (asymm==0 && refl==0 && nonpos==0 && extra==0 &&
- weight<INT_MAX)
- fprintf(output,"Graph OK.\n");
- }
-
- if (asymm || refl || nonpos || extra || weight>=INT_MAX)
- return FALSE;
-
- return TRUE;
-}
-
-
-/*
- * graph_test_regular()
- *
- * Returns the vertex degree for regular graphs, or -1 if the graph is
- * not regular.
- */
-int graph_test_regular(graph_t *g) {
- int i,n;
-
- n=set_size(g->edges[0]);
-
- for (i=1; i < g->n; i++) {
- if (set_size(g->edges[i]) != n)
- return -1;
- }
- return n;
-}
-
-
-
-/*
- * This file contains the vertex reordering routines.
- *
- * Copyright (C) 2002 Sampo Niskanen, Patric <20>sterg<72>rd.
- * Licensed under the GNU GPL, read the file LICENSE for details.
- */
-
-/*
-#include "reorder.h"
-
-#include <time.h>
-#include <sys/times.h>
-#include <stdlib.h>
-
-#include <limits.h>
-*/
-
-
-/*
- * reorder_set()
- *
- * Reorders the set s with a function i -> order[i].
- *
- * Note: Assumes that order is the same size as SET_MAX_SIZE(s).
- */
-void reorder_set(set_t s,int *order) {
- set_t tmp;
- int i,j;
- setelement e;
-
- ASSERT(reorder_is_bijection(order,SET_MAX_SIZE(s)));
-
- tmp=set_new(SET_MAX_SIZE(s));
-
- for (i=0; i<(SET_MAX_SIZE(s)/ELEMENTSIZE); i++) {
- e=s[i];
- if (e==0)
- continue;
- for (j=0; j<ELEMENTSIZE; j++) {
- if (e&1) {
- SET_ADD_ELEMENT(tmp,order[i*ELEMENTSIZE+j]);
- }
- e = e>>1;
- }
- }
- if (SET_MAX_SIZE(s)%ELEMENTSIZE) {
- e=s[i];
- for (j=0; j<(SET_MAX_SIZE(s)%ELEMENTSIZE); j++) {
- if (e&1) {
- SET_ADD_ELEMENT(tmp,order[i*ELEMENTSIZE+j]);
- }
- e = e>>1;
- }
- }
- set_copy(s,tmp);
- set_free(tmp);
- return;
-}
-
-
-/*
- * reorder_graph()
- *
- * Reorders the vertices in the graph with function i -> order[i].
- *
- * Note: Assumes that order is of size g->n.
- */
-void reorder_graph(graph_t *g, int *order) {
- int i;
- set_t *tmp_e;
- int *tmp_w;
-
- ASSERT(reorder_is_bijection(order,g->n));
-
- tmp_e=malloc(g->n * sizeof(set_t));
- tmp_w=malloc(g->n * sizeof(int));
- for (i=0; i<g->n; i++) {
- reorder_set(g->edges[i],order);
- tmp_e[order[i]]=g->edges[i];
- tmp_w[order[i]]=g->weights[i];
- }
- for (i=0; i<g->n; i++) {
- g->edges[i]=tmp_e[i];
- g->weights[i]=tmp_w[i];
- }
- free(tmp_e);
- free(tmp_w);
- return;
-}
-
-
-
-/*
- * reorder_duplicate()
- *
- * Returns a newly allocated duplicate of the given ordering.
- */
-int *reorder_duplicate(int *order,int n) {
- int *new;
-
- new=malloc(n*sizeof(int));
- memcpy(new,order,n*sizeof(int));
- return new;
-}
-
-/*
- * reorder_invert()
- *
- * Inverts the given ordering so that new[old[i]]==i.
- *
- * Note: Asserts that order is a bijection.
- */
-void reorder_invert(int *order,int n) {
- int *new;
- int i;
-
- ASSERT(reorder_is_bijection(order,n));
-
- new=malloc(n*sizeof(int));
- for (i=0; i<n; i++)
- new[order[i]]=i;
- for (i=0; i<n; i++)
- order[i]=new[i];
- free(new);
- return;
-}
-
-/*
- * reorder_reverse()
- *
- * Reverses the given ordering so that new[i] == n-1 - old[i].
