nysol-take 3.0.0

data/ext/macerun/src/sgraph.c

@@ -0,0 +1,360 @@
+/*  graph library by array list
+            12/Feb/2002    by Takeaki Uno
+    homepage:   http://research.nii.ac.jp/~uno/index.html  */
+/* This program is available for only academic use, basically.
+   Anyone can modify this program, but he/she has to write down 
+    the change of the modification on the top of the source code.
+   Neither contact nor appointment to Takeaki Uno is needed.
+   If one wants to re-distribute this code, do not forget to 
+    refer the newest code, and show the link to homepage of 
+    Takeaki Uno, to notify the news about the codes for the users.
+   For the commercial use, please make a contact to Takeaki Uno. */
+
+#ifndef _sgraph_c_
+#define _sgraph_c_
+
+#include"sgraph.h"
+#include"vec.c"
+
+SGRAPH INIT_SGRAPH = {TYPE_SGRAPH,NULL,0,INIT_SETFAMILY_,INIT_SETFAMILY_,INIT_SETFAMILY_,0,NULL,NULL,NULL};
+
+/*  initialization  */
+void SGRAPH_alloc (SGRAPH *G, QUEUE_ID nodes, size_t edge_num, size_t arc_num){
+  if ( edge_num > 0 ){
+    SETFAMILY_alloc (&G->edge, nodes, NULL, nodes, edge_num);
+    if ( G->flag&LOAD_EDGEW && (!ERROR_MES) ) SETFAMILY_alloc_weight (&G->edge);
+  }
+  if ( arc_num > 0 ){
+    SETFAMILY_alloc (&G->in, nodes, NULL, nodes, arc_num);
+    SETFAMILY_alloc (&G->out, nodes, NULL, nodes, arc_num);
+    if ( G->flag&LOAD_EDGEW && (!ERROR_MES) ){
+      SETFAMILY_alloc_weight (&G->in);
+      SETFAMILY_alloc_weight (&G->out);
+    }
+  }
+  if (G->flag&LOAD_NODEW) calloc2 (G->node_w, nodes, G->node_w=0);
+  if ( ERROR_MES ){ SGRAPH_end (G); EXIT; }
+}
+
+/* copy graph G to graph G2. Underconstruction */
+//void SGRAPH_cpy (SGRAPH *G2, SGRAPH *G){}
+
+/* free graph object  */
+void SGRAPH_end (SGRAPH *G){
+  SETFAMILY_end (&G->edge);
+  SETFAMILY_end (&G->in);
+  SETFAMILY_end (&G->out);
+  mfree (G->wbuf, G->perm);
+  *G = INIT_SGRAPH;
+}
+
+
+/*  make an edge between u and v.
+   If they are already connected, it will be a multiple edge */
+void SGRAPH_edge_mk (SGRAPH *G, QUEUE_INT u, QUEUE_INT v, WEIGHT w){
+  if ( G->edge.w ){
+    G->edge.w[u][G->edge.v[u].t] = w;
+    G->edge.w[v][G->edge.v[v].t] = w;
+  }
+  ARY_INS (G->edge.v[u], v);
+  ARY_INS (G->edge.v[v], u);
+  G->edge.eles += 2;
+}
+
+/*  make an arc between u and v.
