First commit on github -- NetBunch 1.0

8 files changed, 664 insertions, 0 deletions

diff --git a/src/include/cum_distr.h b/src/include/cum_distr.h
new file mode 100644
index 0000000..a06336a
--- /dev/null
+++ b/src/include/cum_distr.h
@@ -0,0 +1,60 @@
+/**
+ *  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 __CUM_DISTR_H__
+#define __CUM_DISTR_H__
+
+typedef struct{
+  unsigned int id;
+  long double value;
+} idval_t;
+
+typedef struct{
+  unsigned int N;
+  unsigned int num;
+  idval_t *v;
+  long double sum;
+} cum_distr_t;
+
+cum_distr_t* cum_distr_init(unsigned int N);
+
+int cum_distr_add(cum_distr_t *d, unsigned int id, long double val);
+
+unsigned int cum_distr_sample(cum_distr_t *d);
+
+void cum_distr_dump(cum_distr_t *d);
+
+
+void cum_distr_destroy(cum_distr_t *d);
+
+
+#endif //__CUM_DISTR_H__
diff --git a/src/include/dset.h b/src/include/dset.h
new file mode 100644
index 0000000..0a072e5
--- /dev/null
+++ b/src/include/dset.h
@@ -0,0 +1,65 @@
+/**
+ *  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 __DSET_H__
+#define __DSET_H__
+
+
+typedef struct dset{
+  int rank;
+  struct dset *parent;
+  int id;
+} dset_elem_t;
+
+typedef dset_elem_t* dset_t;
+
+void dset_makeset(dset_t *ds);
+
+void dset_destroy(dset_t ds);
+
+dset_t dset_find(dset_t ds);
+
+void dset_union(dset_t s1, dset_t s2);
+
+void dset_union_opt(dset_t d1, dset_t s2);
+
+dset_t dset_find_opt(dset_t ds);
+
+void dset_makeset_id(dset_t *ds, int id);
+
+int dset_find_id(dset_t ds);
+
+int dset_find_id_opt(dset_t ds);
+
+
+
+#endif /* __DSET_H__ */
diff --git a/src/include/gen_heap.h b/src/include/gen_heap.h
new file mode 100644
index 0000000..0d434bc
--- /dev/null
+++ b/src/include/gen_heap.h
@@ -0,0 +1,84 @@
+/**
+ *  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 __GEN_HEAP__
+#define __GEN_HEAP__
+
+
+#define MAX_HEAP  0x01
+#define MIN_HEAP  0x02
+
+#define SORT_ASC  0x04
+#define SORT_DESC 0x08
+
+#define ERR_DELETE -0x04
+
+typedef struct{
+  int (*compare)(const void *e1, const void *e2);
+  void* (*alloc_vector)(unsigned int N);
+  void (*dealloc_vector)(void *v);
+  void (*dealloc_elem)(void *e);
+  void (*print_elem)(void *e);
+} gen_heap_func_t;
+
+
+typedef struct{
+  int N;
+  int last;
+  void **v;
+  gen_heap_func_t funs;
+  char htype;
+} gen_heap_t;
+
+
+#define PARENT(i) (int)(floor((i-1)/2))
+
+gen_heap_t * gen_heap_init(unsigned int N, char htype, gen_heap_func_t *funs);
+
+void gen_heap_insert(gen_heap_t *h, void *elem);
+
+int gen_heap_delete(gen_heap_t *h, void **val);
+
+void* gen_heap_peek(gen_heap_t *h);
+
+gen_heap_t* gen_heap_from_array(void **v, unsigned int N, unsigned int last, char htype, 
+                                gen_heap_func_t *funs);
+
+void gen_heap_dump(gen_heap_t *h);
+
+void gen_heap_destroy(gen_heap_t *h);
+
+int gen_heap_sort(void *v, unsigned int N, size_t size, 
+                  char dir, int (*compar)(const void*, const void*));
+
+#endif // __GEN_HEAP__
diff --git a/src/include/gen_pqueue.h b/src/include/gen_pqueue.h
new file mode 100644
index 0000000..4dec23b
--- /dev/null
+++ b/src/include/gen_pqueue.h
@@ -0,0 +1,108 @@
+/**
+ *  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 __GEN_PQUEUE_H__
+#define __GEN_PQUEUE_H__
+
+#include "gen_heap.h"
+
+#define KEY_ERROR -1
+#define ID_ERROR  -2
+
+/*
+ * 
+ * This implementation of the priority queue is based on gen_heap, but
+ * requires some additional code to work, since we need to maintain an
+ * array of "handles", i.e. a mapping between elements and their
+ * current positions in the heap
+ *
+ */
+
+typedef struct{
+  int (*compare)(const void *e1, const void *e2); /* compare two elements (standard comparator) */
+  void* (*alloc_vector)(unsigned int N); /* */
+  void (*dealloc_vector)(void *v); /* */
+  void (*dealloc_elem)(void *e); /* deallocate an element */
+  void (*print_elem)(void *e); /* print an element */
+  int  (*get_id)(void *e); /* get the id associated to an element
+                              (used for handles management) */