- */
-void reorder_reverse(int *order,int n) {
- int i;
-
- for (i=0; i<n; i++)
- order[i] = n-1 - order[i];
- return;
-}
-
-/*
- * reorder_is_bijection
- *
- * Checks that an ordering is a bijection {0,...,n-1} -> {0,...,n-1}.
- *
- * Returns TRUE if it is a bijection, FALSE otherwise.
- */
-boolean reorder_is_bijection(int *order,int n) {
- boolean *used;
- int i;
-
- used=calloc(n,sizeof(boolean));
- for (i=0; i<n; i++) {
- if (order[i]<0 || order[i]>=n) {
- free(used);
- return FALSE;
- }
- if (used[order[i]]) {
- free(used);
- return FALSE;
- }
- used[order[i]]=TRUE;
- }
- for (i=0; i<n; i++) {
- if (!used[i]) {
- free(used);
- return FALSE;
- }
- }
- free(used);
- return TRUE;
-}
-
-/*
- * reorder_ident()
- *
- * Returns a newly allocated identity ordering of size n, ie. order[i]==i.
- */
-int *reorder_ident(int n) {
- int i;
- int *order;
-
- order=malloc(n*sizeof(int));
- for (i=0; i<n; i++)
- order[i]=i;
- return order;
-}
-
-
-
-/*** Reordering functions for use in clique_options ***/
-
-/*
- * reorder_by_ident()
- *
- * Returns an identity ordering.
- */
-int *reorder_by_ident(graph_t *g,boolean weighted) {
- return reorder_ident(g->n);
-}
-
-/*
- * reorder_by_reverse()
- *
- * Returns a reverse identity ordering.
- */
-int *reorder_by_reverse(graph_t *g,boolean weighted) {
- int i;
- int *order;
-
- order=malloc(g->n * sizeof(int));
- for (i=0; i < g->n; i++)
- order[i]=g->n-i-1;
- return order;
-}
-
-/*
- * reorder_by_greedy_coloring()
- *
- * Equivalent to reorder_by_weighted_greedy_coloring or
- * reorder_by_unweighted_greedy_coloring according to the value of weighted.
- */
-int *reorder_by_greedy_coloring(graph_t *g,boolean weighted) {
- if (weighted)
- return reorder_by_weighted_greedy_coloring(g,weighted);
- else
- return reorder_by_unweighted_greedy_coloring(g,weighted);
-}
-
-
-/*
- * reorder_by_unweighted_greedy_coloring()
- *
- * Returns an ordering for the graph g by coloring the clique one
- * color at a time, always adding the vertex of largest degree within
- * the uncolored graph, and numbering these vertices 0, 1, ...
- *
- * Experimentally efficient for use with unweighted graphs.
- */
-int *reorder_by_unweighted_greedy_coloring(graph_t *g,boolean weighted) {
- int i,j,v;
- boolean *tmp_used;
- int *degree; /* -1 for used vertices */
- int *order;
- int maxdegree,maxvertex=0;
- boolean samecolor;
-
- tmp_used=calloc(g->n,sizeof(boolean));
- degree=calloc(g->n,sizeof(int));
- order=calloc(g->n,sizeof(int));
-
- for (i=0; i < g->n; i++) {
- for (j=0; j < g->n; j++) {
- ASSERT(!((i==j) && GRAPH_IS_EDGE(g,i,j)));
- if (GRAPH_IS_EDGE(g,i,j))
- degree[i]++;
- }
- }
-
- v=0;
- while (v < g->n) {
- /* Reset tmp_used. */
- memset(tmp_used,0,g->n * sizeof(boolean));
-
- do {
- /* Find vertex to be colored. */
- maxdegree=0;
- samecolor=FALSE;
- for (i=0; i < g->n; i++) {
- if (!tmp_used[i] && degree[i] >= maxdegree) {
- maxvertex=i;
- maxdegree=degree[i];
- samecolor=TRUE;
- }
- }
- if (samecolor) {
- order[v]=maxvertex;
- degree[maxvertex]=-1;
- v++;
-
- /* Mark neighbors not to color with same
- * color and update neighbor degrees. */
- for (i=0; i < g->n; i++) {
- if (GRAPH_IS_EDGE(g,maxvertex,i)) {
- tmp_used[i]=TRUE;
- degree[i]--;
- }
- }
- }
- } while (samecolor);
- }
-
- free(tmp_used);
- free(degree);
- return order;
-}
-
-/*
- * reorder_by_weighted_greedy_coloring()
- *
- * Returns an ordering for the graph g by coloring the clique one
- * color at a time, always adding the vertex that (in order of importance):
- * 1. has the minimum weight in the remaining graph
- * 2. has the largest sum of weights surrounding the vertex
- *
- * Experimentally efficient for use with weighted graphs.
