nysol-take 3.0.0

data/ext/lcmseqrun/src/problem_zero.c

@@ -0,0 +1,439 @@
+/*  Common problem input/output routines /structure
+            25/Nov/2007   by Takeaki Uno  e-mail:uno@nii.jp, 
+    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, please
+    refer the newest code, and show the link to homepage of 
+    Takeaki Uno, to notify the news about the codes for the users. */
+
+/***************************************************/
+
+#ifndef _problem_c_
+#define _problem_c_
+
+#include"problem.h"
+
+#include"stdlib2.c"
+#include"queue.c"
+#include"itemset_zero.c"
+
+void PROBLEM_error (){
+  ERROR_MES = "command explanation";
+  EXIT;
+}
+
+/*************************************************************************/
+/* PROBLEM and ITEMSET initialization */
+/*************************************************************************/
+void PROBLEM_init (PROBLEM *P){
+  P->start_time = clock();
+  RAND_INIT;
+  ERROR_MES = NULL;
+
+#ifdef _FILE2_LOAD_FROM_MEMORY_
+  __load_from_memory_org2__ = __load_from_memory__ = __load_from_memory_org__;
+#endif
+
+  P->problem = P->problem2 = 0;
+  P->prog = 0;
+  P->prog2 = 0;
+  P->input_fname = P->input_fname2 = P->output_fname = P->output_fname2 = NULL;
+  P->workdir = P->workdir2 = NULL;
+  P->weight_fname = P->header_fname = P->table_fname = P->sc_fname = NULL;
+  P->position_fname = P->position2_fname = NULL;
+  P->outperm_fname = NULL;
+
+  P->root = 0;
+  P->dir = P->edge_dir = 0;
+  P->th = P->th2 = P->th3 = 0;
+  P->ratio = P->ratio2 = 0;
+  P->num = P->siz = P->dim = P->len = P->width = P->height = 0;
+  P->rows = 0;
+  P->clms = 0;
+  P->gap_ub = INTHUGE;
+  P->gap_lb = 0;
+  P->xmax = P->ymax = P->pxmax = P->pymax = 0;
+  P->tmax = P->tmin = 0;
+  P->cost = P->cost2 = 0;
+  
+  ITEMSET_init (&P->II);
+  ITEMSET_init (&P->II2);
+
+  P->vf = P->dep = NULL;
+  P->ff = INIT_QUEUE;
+
+  P->shift = NULL;
+  P->occ_w = P->occ_pw = P->occ_w2 = P->occ_pw2 = NULL;
+  P->buf = P->buf_org = NULL;
+  P->buf_end = 0;
+  
+  P->itemjump = P->itemcand = P->vecjump = P->veccand = INIT_QUEUE;  // for delivery
+  P->itemchr = P->vecchr = NULL;
+  P->OQ = P->OQ2 = P->VQ = P->VQ2 = NULL;   // for delivery
+  P->itemary = NULL;
+  P->itemmark = P->itemflag = P->vecmark = P->vecflag = NULL;  // mark for vector
+  P->occ_t = P->vecary = NULL;
+  P->oo = INIT_QUEUE;
+  P->vecw = NULL;
+  
+  P->pat = NULL;
+  P->plen = P->perr = 0;
+
+#ifdef _base_h_
+  P->B = INIT_BASE;
+#endif
+
+#ifdef _alist_h_
+  P->occ = INIT_MALIST;
+  P->itemlist = INIT_ALIST;
+  P->veclist = INIT_ALIST;
+#endif
+
+#ifdef _trsact_h_
+  TRSACT_init (&P->TT);
+  TRSACT_init (&P->TT2);
+#endif
+#ifdef _sgraph_h_
+  P->SG = INIT_SGRAPH;
+  P->SG2 = INIT_SGRAPH;
+#endif
+#ifdef _agraph_h_
+  P->AG = INIT_AGRAPH;
+  P->AG2 = INIT_AGRAPH;
+#endif
+#ifdef _seq_h_
+  SEQ_init (&P->SS);
+  SEQ_init (&P->SS2);
+#endif
+#ifdef _pos_h_
+  POS_init (&P->PS);
+  POS_init (&P->PS2);
+  P->PS.S = &P->SS;
+  P->PS2.S = &P->SS2;
+  P->PS.I = &P->II;
+  P->PS2.I = &P->II;
+#endif
+#ifdef _fstar_h_
+  P->FS = INIT_FSTAR;
+  P->FS2 = INIT_FSTAR;
+#endif
+
+#ifdef _vec_h_
+  P->MM = INIT_MAT;
+  P->MM2 = INIT_MAT;
+  P->SM = INIT_SMAT;
+  P->SM2 = INIT_SMAT;
+  P->FF = INIT_SETFAMILY;
+  P->FF2 = INIT_SETFAMILY;
+#endif
+
+#ifdef _barray_h_
+  P->BA = INIT_BARRAY;
+  P->BA2 = INIT_BARRAY;
+#endif
+}
+
+/*************************************************************************/
+/* PROBLEM load */