+   If they are already connected, it will be a multiple arc */
+void SGRAPH_arc_mk (SGRAPH *G, QUEUE_INT u, QUEUE_INT v, WEIGHT w){
+  if ( G->out.w ) G->out.w[u][G->out.v[u].t] = w;
+  if ( G->in.w ) G->in.w[v][G->in.v[v].t] = w;
+  ARY_INS (G->out.v[u], v);
+  ARY_INS (G->in.v[v], u);
+  G->in.eles++;
+  G->out.eles++;
+}
+
+/* Delete the edge connecting u and v. If edge (u,v) does not exist, nothing will occur. */
+void SGRAPH_edge_rm_iter (SETFAMILY *M, QUEUE_INT u, QUEUE_INT v){
+  QUEUE_INT i;
+  if ( (i = (QUEUE_INT)QUEUE_ele (&M->v[u], v)) >= 0 ){
+    QUEUE_rm (&M->v[u], i);
+    if ( M->w ) M->w[u][i] = M->w[u][M->v[u].t];
+    M->eles--;
+  }
+}
+
+/* Delete the edge connecting u and v. If edge (u,v) does not exist, nothing will occur. */
+void SGRAPH_edge_rm (SGRAPH *G, QUEUE_INT u, QUEUE_INT v){
+  SGRAPH_edge_rm_iter (&G->edge, u, v);
+  SGRAPH_edge_rm_iter (&G->edge, v, u);
+}
+
+/* Delete the arc connecting u and v. If arc (u,v) does not exist, nothing will occur. */
+void SGRAPH_arc_rm (SGRAPH *G, QUEUE_INT u, QUEUE_INT v){
+  SGRAPH_edge_rm_iter (&G->out, u, v);
+  SGRAPH_edge_rm_iter (&G->in, v, u);
+}
+
+/*  print graph by numbers  */
+void SGRAPH_print (SGRAPH *G){
+  VEC_ID i, j;
+  QUEUE_INT e;
+  
+  printf ("#node "VEC_IDF" ,#edge %zd ,#arc %zd\n", SGRAPH_NODE_NUM(*G), G->edge.eles, G->in.eles);
+  FLOOP (i, 0, SGRAPH_NODE_NUM(*G)){
+    printf ("NODE "VEC_IDF" ", i);
+    if ( G->node_w ){ putchar ('('); print_WEIGHT (G->node_w[i]); putchar (')'); }
+    printf (" >>\n");
+    if ( G->edge.v && G->edge.v[i].t ){
+      printf ("    edge      : ");
+      for (j=0; j<G->edge.v[i].t ; j++){
+        e = G->edge.v[i].v[j];
+        printf (VEC_IDF, e);
+        if ( G->edge.w ){ putchar ('('); print_WEIGHT (G->edge.w[i][j]); putchar (')'); }
+        putchar (',');
+      }
+      putchar ('\n');
+    }
+    if ( G->in.w ){
+      if ( G->in.v[i].t ){
+        printf ("    in-arc      : ");
+        for (j=0; j<G->in.v[i].t ; j++){
+          e = G->in.v[i].v[j];
+          printf (VEC_IDF, e);
+          if ( G->in.w ){ putchar ('('); print_WEIGHT (G->in.w[i][j]); putchar (')'); }
+          putchar (',');
+        }
+        putchar ('\n');
+      }
+    }
+    if ( G->out.w ){
+      if ( G->out.v[i].t ){
+        printf ("    out-arc      : ");
+        for (j=0; j<G->out.v[i].t ; j++){
+          e = G->out.v[i].v[j];
+          printf (VEC_IDF, e);
+          if ( G->out.w ){ putchar ('('); print_WEIGHT (G->out.w[i][j]); putchar (')');}
+          putchar (',');
+        }
+        putchar ('\n');
+      }
+    }
+  }
+}
+
+/* Output a graph to file
+  Vertices, edges, arcs less than node_num, edge_num, arc_num are written to the file. Input parameters are
+  (graph) (file name) (flag)
+  SGRAPH_READ_NODEW 512 // read node weight
+  SGRAPH_READ_EDGEW 1024 // read edge weight
+*/
+/*
+  format of file:(including notifications to make input file)
+   
+  the ith row corresponds to node i-1, and
+    ID list of nodes adjacent to i, and having ID > i, for undirected graph
+    ID list of nodes adjacent to i by out-going arc of i, for directed graph
+   Separator is ",", but graph load routine accepts any letter for 
+    separator but not a number.
+   If the graph has both edges and arcs, write them in two lines separately,
+    so a node then uses two lines, and #nodes = #lines/2.
+  
+    ==  Notifications to make input file ==
+   Notice that if 0th line has node 2, and the 2nd line has 0, then there
+    will be multiple edge (0,2) and (2,0).
+   The read routine does not make error with multiple edges, it is allowed.
+
+   The ID of nodes begin from 0. After reading graph, node_num is set to
+    node_end.