- */
-int *reorder_by_weighted_greedy_coloring(graph_t *g, boolean weighted) {
- int i,j,p=0;
- int cnt;
- int *nwt; /* Sum of surrounding vertices' weights */
- int min_wt,max_nwt;
- boolean *used;
- int *order;
-
- nwt=malloc(g->n * sizeof(int));
- order=malloc(g->n * sizeof(int));
- used=calloc(g->n,sizeof(boolean));
-
- for (i=0; i < g->n; i++) {
- nwt[i]=0;
- for (j=0; j < g->n; j++)
- if (GRAPH_IS_EDGE(g, i, j))
- nwt[i] += g->weights[j];
- }
-
- for (cnt=0; cnt < g->n; cnt++) {
- min_wt=INT_MAX;
- max_nwt=-1;
- for (i=g->n-1; i>=0; i--)
- if ((!used[i]) && (g->weights[i] < min_wt))
- min_wt=g->weights[i];
- for (i=g->n-1; i>=0; i--) {
- if (used[i] || (g->weights[i] > min_wt))
- continue;
- if (nwt[i] > max_nwt) {
- max_nwt=nwt[i];
- p=i;
- }
- }
- order[cnt]=p;
- used[p]=TRUE;
- for (j=0; j < g->n; j++)
- if ((!used[j]) && (GRAPH_IS_EDGE(g, p, j)))
- nwt[j] -= g->weights[p];
- }
-
- free(nwt);
- free(used);
-
- ASSERT(reorder_is_bijection(order,g->n));
-
- return order;
-}
-
-/*
- * reorder_by_degree()
- *
- * Returns a reordering of the graph g so that the vertices with largest
- * degrees (most neighbors) are first.
- */
-int *reorder_by_degree(graph_t *g, boolean weighted) {
- int i,j,v;
- int *degree;
- int *order;
- int maxdegree,maxvertex=0;
-
- degree=calloc(g->n,sizeof(int));
- order=calloc(g->n,sizeof(int));
-
- for (i=0; i < g->n; i++) {
- for (j=0; j < g->n; j++) {
- ASSERT(!((i==j) && GRAPH_IS_EDGE(g,i,j)));
- if (GRAPH_IS_EDGE(g,i,j))
- degree[i]++;
- }
- }
-
- for (v=0; v < g->n; v++) {
- maxdegree=0;
- for (i=0; i < g->n; i++) {
- if (degree[i] >= maxdegree) {
- maxvertex=i;
- maxdegree=degree[i];
- }
- }
- order[v]=maxvertex;
- degree[maxvertex]=-1; /* used */
-/*** Max. degree withing unselected graph:
- for (i=0; i < g->n; i++) {
- if (GRAPH_IS_EDGE(g,maxvertex,i))
- degree[i]--;
- }
-***/
- }
-
- free(degree);
- return order;
-}
-
-/*
- * reorder_by_random()
- *
- * Returns a random reordering for graph g.
- * Note: Used the functions rand() and srand() to generate the random
- * numbers. srand() is re-initialized every time reorder_by_random()
- * is called using the system time.
- */
-int *reorder_by_random(graph_t *g, boolean weighted) {
- /* struct tms t; */
- int i,r;
- int *new;
- boolean *used;
-
-/*
- srand(times(&t)+time(NULL));
-*/
- INITRANBYTIME;
-
- new=calloc(g->n, sizeof(int));
- used=calloc(g->n, sizeof(boolean));
- for (i=0; i < g->n; i++) {
- do {
- r=NEXTRAN % g->n;
- } while (used[r]);
- new[i]=r;
- used[r]=TRUE;
- }
- free(used);
- return new;
-}
-
/************************************************************************/
/* This is an interface between nauty and cliquer for finding
--- a/nautycliquer.h
+++ b/nautycliquer.h
@@ -6,637 +6,7 @@
#include "nauty.h"
#include "gtools.h"
-#include <limits.h>
-
-/**********************************************************************
-#include "cliquerconf.h"
-*/
-
-/*
- * setelement is the basic memory type used in sets. It is often fastest
- * to be as large as can fit into the CPU registers.