+  void* (*get_key)(void *e);/* get the current key of element e */
+  void (*set_key)(void *e, void *k); /* set a new key to element e */
+  int (*compare_to_key)(void *e, void *key); /* compare a key with the one of element e */
+} gen_pqueue_func_t;
+
+
+
+typedef struct{
+  int N;
+  int last;
+  void **v;
+  gen_pqueue_func_t funs;
+  char qtype;
+  int *handles;
+} gen_pqueue_t;
+
+
+
+#define MIN_QUEUE 0x01
+#define MAX_QUEUE 0x02
+
+
+
+gen_pqueue_t * gen_pqueue_init(unsigned int N, char htype, gen_pqueue_func_t *funs);
+
+void gen_pqueue_insert(gen_pqueue_t *h, void *elem);
+
+int gen_pqueue_delete(gen_pqueue_t *h, void **val);
+
+void* gen_pqueue_peek(gen_pqueue_t *h);
+
+gen_pqueue_t* gen_pqueue_from_array(void **v, unsigned int N, unsigned int last, char htype, 
+                                gen_pqueue_func_t *funs);
+
+int gen_pqueue_change_key(gen_pqueue_t *q, unsigned int i, void *key);
+
+int gen_pqueue_force_key(gen_pqueue_t *q, unsigned int idx, void *key);
+
+void gen_pqueue_dump(gen_pqueue_t *h);
+
+void gen_pqueue_destroy(gen_pqueue_t *h);
+
+int gen_pqueue_get_handle(gen_pqueue_t *q, int id);
+
+void* gen_pqueue_get_key(gen_pqueue_t *q, int idx);
+
+
+
+
+#endif // __GEN_PQUEUE_H__
diff --git a/src/include/gen_stack.h b/src/include/gen_stack.h
new file mode 100644
index 0000000..2dc46c5
--- /dev/null
+++ b/src/include/gen_stack.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:
+ *
+ ***********************************************************************
+ */
+
+#ifndef __GEN_STACK_H__
+#define __GEN_STACK_H__
+
+typedef struct{
+  unsigned int size;
+  int head;
+  void **v;
+} gen_stack_t;
+
+
+void gen_stack_create(gen_stack_t *s);
+
+void gen_stack_push(gen_stack_t *s, void *elem);
+
+int gen_stack_pop(gen_stack_t *s, void **res);
+
+int gen_stack_empty(gen_stack_t *s);
+
+int gen_stack_size(gen_stack_t *s);
+
+
+#endif //__GEN_STACK_H__
diff --git a/src/include/iltree.h b/src/include/iltree.h
new file mode 100644
index 0000000..d30dc83
--- /dev/null
+++ b/src/include/iltree.h
@@ -0,0 +1,93 @@
+/**
+ *  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 __ILTREE_H__
+#define __ILTREE_H__
+
+
+typedef struct node{
+  void* info;
+  struct node* left;
+  struct node* right;
+} node_t;
+
+typedef struct{
+  void* (*alloc)();
+  void (*dealloc)(void*);
+  void (*copy)(void *src, void *dst);
+  int (*compare)(void*, void*);
+  void (*print)(void*, void*);
+  void *fileout;
+} ilfunc_t;
+
+
+typedef struct {
+  node_t* root;
+  ilfunc_t funs;
+} iltree_struct_t;
+
+
+
+typedef iltree_struct_t* iltree_t;
+
+
+void iltree_set_funs(iltree_t, ilfunc_t *);
+
+void iltree_destroy(iltree_t);
+
+void iltree_empty(iltree_t);
+
+void iltree_insert(iltree_t, void*);
+
+void* iltree_lookup(iltree_t, void*);
+
+void iltree_view_pre(iltree_t);
+
+iltree_t iltree_create(iltree_t);
+
+void iltree_empty_cache(iltree_t);
+
+void iltree_map(iltree_t, void (*func)(void*));
+
+void iltree_map_args(iltree_t, void (*func)(void*, void*), void*);
+
+void* iltree_get_fileout(iltree_t t);
+
+void iltree_set_fileout(iltree_t t, void *f);
+
+void* iltree_getmin(iltree_t t);
+
+void* iltree_getmax(iltree_t t);
+
+
+
+#endif /* __ILTREE_H__*/
diff --git a/src/include/iltree_double.h b/src/include/iltree_double.h
new file mode 100644
index 0000000..f294aae
--- /dev/null
+++ b/src/include/iltree_double.h
@@ -0,0 +1,62 @@
+/**
+ *  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
+ *
+ ***********************************************************************
+ *
+ *  Implementation of the iltree data structure with keys of type
+ *  "long double"
+ *
+ */
+
+#ifndef __ILTREE_DOUBLE_H__
+#define __ILTREE_DOUBLE_H__
+
+
+
+#include "iltree.h"
+
+iltree_t iltree_double_init(iltree_t t, void *fileout);
+
+
+void* alloc_double();
+
+void dealloc_double(void *elem);
+
+void copy_double(void *elem1, void *elem2);
+
+int compare_long_double(void *elem1, void *elem2);
+
+void print_long_double(void *elem, void *fileout);
+
+
+
