First commit on github -- NetBunch 1.0

5 files changed, 938 insertions, 0 deletions

diff --git a/src/kruskal/Makefile.am b/src/kruskal/Makefile.am
new file mode 100644
index 0000000..6db35f0
--- /dev/null
+++ b/src/kruskal/Makefile.am
@@ -0,0 +1,6 @@
+include ../common.mk 
+bin_PROGRAMS = kruskal
+kruskal_SOURCES = kruskal.c  edge_w_funs.c edge_w_funs.h \
+../utils/utils.c ../utils/dset.c ../utils/gen_heap.c \
+../include/utils.h ../include/dset.h ../include/gen_heap.h 
+kruskal_LDADD = -lm
diff --git a/src/kruskal/Makefile.in b/src/kruskal/Makefile.in
new file mode 100644
index 0000000..252117e
--- /dev/null
+++ b/src/kruskal/Makefile.in
@@ -0,0 +1,590 @@
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+	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+	    install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+	    "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+	fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-rm -f ../utils/$(DEPDIR)/$(am__dirstamp)
+	-rm -f ../utils/$(am__dirstamp)
+
+maintainer-clean-generic:
+	@echo "This command is intended for maintainers to use"
+	@echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+	distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+	-rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+	-rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+	clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+	distclean distclean-compile distclean-generic distclean-tags \
+	distdir dvi dvi-am html html-am info info-am install \
+	install-am install-binPROGRAMS install-data install-data-am \
+	install-dvi install-dvi-am install-exec install-exec-am \
+	install-html install-html-am install-info install-info-am \
+	install-man install-pdf install-pdf-am install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs maintainer-clean maintainer-clean-generic \
+	mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+	ps ps-am tags tags-am uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/kruskal/edge_w_funs.c b/src/kruskal/edge_w_funs.c
new file mode 100644
index 0000000..09568ef
--- /dev/null
+++ b/src/kruskal/edge_w_funs.c
@@ -0,0 +1,73 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ */
+
+
+#include "edge_w_funs.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+int compare_edge_w(const void *e1, const void *e2){
+  
+  edge_w_t *t1, *t2;
+  
+  t1 = (edge_w_t*) e1;
+  t2 = (edge_w_t*) e2;
+  
+  return (t1->w == t2->w? 0 : (t1->w < t2->w? -1 :1));
+}
+
+
+void* alloc_vector_edge_w(unsigned int N){
+  
+  return malloc(N * sizeof(edge_w_t*));
+}
+
+void dealloc_vector_edge_w(void *v){
+  
+  free(v);
+}
+
+void dealloc_elem_edge_w(void *e){
+  
+  free(e);
+}
+
+void print_elem_edge_w(void *e){
+  
+  edge_w_t *elem;
+
+  elem = (edge_w_t*)e;
+  
+  printf("%d %d %2.8g\n", elem->i, elem->j, elem->w);
+}
+
+
diff --git a/src/kruskal/edge_w_funs.h b/src/kruskal/edge_w_funs.h
new file mode 100644
index 0000000..bb6fd9c
--- /dev/null
+++ b/src/kruskal/edge_w_funs.h
@@ -0,0 +1,54 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ */
+
+#ifndef __EDGE_W_FUNS_H__
+#define __EDGE_W_FUNS_H__
+
+typedef struct{
+  unsigned int i;
+  unsigned int j;
+  double w;
+} edge_w_t;
+
+
+int compare_edge_w(const void *e1, const void *e2);
+
+void* alloc_vector_edge_w(unsigned int N);
+
+void dealloc_vector_edge_w(void *v);
+
+void dealloc_elem_edge_w(void *e);
+
+void print_elem_edge_w(void *e);
+
+
+#endif //__EDGE_W_FUNS_H__
diff --git a/src/kruskal/kruskal.c b/src/kruskal/kruskal.c
new file mode 100644
index 0000000..2aa3660
--- /dev/null
+++ b/src/kruskal/kruskal.c
@@ -0,0 +1,215 @@
+/**
+ *  This program is free software: you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License as
+ *  published by the Free Software Foundation, either version 3 of the
+ *  License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see
+ *  <http://www.gnu.org/licenses/>.
+ *
+ *  (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk>
+ * 
+ *  This file is part of NetBunch, a package for complex network
+ *  analysis and modelling. For more information please visit:
+ *
+ *             http://www.complex-networks.net/
+ *
+ *  If you use this software, please add a reference to 
+ *
+ *               V. Latora, V. Nicosia, G. Russo             
+ *   "Complex Networks: Principles, Methods and Applications"
+ *              Cambridge University Press (2017) 
+ *                ISBN: 9781107103184
+ *
+ ***********************************************************************
+ *
+ *  This program finds the minimum/maximum spanning tree of a graph
+ *  given as input, using the Kruskal's algorithm 
+ *
+ *
+ *  References:
+ *  
+ * [1] J. B. Kruskal. "On the shortest spanning subtree of a graph and
+ *     the traveling sales-man problem". P. Am. Math. Soc. 7 (1956),
+ *     48-48.  