- *
- * ELEMENTSIZE is the size of one setelement, measured in bits. It must
- * be either 16, 32 or 64 (otherwise additional changes must be made to
- * the source).
- *
- * The default is to use "unsigned long int" and attempt to guess the
- * size using <limits.h>, which should work pretty well. Check functioning
- * with "make test".
- */
-
-/* typedef unsigned long int setelement; */
-/* #define ELEMENTSIZE 64 */
-
-/*
- * INLINE is a command prepended to function declarations to instruct the
- * compiler to inline the function. If inlining is not desired, define blank.
- *
- * The default is to use "inline", which is recognized by most compilers.
- */
-
-/* #define INLINE */
-/* #define INLINE __inline__ */
-
-
-/*
- * Set handling functions are defined as static functions in set.h for
- * performance reasons. This may cause unnecessary warnings from the
- * compiler. Some compilers (such as GCC) have the possibility to turn
- * off the warnings on a per-function basis using a flag prepended to
- * the function declaration.
- *
- * The default is to use the correct attribute when compiling with GCC,
- * or no flag otherwise.
- */
-
-/* #define UNUSED_FUNCTION __attribute__((unused)) */
-/* #define UNUSED_FUNCTION */
-
-/*
- * Uncommenting the following will disable all assertions (checks that
- * function arguments and other variables are correct). This is highly
- * discouraged, as it allows bugs to go unnoticed easier. The assertions
- * are set so that they do not slow down programs notably.
- */
-
-/* #define ASSERT(x) */
-
-/**********************************************************************
-#include "misc.h"
-*/
-
-/*
- * We #define boolean instead of using a typedef because nauty.h uses it
- * also. AFAIK, there is no way to check for an existing typedef, and
- * re-typedefing is illegal (even when using exactly the same datatype!).
-#ifndef boolean
-#define boolean int
-#endif
-
-BDM: In nauty's version we will use nauty's boolean (which is int anyway).
- */
-
-/*
- * Default value for UNUSED_FUNCTION: use "__attribute__((unused))" for
- * GCC versions that support it, otherwise leave blank.
- */
-#ifndef UNUSED_FUNCTION
-# if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4)
-# define UNUSED_FUNCTION __attribute__((unused))
-# else
-# define UNUSED_FUNCTION
-# endif
-#endif /* !UNUSED_FUNCTION */
-
-/*
- * Default inlining directive: "inline"
- */
-#ifndef INLINE
-#define INLINE inline
-#endif
-
-#ifndef ASSERT
-#define ASSERT(expr) \
- if (!(expr)) { \
- fprintf(stderr,"cliquer file %s: line %d: assertion failed: " \
- "(%s)\n",__FILE__,__LINE__,#expr); \
- abort(); \
- }
-#endif /* !ASSERT */
-
-
-#ifndef FALSE
-#define FALSE (0)
-#endif
-#ifndef TRUE
-#define TRUE (!FALSE)
-#endif
-
-
-#ifndef MIN
-#define MIN(a,b) (((a)<(b))?(a):(b))
-#endif
-#ifndef MAX
-#define MAX(a,b) (((a)>(b))?(a):(b))
-#endif
-#ifndef ABS
-#define ABS(v) (((v)<0)?(-(v)):(v))
-#endif
-
-/**********************************************************************
-#include "set.h"
-*/
-
-/*
- * This file contains the set handling routines.
- *
- * Copyright (C) 2002 Sampo Niskanen, Patric Östergård.
- * Licensed under the GNU GPL, read the file LICENSE for details.
- */
-
-/*
- * Sets are arrays of setelement's (typically unsigned long int's) with
- * representative bits for each value they can contain. The values
- * are numbered 0,...,n-1.