+void iltree_double_dump_edges(iltree_t t);
+
+
+#endif // __ILTREE_DOUBLE_H__
diff --git a/src/include/utils.h b/src/include/utils.h
new file mode 100644
index 0000000..599a287
--- /dev/null
+++ b/src/include/utils.h
@@ -0,0 +1,138 @@
+/**
+ *  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 __UTILS_H__
+#define __UTILS_H__
+
+#define VALID_PTR_OR_EXIT(ptr, status) \
+  if (!ptr){\
+    fprintf(stderr, "Error in %s at line %d -- Exiting!!!\n", \
+            __FILE__, __LINE__);\
+    exit(status);\
+  }
+
+
+int read_deg_distr(FILE *filein, unsigned int **degs, unsigned int **Nk, double **p);
+
+int read_deg_seq(FILE *filein, unsigned int **nodes);
+
+int read_stubs(FILE *filein, unsigned int **S);
+
+int read_ij(FILE *filein, unsigned int **i, unsigned int **j);
+
+int read_ij_w(FILE *filein, unsigned int **i, unsigned int **j, double **w);
+
+void read_slap(FILE *filein, unsigned int *K, unsigned int *N, 
+               unsigned int **J_slap, unsigned int **r_slap);
+
+void read_slap_w(FILE *filein, unsigned int *K, unsigned int *N, 
+                 unsigned int **J_slap, unsigned int **r_slap, double **W_slap);
+
+void read_slap_dir(FILE *filein, unsigned int *K, unsigned int *N, 
+               unsigned int **J_slap, unsigned int **r_slap);
+
+void read_slap_dir_incoming(FILE *filein, unsigned int *K, unsigned int *N, 
+               unsigned int **J_slap, unsigned int **r_slap);
+
+
+int convert_ij2slap(unsigned int *I, unsigned int *J, unsigned int K, 
+                    unsigned int ** r_slap, unsigned int **J_slap);
+
+int convert_ij2slap_N(unsigned int *I, unsigned int *J, unsigned int K,   
+                      unsigned int N, unsigned int ** r_slap, 
+                      unsigned int **J_slap);
+
+int convert_ij2slap_w(unsigned int *I, unsigned int *J, double *W,  unsigned int K, 
+                      unsigned int ** r_slap, unsigned int **J_slap, 
+                      double **W_slap);
+  
+
+void write_edges(FILE *fileout, unsigned int *J_slap, 
+                 unsigned int *r_slap, unsigned int N);
+  
+void write_edges_dir(FILE *fileout, unsigned int *J_slap, 
+                 unsigned int *r_slap, unsigned int N);
+  
+
+void dump_deg_distr(unsigned int *degs, double *p, int n);
+
+void dump_deg_seq(unsigned int *nodes, int N);
+
+
+FILE* openfile_or_exit(char *filename, char *mode, int exitcode);
+
+int compare_int(const void *x1, const void *x2);
+
+int compare_double(const void *x1, const void *x2);
+
+void print_int(void *elem);
+
+void print_double(void *elem);
+
+unsigned int find_max(unsigned int *, unsigned int);
+
+int is_neigh(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+             unsigned int i, unsigned int j);
+
+int is_neigh_bs(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+             unsigned int i, unsigned int j);
+
+double get_neigh_weight(unsigned int *J_slap, unsigned int *r_slap, double *W_slap, 
+                        unsigned int N,  unsigned int i, unsigned int j);
+
+/* sort the adjacency list of neighbours of each node in ascending order */
+void sort_neighbours(unsigned int *J_slap, unsigned int *r_slap, unsigned int N);
+
+double strength(unsigned int *r_slap,  double *W_slap, int i);
+
+void convert_slap2ij(unsigned int *J_slap, unsigned int *r_slap, int N, unsigned int *I, unsigned int *J);
+
+/* Show a simple progress message */
+void show_progress(FILE *fout, char *s, unsigned int progress, unsigned int total);
+
+
+/* find the position of a neghbour of i (node j) in J_slap */
+int find_neigh_in_Jslap(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, 
+                        unsigned int i, unsigned int j, unsigned int *ret);
+
+
+/* shuffle a vector of integers in-place */
+void shuffle_vector(unsigned int *v, unsigned int N);
+
+
+unsigned int read_partition(FILE *fin, unsigned int N, unsigned int *part);
+
+int degree (unsigned int *r_slap, unsigned int i);
+
+int my_strcasecmp(const char *s1, const char *s2);
+
+#endif /*__UTILS_H__*/