+/*************************************************************************/
+void PROBLEM_load (PROBLEM *P){
+  int f=0;
+  ITEMSET *II = &P->II;
+/******************************/
+#ifdef _trsact_h_
+  if ( P->TT.fname ){ TRSACT_load (&P->TT);       if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->TT2.fname ){ TRSACT_load (&P->TT2);       if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _sgraph_h_
+  if ( P->SG.fname ){ SGRAPH_load (&P->SG);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->SG2.fname ){ SGRAPH_load (&P->SG);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _agraph_h_
+  if ( P->AG.fname ){ AGRAPH_load (&P->AG);    if (ERROR_MES) goto ERR;}
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->AG2.fname ){ AGRAPH_load (&P->AG2);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _fstar_h_
+  if ( P->FS.fname ){ FSTAR_load (&P->FS);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FS2.fname ){ FSTAR_load (&P->FS2);     if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _vec_h_
+  if ( P->MM.fname ){ MAT_load (&P->MM);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->MM2.fname ){ MAT_load (&P->MM2);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->SM.fname ){ SMAT_load (&P->SM);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->SM2.fname ){ SMAT_load (&P->SM2);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF.fname ){ SETFAMILY_load (&P->FF);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF2.fname ){ SETFAMILY_load (&P->FF2);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF.wfname ){ SETFAMILY_load_weight (&P->FF);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF2.wfname ){ SETFAMILY_load_weight (&P->FF2);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF.cwfname ){ SETFAMILY_load_column_weight (&P->FF);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF2.cwfname ){ SETFAMILY_load_column_weight (&P->FF2);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF.rwfname ){ SETFAMILY_load_row_weight (&P->FF);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->FF2.rwfname ){ SETFAMILY_load_row_weight (&P->FF2);   if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _seq_h_
+  if ( P->SS.fname ){ SEQ_load (&P->SS);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->SS2.fname ){ SEQ_load (&P->SS2);     if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+#ifdef _barray_h_
+  if ( P->BA.fname ){ BARRAY_load (&P->BA);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+  if ( P->BA2.fname ){ BARRAY_load (&P->BA2);    if (ERROR_MES) goto ERR; }
+ #ifdef _FILE2_LOAD_FROM_MEMORY_
+   __load_from_memory_org__ = __load_from_memory__;
+ #endif
+#endif
+
+  if (P->input_fname){ f=1; print_mes (II, " input: %s", P->input_fname); }
+  if (P->weight_fname){ f=1; print_mes (II, " weight: %s", P->weight_fname); }
+  if (P->output_fname){ f=1; print_mes (II, " output to: %s",P->output_fname); }
+  if ( f ) print_mes (II, "\n");
+
+/******************************/
+
+  if ( !ERROR_MES ) return;
+  ERR:;
+  PROBLEM_end (P);
+  EXIT;
+}
+
+/* termination of problem */
+void PROBLEM_end (PROBLEM *P){
+  ITEMSET *II = &P->II;
+
+#ifdef _trsact_h_
+  TRSACT_end (&P->TT);
+  TRSACT_end (&P->TT2);
+#endif
+#ifdef _sgraph_h_
+  SGRAPH_end (&P->SG);
+  SGRAPH_end (&P->SG2);
+#endif
+#ifdef _agraph_h_
+  AGRAPH_end (&P->AG);
+  AGRAPH_end (&P->AG2);
+#endif
+#ifdef _seq_h_
+  SEQ_end (&P->SS);
+  SEQ_end (&P->SS2);
+#endif