- */
-
-
-/*** Variable types and constants. ***/
-
-
-/*
- * If setelement hasn't been declared:
- * - use "unsigned long int" as setelement
- * - try to deduce size from ULONG_MAX
- */
-
-#ifndef ELEMENTSIZE
-typedef unsigned long int setelement;
-# if (ULONG_MAX == 65535)
-# define ELEMENTSIZE 16
-# elif (ULONG_MAX == 4294967295)
-# define ELEMENTSIZE 32
-# else
-# define ELEMENTSIZE 64
-# endif
-#endif /* !ELEMENTSIZE */
-
-typedef setelement * set_t;
-
-
-/*** Counting amount of 1 bits in a setelement ***/
-
-/* Array for amount of 1 bits in a byte. */
-static int set_bit_count[256] = {
- 0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,
- 1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
- 1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
- 1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
- 2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,
- 3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
- 3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,
- 4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8 };
-
-/* The following macros assume that all higher bits are 0.
- * They may in some cases be useful also on with other ELEMENTSIZE's,
- * so we define them all. */
-#define SET_ELEMENT_BIT_COUNT_8(a) (set_bit_count[(a)])
-#define SET_ELEMENT_BIT_COUNT_16(a) (set_bit_count[(a)>>8] + \
- set_bit_count[(a)&0xFF])
-#define SET_ELEMENT_BIT_COUNT_32(a) (set_bit_count[(a)>>24] + \
- set_bit_count[((a)>>16)&0xFF] + \
- set_bit_count[((a)>>8)&0xFF] + \
- set_bit_count[(a)&0xFF])
-#define SET_ELEMENT_BIT_COUNT_64(a) (set_bit_count[(a)>>56] + \
- set_bit_count[((a)>>48)&0xFF] + \
- set_bit_count[((a)>>40)&0xFF] + \
- set_bit_count[((a)>>32)&0xFF] + \
- set_bit_count[((a)>>24)&0xFF] + \
- set_bit_count[((a)>>16)&0xFF] + \
- set_bit_count[((a)>>8)&0xFF] + \
- set_bit_count[(a)&0xFF])
-#if (ELEMENTSIZE==64)
-# define SET_ELEMENT_BIT_COUNT(a) SET_ELEMENT_BIT_COUNT_64(a)
-# define FULL_ELEMENT ((setelement)0xFFFFFFFFFFFFFFFF)
-#elif (ELEMENTSIZE==32)
-# define SET_ELEMENT_BIT_COUNT(a) SET_ELEMENT_BIT_COUNT_32(a)
-# define FULL_ELEMENT ((setelement)0xFFFFFFFF)
-#elif (ELEMENTSIZE==16)
-# define SET_ELEMENT_BIT_COUNT(a) SET_ELEMENT_BIT_COUNT_16(a)
-# define FULL_ELEMENT ((setelement)0xFFFF)
-#else
-# error "SET_ELEMENT_BIT_COUNT(a) not defined for current ELEMENTSIZE"
-#endif
-
-/*** Macros and functions ***/
-
-/*
- * Gives a value with bit x (counting from lsb up) set.
- *
- * Making this as a table might speed up things on some machines
- * (though on most modern machines it's faster to shift instead of
- * using memory). Making it a macro makes it easy to change.
- */
-#define SET_BIT_MASK(x) ((setelement)1<<(x))
-
-/* Set element handling macros */
-
-#define SET_ELEMENT_INTERSECT(a,b) ((a)&(b))
-#define SET_ELEMENT_UNION(a,b) ((a)|(b))
-#define SET_ELEMENT_DIFFERENCE(a,b) ((a)&(~(b)))
-#define SET_ELEMENT_CONTAINS(e,v) ((e)&SET_BIT_MASK(v))
-
-/* Set handling macros */
-
-#define SET_ADD_ELEMENT(s,a) \
- ((s)[(a)/ELEMENTSIZE] |= SET_BIT_MASK((a)%ELEMENTSIZE))
-#define SET_DEL_ELEMENT(s,a) \
- ((s)[(a)/ELEMENTSIZE] &= ~SET_BIT_MASK((a)%ELEMENTSIZE))
-#define SET_CONTAINS_FAST(s,a) (SET_ELEMENT_CONTAINS((s)[(a)/ELEMENTSIZE], \
- (a)%ELEMENTSIZE))
-#define SET_CONTAINS(s,a) (((a)<SET_MAX_SIZE(s))?SET_CONTAINS_FAST(s,a):FALSE)
-
-/* Sets can hold values between 0,...,SET_MAX_SIZE(s)-1 */
-#define SET_MAX_SIZE(s) ((s)[-1])
-/* Sets consist of an array of SET_ARRAY_LENGTH(s) setelements */
-#define SET_ARRAY_LENGTH(s) (((s)[-1]+ELEMENTSIZE-1)/ELEMENTSIZE)
-
-/*
- * set_new()
- *
- * Create a new set that can hold values in the range 0,...,size-1.