+
+   Input file example, without weights, E={(0,1),(0,2),(1,1),(1,3),(2,3)}
+===========
+   1,2
+   1 3
+   3
+   
+   [EOF]
+=========
+   Nodes are 0,1, and 2, both edges and arcs exist, with node/edge/arc weights)
+   5000,1,30
+   0,50,1,20,
+   100,1,3
+   2,20
+   200
+   
+   [EOF]
+=======
+   where node weights are 5000, 100, 200, and edges and their weights are
+    (0,1),30,   (1,1),3
+    arcs and their weights are (0,0),50,   (0,1), 20,   (1,2), 20
+
+    In the case of bipartite graph, write the adjacent-node lists only for 
+     the node in node set one.
+     
+    
+*/
+
+/* graph load routine. Allocate memory as much as the size of input file.
+   parameters are, 
+   (graph) (file name) 
+ LOAD_EDGE // read undirected edge from file
+ LOAD_ARC // read directed arc from file
+ LOAD_BIPARTITE // load bipartite graph
+ LOAD_NODEW // read node weight
+ LOAD_EDGEW // read edge weight
+*/
+/* In the bipartite case, even if the IDs of node set 2 begin from 0, i.e.,
+   overlaps with node 1, the routine automatically correct them. */
+/* Directed bipartite graph, all arcs are considered to be from node set 1
+ to node set 2. If both directions exist, read as a general graph, and set
+  node1_num later in some way. */
+/* The routine compares the maximum node index and #lines, and set #node
+  to the larger one. However, if node weight exists, weights will be included 
+  in the candidates of maximum index, thus in this case we fix #node := #lines.
+  In the case of bipartite graph, the routine compares, but the weights of 
+   non-existing lines will be -1. */
+
+/* make the opposite direction edge, for each edge; buffers have to be already doubly allocated */
+void SGRAPH_load_delivery (SGRAPH *G, SETFAMILY *OO, SETFAMILY *MM, QUEUE_ID *c){
+  VEC_ID i;
+  QUEUE_ID j;
+  QUEUE_INT e;
+  FLOOP (i, 0, MM->t) c[i] = MM->v[i].t;
+  FLOOP (i, 0, MM->t){
+    FLOOP (j, 0, c[i]){
+      e = MM->v[i].v[j];
+      if ( OO->w ) OO->w[e][OO->v[e].t] = MM->w[i][j];
+      ARY_INS (OO->v[e], i);
+    }
+  }
+}
+
+/* make the opposite direction edge, for each edge; buffers have to be already doubly allocated */
+void SGRAPH_mk_opposite_edge (SGRAPH *G, QUEUE_ID *c){
+  VEC_ID i;
+  size_t j, jj;
+  j = G->edge.eles;  // shift the arrays to insert edges of opposite directions
+  BLOOP (i, G->edge.t, 0){
+    j -= G->edge.v[i].t+c[i];
+    jj = G->edge.v[i].t+1;
+    do {
+      jj--;
+      G->edge.buf[j+i+jj] = G->edge.v[i].v[jj];
+    } while ( jj>0 );
+    G->edge.v[i].end += c[i];
+    G->edge.v[i].v = &G->edge.buf[j+i];
+    if ( G->edge.w ){
+      memcpy ( &G->edge.buf[j], G->edge.w[i], sizeof(WEIGHT)*G->edge.v[i].t );
+      G->edge.w[i] = &G->edge.wbuf[j];
+    }
+  }
+}
+
+/* load edges/arcs (determined by G->flag) from file */
+void SGRAPH_load (SGRAPH *G){
+  VEC_ID i;
+  QUEUE_ID *c;
+  SETFAMILY *F1, *F2;
+  if ( G->flag & LOAD_ELE ){
+    G->edge.flag |= LOAD_ELE;
+    G->in.flag |= LOAD_ELE;
+    G->out.flag |= LOAD_ELE;
+  }
+  if ( G->flag&LOAD_EDGE ){ F1 = F2 = &G->edge; G->edge.flag |= LOAD_DBLBUF; }
+  else { F1 = &G->in; F2 = &G->out; }
+  F1->fname = G->fname; F1->wfname = F1->wfname;
+  SETFAMILY_load (F1);
+    // adjact so that #rows and #colums are the same
+  if ( !(G->flag&LOAD_BIPARTITE)){
+    if ( F1->clms < F1->t ){
+      F1->clms = F1->t;