+ *
+ */
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "dset.h"
+#include "gen_heap.h"
+#include "utils.h"
+#include "edge_w_funs.h"
+
+
+void usage(int argc, char *argv[]){
+
+  printf("********************************************************************\n"
+         "**                                                                **\n"
+         "**                        -*-   kruskal  -*-                      **\n"
+         "**                                                                **\n"
+         "**   Find the minimum/maximum spanning tree of a weighted graph   **\n"
+         "**   'graph_in' provided as input.                                **\n"
+         "**                                                                **\n"
+         "**   The input file 'graph_in' is a weighted edge-list:           **\n"
+         "**                                                                **\n"
+         "**                        I_1 J_1 W_1                             **\n"
+         "**                        I_2 J_2 W_2                             **\n"
+         "**                        I_3 J_3 W_3                             **\n"
+         "**                        ... ...                                 **\n"
+         "**                        I_K J_K W_K                             **\n"
+         "**                                                                **\n"
+         "**    The program computes by default the minimum spanning tree   **\n"
+         "**    of 'graph_in', unless the second parameter 'MAX' is         **\n"
+         "**    specified.                                                  **\n"
+         "**                                                                **\n"
+         "**    The program prints on STDOUT the weighted edge-list of the  **\n"
+         "**    minimum/maximum spanning tree of 'graph_in'.                **\n"
+         "**                                                                **\n"
+         "**    If 'graph_in' is an unweighted graph, the program prints    **\n"
+         "**    on output one of the spanning trees of the graph.           **\n"
+         "**                                                                **\n"
+         "********************************************************************\n"
+         " This is Free Software - You can use and distribute it under \n"
+         " the terms of the GNU General Public License, version 3 or later\n\n"
+         " Please visit http://www.complex-networks.net for more information\n\n"
+         " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n"
+         "********************************************************************\n\n"
+         );
+  printf("Usage: %s <graph_in> [MAX]\n", argv[0]);
+}
+
+
+void kruskal(gen_heap_t *h, unsigned int N){
+  
+  dset_t *nodes, set1, set2;
+  edge_w_t *elem;
+  unsigned int i;
+  
+  
+  nodes = malloc(N * sizeof(dset_t));
+  
+  for(i=0; i<N; i++){
+    nodes[i] = NULL;
+    dset_makeset(nodes + i);
+  }
+  
+  while(! gen_heap_delete(h, (void**)(&elem))){
+    /* get the next edge */
+    set1 = dset_find(nodes[elem->i]);
+    set2 = dset_find(nodes[elem->j]);
+    /* if i and j do not belong to the same disjoint set...*/
+    if (set1 != set2){
+      /* ... the edge (i,j) belongs to the spanning tree, */
+      /* so we print it...*/
+      print_elem_edge_w(elem);
+      /* ...then merge the two sets... */
+      dset_union(nodes[elem->i], nodes[elem->j]);
+    }
+    free(elem);
+  }
+  /* We now destroy all the disjoint sets... */
+  for (i=0;i<N;i++){
+    dset_destroy(nodes[i]);
+  }
+  free(nodes);
+  
+}
+
+void load_edges_into_heap(FILE *filein, gen_heap_t *h){
+  
+  char buff[256];
+  char *ptr;
+  edge_w_t *elem;
+  
+  
+  while(fgets(buff, 256, filein)){
+    if (buff[0] == '#')
+      continue;
+    elem = malloc(sizeof(edge_w_t));
+    ptr = strtok(buff, " "); /* read the first node */
+    VALID_PTR_OR_EXIT(ptr, 7);
+    elem->i = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the second node */
+    VALID_PTR_OR_EXIT(ptr, 7);
+    elem->j = atoi(ptr);
+    ptr = strtok(NULL, " "); /* read the weight */
+    if (!ptr)
+      /* if no weight is specified, assume it is set to 1.0 */
+      elem->w = 1.0;
+    else
+      elem->w = atof(ptr);
+    /* put the edge in the heap */
+    gen_heap_insert(h, elem);
+  }
+  
+}
+
+int count_num_lines(FILE *filein){
+  
+  int i, ch ;
+
+  i = 0;
+  
+  while ((ch = fgetc(filein)) != EOF){
+      if (ch == '\n')
+        i ++;
+  }
+  rewind(filein);
+  return i;
+}
+
+
+int main(int argc, char *argv[]){
+  
+  gen_heap_t *h;
+  unsigned int N;
+  FILE *filein;
+  char htype;
+  gen_heap_func_t  *funs;
+  
+  if(argc < 2){
+    usage(argc, argv);
+    exit(1);
+  }
+
+  htype = MIN_HEAP;
+  if (argc > 2 && !my_strcasecmp(argv[2], "MAX")){
+    htype = MAX_HEAP;
+  }
+
+  /* Initialisation of functions for gen_heap*/
+  funs = malloc(sizeof(gen_heap_func_t));
+  (*funs).compare = compare_edge_w;
+  (*funs).alloc_vector = alloc_vector_edge_w;
+  (*funs).dealloc_vector = dealloc_vector_edge_w;
+  (*funs).dealloc_elem = dealloc_elem_edge_w;
+  (*funs).print_elem = print_elem_edge_w;
+
+
+  
+  filein = openfile_or_exit(argv[1], "r", 2);
+  
+  N = count_num_lines(filein);
+
+  h = gen_heap_init(N, htype, funs);
+  
+  load_edges_into_heap(filein, h);
+
+  fclose(filein);
+  
+  kruskal(h, N);
+  gen_heap_destroy(h);
+  free(funs);
+}