- */
-UNUSED_FUNCTION
-static set_t set_new(int size) {
- int n;
- set_t s;
-
- ASSERT(size>0);
-
- n=(size/ELEMENTSIZE+1)+1;
- s=calloc(n,sizeof(setelement));
- s[0]=size;
-
- return &(s[1]);
-}
-
-/*
- * set_free()
- *
- * Free the memory associated with set s.
- */
-UNUSED_FUNCTION INLINE
-static void set_free(set_t s) {
- ASSERT(s!=NULL);
- free(&(s[-1]));
-}
-
-/*
- * set_resize()
- *
- * Resizes set s to given size. If the size is less than SET_MAX_SIZE(s),
- * the last elements are dropped.
- *
- * Returns a pointer to the new set.
- */
-UNUSED_FUNCTION INLINE
-static set_t set_resize(set_t s, int size) {
- int n;
-
- ASSERT(size>0);
-
- n=(size/ELEMENTSIZE+1);
- s=((setelement *)realloc(s-1,(n+1)*sizeof(setelement)))+1;
-
- if (n>SET_ARRAY_LENGTH(s))
- memset(s+SET_ARRAY_LENGTH(s),0,
- (n-SET_ARRAY_LENGTH(s))*sizeof(setelement));
- if (size < SET_MAX_SIZE(s))
- s[(size-1)/ELEMENTSIZE] &= (FULL_ELEMENT >>
- (ELEMENTSIZE-size%ELEMENTSIZE));
- s[-1]=size;
-
- return s;
-}
-
-/*
- * set_size()
- *
- * Returns the number of elements in set s.
- */
-UNUSED_FUNCTION INLINE
-static int set_size(set_t s) {
- int count=0;
- setelement *c;
-
- for (c=s; c < s+SET_ARRAY_LENGTH(s); c++)
- count+=SET_ELEMENT_BIT_COUNT(*c);
- return count;
-}
-
-/*
- * set_duplicate()
- *
- * Returns a newly allocated duplicate of set s.
- */
-UNUSED_FUNCTION INLINE
-static set_t set_duplicate(set_t s) {
- set_t new;
-
- new=set_new(SET_MAX_SIZE(s));
- memcpy(new,s,SET_ARRAY_LENGTH(s)*sizeof(setelement));
- return new;
-}
-
-/*
- * set_copy()
- *
- * Copies set src to dest. If dest is NULL, is equal to set_duplicate.
- * If dest smaller than src, it is freed and a new set of the same size as
- * src is returned.
- */
-UNUSED_FUNCTION INLINE
-static set_t set_copy(set_t dest,set_t src) {
- if (dest==NULL)
- return set_duplicate(src);
- if (SET_MAX_SIZE(dest)<SET_MAX_SIZE(src)) {
- set_free(dest);
- return set_duplicate(src);
- }
- memcpy(dest,src,SET_ARRAY_LENGTH(src)*sizeof(setelement));
- memset(dest+SET_ARRAY_LENGTH(src),0,((SET_ARRAY_LENGTH(dest) -
- SET_ARRAY_LENGTH(src)) *
- sizeof(setelement)));
- return dest;
-}
-
-/*
- * set_empty()
- *
- * Removes all elements from the set s.
- */
-UNUSED_FUNCTION INLINE
-static void set_empty(set_t s) {
- memset(s,0,SET_ARRAY_LENGTH(s)*sizeof(setelement));
- return;
-}
-
-/*
- * set_intersection()
- *
- * Store the intersection of sets a and b into res. If res is NULL,
- * a new set is created and the result is written to it. If res is
- * smaller than the larger one of a and b, it is freed and a new set
- * is created and the result is returned.
- *
- * Returns either res or a new set that has been allocated in its stead.
- *
- * Note: res may not be a or b.