+      FLOOP (i, 0, F1->t) F1->v[i].v[F1->v[i].t] = F1->t; // re-set endmark
+    } else if ( F1->clms > F1->t ){
+      reallocx_ (F1->v, F1->t, F1->clms, INIT_QUEUE, EXIT);
+      FLOOP (i, F1->t, F1->clms){
+        F1->v[i].v = F1->v[F1->t -1].v +F1->v[F1->t -1].t +1 +(i -(F1->t-1));
+        F1->v[i].v[0] = F1->clms;
+      } // re-set endmark
+      F1->t = F1->clms;
+    }
+  }
+
+  calloc2 (c, F1->t, EXIT);
+  QUEUE_delivery (NULL, c, NULL, F1->v, NULL, F1->t, F1->t);
+
+  if ( F1 != F2 ) SETFAMILY_alloc (F2, F1->t, c, F1->t, 0);
+  else {
+    G->edge.eles *= 2;  G->edge.ele_end *= 2;
+    SGRAPH_mk_opposite_edge (G, c); // shift the arrays to insert edges of opposite directions
+  }
+
+  SGRAPH_load_delivery (G, F2, F1, c);
+  free (c);
+  F2->clms = F2->t; FLOOP (i, 0, F2->t) F2->v[i].v[F2->v[i].t] = F2->t; // re-set endmark
+
+  F1->flag |= G->flag; SETFAMILY_sort (F1);
+  if ( F1 != F2 ){ F2->flag |= G->flag; SETFAMILY_sort (F2); }
+  print_mes (G, "sgraph: %s ,#nodes %d ,#edges %zd ,#arcs %zd", G->fname, SGRAPH_NODE_NUM(*G), G->edge.eles/2,  G->in.eles);
+  if ( G->wfname ) print_mes (G, " ,weight file: %s", G->wfname);
+  print_mes (G, "\n");
+}
+
+/* replace node i by perm[i] */
+void SGRAPH_replace_index (SGRAPH *G, PERM *perm, PERM *invperm){
+  QUEUE_INT *x;
+  VEC_ID i;
+  QUEUE Q;
+  WEIGHT *w, ww;
+  
+  FLOOP (i, 0, G->edge.t)
+  if ( G->edge.v ){
+    MQUE_FLOOP (G->edge.v[i], x) *x = perm[*x];
+    ARY_INVPERMUTE (G->edge.v, invperm, Q, G->edge.t, EXIT);
+  }
+  if ( G->in.v ){
+    MQUE_FLOOP (G->in.v[i], x) *x = perm[*x];
+    ARY_INVPERMUTE (G->in.v, invperm, Q, G->edge.t, EXIT);
+  }
+  if ( G->out.v ){
+    MQUE_FLOOP (G->out.v[i], x) *x = perm[*x];
+    ARY_INVPERMUTE (G->out.v, invperm, Q, G->edge.t, EXIT);
+  }
+  if ( G->edge.w ) ARY_INVPERMUTE (G->edge.w, invperm, w, G->edge.t, EXIT);
+  if ( G->in.w ) ARY_INVPERMUTE (G->in.w, invperm, w, G->edge.t, EXIT);
+  if ( G->out.w ) ARY_INVPERMUTE (G->out.w, invperm, w, G->edge.t, EXIT);
+  if ( G->node_w ) ARY_INVPERMUTE (G->node_w, invperm, ww, G->edge.t, EXIT);
+  G->perm = perm;
+}
+
+/* sort the nodes according to the permutation *tmp */
+void SGRAPH_perm_node (SGRAPH *G, PERM *tmp){
+  VEC_ID c1=0, c2=G->node1_num, i;
+  PERM *perm;
+  malloc2 (perm, G->edge.t, {free(tmp);EXIT;});
+  FLOOP (i, 0, G->edge.t)
+      if ( tmp[i]<G->node1_num ) perm[tmp[i]] = c1++; else perm[tmp[i]] = c2++;
+  ARY_INV_PERM_ (tmp, perm, G->edge.t);
+  SGRAPH_replace_index (G, perm, tmp);
+  free2 (tmp);
+}
+
+/* sort the nodes by Q->t, increasing if flag=1, decreasing if flag=-1 */
+void SGRAPH_sort_node (SGRAPH *G, int flag){
+  PERM *tmp;
+  tmp = qsort_perm_VECt ((VEC *)(G->edge.v), G->edge.t, flag==1?sizeof(QUEUE):-sizeof(QUEUE));
+  SGRAPH_perm_node (G, tmp);
+}
+
+/* remove all selfloops (assumption, selfloop is at most one for each vertex) */
+void SGRAPH_rm_selfloop (SGRAPH *G){
+  QUEUE_INT i, *x;
+  FLOOP (i, 0, G->edge.t){
+    MQUE_FLOOP (G->edge.v[i], x){
+      if ( *x == i ){
+        G->edge.v[i].t--;
+        while ( x < G->edge.v[i].v + G->edge.v[i].t ){ *x = *(x+1); x++; }
+        break;
+      }
+    }
+  }
+}
+#endif

data/ext/macerun/src/sgraph.h

@@ -0,0 +1,174 @@
+/*  graph library by array list
+            12/Feb/2002    by Takeaki Uno
+    homepage:   http://research.nii.ac.jp/~uno/index.html  */
+/* This program is available for only academic use, basically.
+   Anyone can modify this program, but he/she has to write down 
+    the change of the modification on the top of the source code.
+   Neither contact nor appointment to Takeaki Uno is needed.
+   If one wants to re-distribute this code, do not forget to 
+    refer the newest code, and show the link to homepage of 
+    Takeaki Uno, to notify the news about the codes for the users.
+   For the commercial use, please make a contact to Takeaki Uno. */
+
+/****************************************************************************/
+/* d = degree of node i := G->edge/in/out.v[i].t
+   d = max/min (in/out) degree := VEC_MAXT(d,G->edge.v/in.v/out.v,0,...->t)  (VEC_MINT, resp.)
+   #nodes :=  SGRAPH_NODE_NUM(G)
+   #edges :=  G->edge.eles/2
+   #arcs :=   G->in.eles or G->out.eles
+   load_node_weight := ARY_LOAD_WEIGHT(G->node_w,WEIGHT,filename,counter,"errormes", EXIT) 
+   load_node_weight := ARY_LOAD_WEIGHT(G->node_w,WEIGHT,filename,counter,"errormes", EXIT) 
+
+   sort_node by size := SGRAPH_sort_node_iter (G, qsort_perm_VECt ((VEC *)Q, G->node_end, flag)
+   sort_node by weight := SGRAPH_sort_node_iter (G, qsort_perm_WEIGHT (w, G->node_end, flag)
+*/
+/****************************************************************************/
+
+#ifndef _sgraph_h_
+#define _sgraph_h_
+
+#include"stdlib2.h"
+#include"vec.h"
+
+
+/*  structure for graph  */
+typedef struct {
+  unsigned char type;   // structure type flag
+  char *fname;      // input file name
+  int flag;         // flag for load routine
+
+  SETFAMILY edge, in, out;  // setfamily for edge, in-arc, out-arc
+  QUEUE_INT node1_num;   // the size of vertex set 1, bipartite case. otherwise 0
+  WEIGHT *node_w, *wbuf;    // pointer to the node weight array(int)
+  PERM *perm;       // node permutation (nodes->original)
+  char *wfname;     // weight file name
+} SGRAPH;
+extern SGRAPH INIT_SGRAPH;
+
+#define SGRAPH_NODE_NUM(G)    MAX((G).edge.t,(G).in.t)
+
+/*************** initialization/termination ***********************/
+
+/*  initialization, termination, allocate arrays for weights, copy and duplication */
+void SGRAPH_alloc (SGRAPH *G, int node_num, size_t edge_num, size_t arc_num);
+void SGRAPH_cpy (SGRAPH *G2, SGRAPH *G);
+void SGRAPH_end (SGRAPH *G);
+
+
+/**************** addition/deletion **********************************/
+
+/*  make/take/remove edge e as connecting vertices u and v,
+ and  edge (u,v). 
+  do nothing if when make already existing edge, or delete non-existing edge.