- */
-UNUSED_FUNCTION INLINE
-static set_t set_intersection(set_t res,set_t a,set_t b) {
- int i,max;
-
- if (res==NULL) {
- res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
- } else if (SET_MAX_SIZE(res) < MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b))) {
- set_free(res);
- res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
- } else {
- set_empty(res);
- }
-
- max=MIN(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
- for (i=0; i<max; i++) {
- res[i]=SET_ELEMENT_INTERSECT(a[i],b[i]);
- }
-
- return res;
-}
-
-/*
- * set_union()
- *
- * Store the union of sets a and b into res. If res is NULL, a new set
- * is created and the result is written to it. If res is smaller than
- * the larger one of a and b, it is freed and a new set is created and
- * the result is returned.
- *
- * Returns either res or a new set that has been allocated in its stead.
- *
- * Note: res may not be a or b.
- */
-UNUSED_FUNCTION INLINE
-static set_t set_union(set_t res,set_t a,set_t b) {
- int i,max;
-
- if (res==NULL) {
- res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
- } else if (SET_MAX_SIZE(res) < MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b))) {
- set_free(res);
- res = set_new(MAX(SET_MAX_SIZE(a),SET_MAX_SIZE(b)));
- } else {
- set_empty(res);
- }
-
- max=MAX(SET_ARRAY_LENGTH(a),SET_ARRAY_LENGTH(b));
- for (i=0; i<max; i++) {
- res[i]=SET_ELEMENT_UNION(a[i],b[i]);
- }
-
- return res;
-}
-
-
-/*
- * set_return_next()
- *
- * Returns the smallest value in set s which is greater than n, or -1 if
- * such a value does not exist.
- *
- * Can be used to iterate through all values of s:
- *
- * int i=-1;
- * while ((i=set_return_next(s,i))>=0) {
- * // i is in set s
- * }
- */
-UNUSED_FUNCTION INLINE
-static int set_return_next(set_t s, int n) {
- if (n<0)
- n=0;
- else
- n++;
- if (n >= SET_MAX_SIZE(s))
- return -1;
-
- while (n%ELEMENTSIZE) {
- if (SET_CONTAINS(s,n))
- return n;
- n++;
- if (n >= SET_MAX_SIZE(s))
- return -1;
- }
-
- while (s[n/ELEMENTSIZE]==0) {
- n+=ELEMENTSIZE;
- if (n >= SET_MAX_SIZE(s))
- return -1;
- }
- while (!SET_CONTAINS(s,n)) {
- n++;
- if (n >= SET_MAX_SIZE(s))
- return -1;
- }
- return n;
-}
-
-
-/*
- * set_print()
- *
- * Prints the size and contents of set s to stdout.
- * Mainly useful for debugging purposes and trivial output.
- */
-UNUSED_FUNCTION
-static void set_print(set_t s) {
- int i;
- printf("size=%d(max %d)",set_size(s),(int)SET_MAX_SIZE(s));
- for (i=0; i<SET_MAX_SIZE(s); i++)
- if (SET_CONTAINS(s,i))
- printf(" %d",i);
- printf("\n");
- return;
-}
-
-/********************************************************************
-#include "graph.h"
-*/
-
-typedef struct _graph_t graph_t;
-struct _graph_t {
- int n; /* Vertices numbered 0...n-1 */
- set_t *edges; /* A list of n sets (the edges). */
- int *weights; /* A list of n vertex weights. */
-};
-
-
-#define GRAPH_IS_EDGE_FAST(g,i,j) (SET_CONTAINS_FAST((g)->edges[(i)],(j)))
-#define GRAPH_IS_EDGE(g,i,j) (((i)<((g)->n))?SET_CONTAINS((g)->edges[(i)], \
- (j)):FALSE)
-#define GRAPH_ADD_EDGE(g,i,j) do { \
- SET_ADD_ELEMENT((g)->edges[(i)],(j)); \
- SET_ADD_ELEMENT((g)->edges[(j)],(i)); \
-} while (FALSE)
-#define GRAPH_DEL_EDGE(g,i,j) do { \
- SET_DEL_ELEMENT((g)->edges[(i)],(j)); \
- SET_DEL_ELEMENT((g)->edges[(j)],(i)); \
-} while (FALSE)
-
-
-extern graph_t *graph_new(int n);
-extern void graph_free(graph_t *g);
-extern void graph_resize(graph_t *g, int size);
-extern void graph_crop(graph_t *g);
-
-extern boolean graph_weighted(graph_t *g);
-extern int graph_edge_count(graph_t *g);
-
-extern graph_t *graph_read_dimacs(FILE *fp);
-extern graph_t *graph_read_dimacs_file(char *file);