+  with range check of parameters */
+
+void SGRAPH_edge_mk (SGRAPH *G, QUEUE_INT u, QUEUE_INT v, WEIGHT w);
+void SGRAPH_edge_rm (SGRAPH *G, QUEUE_INT u, QUEUE_INT v);
+void SGRAPH_arc_mk (SGRAPH *G, QUEUE_INT u, QUEUE_INT v, WEIGHT w);
+void SGRAPH_arc_rm (SGRAPH *G, QUEUE_INT u, QUEUE_INT v);
+
+
+/******************* node/edge sort, and duplication reduction *********************/
+
+/* subroutine of sort_edge_list */
+void SGRAPH_sort_edge_list_iter (QUEUE *Q, WEIGHT **w, PERM *invperm, VEC_ID i, int flag);
+
+/* sort each array list, increasing if flag=1, and decreasing if flag=-1 */
+void SGRAPH_sort_edge_list (SGRAPH *G, int flag);
+
+/* replace node i by perm and invperm */
+void SGRAPH_replace_index (SGRAPH *G, PERM *perm, PERM *invperm);
+
+/* sort the nodes by permutation given by tmp */
+PERM *SGRAPH_sort_node_iter (SGRAPH *G, PERM *tmp);
+
+/* sort the nodes by degrees, increasing if flag=1, decreasing if flag=-1 */
+PERM *SGRAPH_sort_node_t (SGRAPH *G, QUEUE *Q, int flag);
+
+/* sort the nodes by node_weight, increasing if flag=1, decreasing if flag=-1 */
+PERM *SGRAPH_sort_node_w (SGRAPH *G, WEIGHT *w, int flag);
+
+/* remove multiple edges/arcs and self loops 
+   it works only when after applying sort_incident_edges */
+void SGRAPH_simple (SGRAPH *G, int flag);
+
+
+
+
+/******************* print routines *************************************/
+
+
+/*  print graph by numbers  */
+void SGRAPH_print (SGRAPH *G);
+
+/* Write the graph to file. Edges, arcs, and nodes from 0 to node_num/edge_num/arc_num are written to file. Parameters are
+  (graph) (file name) (not write edge weight => 0) (not write node weight => 0) */
+void SGRAPH_save (SGRAPH *G, char *fname);
+
+/* graph load routine. Allocate memory as much as the size of input file.
+   parameters are, 
+   (graph) (file name) (read edges?) (read arcs?) (read node weights?) (read edge weight?) (bipartite?) */
+/* In the row of each vertex, write only vertices larger than it connected by an edge */
+void SGRAPH_load (SGRAPH *G);
+void SGRAPH_load_node_weight (SGRAPH *G, char *filename);
+
+void SGRAPH_rm_selfloop (SGRAPH *G);
+/*
+  format of file:(including notifications to make input file)
+   
+  the ith row corresponds to node i-1, and
+    ID list of nodes adjacent to i, and having ID > i, for undirected graph
+    ID list of nodes adjacent to i by out-going arc of i, for directed graph
+   Separator is ",", but graph load routine accepts any letter for 
+    separator but not a number.
+   If the graph has both edges and arcs, write them in two lines separately,
+    so a node then uses two lines, and #nodes = #lines/2.
+  
+    ==  Notifications to make input file ==
+   Notice that if 0th line has node 2, and the 2nd line has 0, then there
+    will be multiple edge (0,2) and (2,0).
+   The read routine does not make error with multiple edges, it is allowed.
+
+   The ID of nodes begin from 0. After reading graph, node_num is set to
+    node_end.
+
+   Input file example, without weights, E={(0,1),(0,2),(1,1),(1,3),(2,3)}
+===========
+   1,2
+   1 3
+   3
+   
+   [EOF]
+=========
+   Nodes are 0,1, and 2, both edges and arcs exist, with node/edge/arc weights)
+   5000,1,30
+   0,50,1,20,
+   100,1,3
+   2,20
+   200
+   
+   [EOF]
+=======
+   where node weights are 5000, 100, 200, and edges and their weights are
+    (0,1),30,   (1,1),3
+    arcs and their weights are (0,0),50,   (0,1), 20,   (1,2), 20
+
+    In the case of bipartite graph, write the adjacent-node lists only for 
+     the node in node set one.
+     
+    
+*/
+  
+
+/*************************************************************************/
+   
+
+#endif 
+
+
+
+
+
+
+
+