-extern boolean graph_write_dimacs_ascii(graph_t *g, char *comment,FILE *fp);
-extern boolean graph_write_dimacs_ascii_file(graph_t *g,char *comment,
- char *file);
-extern boolean graph_write_dimacs_binary(graph_t *g, char *comment,FILE *fp);
-extern boolean graph_write_dimacs_binary_file(graph_t *g, char *comment,
- char *file);
-
-extern void graph_print(graph_t *g);
-extern boolean graph_test(graph_t *g, FILE *output);
-extern int graph_test_regular(graph_t *g);
-
-UNUSED_FUNCTION INLINE
-static int graph_subgraph_weight(graph_t *g,set_t s) {
- int i,j;
- int count=0;
- setelement e;
-
- for (i=0; i<SET_ARRAY_LENGTH(s); i++) {
- if (s[i]) {
- e=s[i];
- for (j=0; j<ELEMENTSIZE; j++) {
- if (e&1)
- count+=g->weights[i*ELEMENTSIZE+j];
- e = e>>1;
- }
- }
- }
- return count;
-}
-
-UNUSED_FUNCTION INLINE
-static int graph_vertex_degree(graph_t *g, int v) {
- return set_size(g->edges[v]);
-}
-
-/********************************************************************
-#include "reorder.h"
-*/
-
-extern void reorder_set(set_t s,int *order);
-extern void reorder_graph(graph_t *g, int *order);
-extern int *reorder_duplicate(int *order,int n);
-extern void reorder_invert(int *order,int n);
-extern void reorder_reverse(int *order,int n);
-extern int *reorder_ident(int n);
-extern boolean reorder_is_bijection(int *order,int n);
-
-
-#define reorder_by_default reorder_by_greedy_coloring
-extern int *reorder_by_greedy_coloring(graph_t *g, boolean weighted);
-extern int *reorder_by_weighted_greedy_coloring(graph_t *g, boolean weighted);
-extern int *reorder_by_unweighted_greedy_coloring(graph_t *g,boolean weighted);
-extern int *reorder_by_degree(graph_t *g, boolean weighted);
-extern int *reorder_by_random(graph_t *g, boolean weighted);
-extern int *reorder_by_ident(graph_t *g, boolean weighted);
-extern int *reorder_by_reverse(graph_t *g, boolean weighted);
-
-
-typedef struct _clique_options clique_options;
-struct _clique_options {
- int *(*reorder_function)(graph_t *, boolean);
- int *reorder_map;
-
- /* arguments: level, n, max, user_time, system_time, opts */
- boolean (*time_function)(int,int,int,int,double,double,
- clique_options *);
- FILE *output;
-
- boolean (*user_function)(set_t,graph_t *,clique_options *);
- void *user_data;
- set_t *clique_list;
- int clique_list_length;
-};
-
-extern clique_options *clique_default_options;
-
-/* Weighted clique functions */
-extern int clique_max_weight(graph_t *g,clique_options *opts);
-extern set_t clique_find_single(graph_t *g,int min_weight,int max_weight,
- boolean maximal, clique_options *opts);
-extern int clique_find_all(graph_t *g, int req_weight, boolean exact,
- boolean maximal, clique_options *opts);
-
-/* Unweighted clique functions */
-#define clique_unweighted_max_size clique_unweighted_max_weight
-extern int clique_unweighted_max_weight(graph_t *g, clique_options *opts);
-extern set_t clique_unweighted_find_single(graph_t *g,int min_size,
- int max_size,boolean maximal,
- clique_options *opts);
-extern int clique_unweighted_find_all(graph_t *g, int min_size, int max_size,
- boolean maximal, clique_options *opts);
-
-/* Time printing functions */
-extern boolean clique_print_time(int level, int i, int n, int max,
- double cputime, double realtime,
- clique_options *opts);
-extern boolean clique_print_time_always(int level, int i, int n, int max,
- double cputime, double realtime,
- clique_options *opts);
-
-
-/* Alternate spelling (let's be a little forgiving): */
-#define cliquer_options clique_options
-#define cliquer_default_options clique_default_options
+#include <cliquer.h>
/* Procedures defined in nautycliquer.c */
extern int find_clique(graph *g, int m, int n,
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