+#ifdef _fstar_h_
+  FSTAR_end (&P->FS);
+  FSTAR_end (&P->FS2);
+#endif
+#ifdef _vec_h_
+  MAT_end (&P->MM);
+  MAT_end (&P->MM2);
+  SMAT_end (&P->SM);
+  SMAT_end (&P->SM2);
+  SETFAMILY_end (&P->FF);
+  SETFAMILY_end (&P->FF2);
+#endif
+#ifdef _pos_h_
+  POS_end (&P->PS);
+  POS_end (&P->PS2);
+#endif
+#ifdef _barray_h_
+  BARRAY_end (&P->BA);
+  BARRAY_end (&P->BA2);
+#endif
+
+/******************************/
+
+  mfree (P->vf, P->dep);
+  QUEUE_end (&P->ff);
+
+  ITEMSET_end (II);
+  ITEMSET_end (&P->II2);
+
+  if ( P->occ_pw2 != P->occ_pw && P->occ_pw2 != P->occ_w2 ) free2 (P->occ_pw2);
+  if ( P->occ_w2 != P->occ_w ) free2 (P->occ_w2);
+  if ( P->occ_pw != P->occ_w ) free2 (P->occ_pw);
+  mfree (P->shift, P->occ_t, P->occ_w);
+
+  if ( P->OQ ) free2 (P->OQ[0].v);
+  if ( P->OQ2 ) free2 (P->OQ2[0].v);
+  if ( P->VQ ) free2 (P->VQ[0].v);
+  if ( P->VQ2 ) free2 (P->VQ2[0].v);
+  mfree (P->OQ, P->OQ2, P->VQ, P->VQ2, P->itemchr, P->vecchr);
+
+  mfree (P->itemary, P->itemflag, P->itemmark, P->vecary, P->vecflag, P->vecmark, P->vecw);
+  QUEUE_end (&P->itemcand);
+  QUEUE_end (&P->itemjump);
+
+  QUEUE_end (&P->veccand);
+  QUEUE_end (&P->vecjump);
+  QUEUE_end (&P->oo);
+
+  free2 (P->buf_org);
+ 
+#ifdef _alist_h_
+  MALIST_end (&P->occ);
+  ALIST_end (&P->itemlist);
+  ALIST_end (&P->veclist);
+#endif
+
+#ifdef _undo_h_
+  ALISTundo_end ();
+#endif
+
+  P->end_time = clock();
+  if ( print_time_flag )
+   print_mes (II, "computation_time= %3f\n", ((double)(P->end_time-P->start_time))/CLOCKS_PER_SEC);
+
+#ifdef _FILE2_LOAD_FROM_MEMORY_
+  __load_from_memory_org__ = __load_from_memory_org2__;
+  __write_to_memory__ = __write_to_memory_org__;
+#endif
+
+  PROBLEM_init (P);
+}
+
+/* allocate arrays and structures */
+void PROBLEM_alloc (PROBLEM *P, QUEUE_ID siz, QUEUE_ID siz2, size_t siz3, PERM *perm, int f){
+  PERM *p;
+#ifdef _alist_h_
+  ALIST_ID i=0;
+#endif
+  int j;
+
+  if ( f&PROBLEM_SHIFT ) calloc2 (P->shift, siz+2, goto ERR);
+  if ( f&PROBLEM_OCC_T ) calloc2 (P->occ_t, siz+2, goto ERR);
+  if ( f&(PROBLEM_OCC_W+PROBLEM_OCC_PW) ) calloc2 (P->occ_w, siz+2, goto ERR);
+  if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw, siz+2, goto ERR);
+  else P->occ_pw = P->occ_w;
+  if ( f&PROBLEM_OCC_W2 ){
+    calloc2 (P->occ_w2, siz+2, goto ERR);
+    if ( f&PROBLEM_OCC_PW ) calloc2 (P->occ_pw2, siz+2, goto ERR);
+    else P->occ_pw2 = P->occ_w2;
+  } else { P->occ_w2 = P->occ_w; P->occ_pw2 = P->occ_pw; }
+
+  if ( f&PROBLEM_ITEMFLAG ) calloc2 (P->itemflag, siz+2, goto ERR);
+  if ( f&PROBLEM_ITEMMARK ) calloc2 (P->itemmark, siz+2, goto ERR);
+  if ( f&PROBLEM_ITEMARY ) calloc2(P->itemary, siz+2, goto ERR);
+  if ( f&PROBLEM_ITEMCHR ) calloc2(P->itemchr, siz+2, goto ERR);
+  if ( f&PROBLEM_ITEMJUMP ) QUEUE_alloc (&P->itemjump, siz+2);
+  if ( f&PROBLEM_ITEMCAND ) QUEUE_alloc (&P->itemcand, siz+2);
+
+  if ( f&PROBLEM_VECFLAG ) calloc2 (P->vecflag, siz2+2, goto ERR);
+  if ( f&PROBLEM_VECMARK ) calloc2 (P->vecmark, siz2+2, goto ERR);
+  if ( f&PROBLEM_VECARY ) calloc2 (P->vecary, siz2+2, goto ERR);
+  if ( f&PROBLEM_VECCHR ) calloc2 (P->vecchr, siz2+2, goto ERR);
+  if ( f&PROBLEM_VECJUMP ) QUEUE_alloc (&P->vecjump, siz2+2);
+  if ( f&PROBLEM_VECCAND ) QUEUE_alloc (&P->veccand, siz2+2);
+  if ( f&PROBLEM_VECW ) calloc2 (P->vecw, siz2+2, goto ERR);
+
+#ifdef _alist_h_
+  if ( f&PROBLEM_ITEMLIST ) ALIST_alloc (&P->itemlist, siz+2);
+  if ( f&PROBLEM_VECLIST ) ALIST_alloc (&P->veclist, siz2+2);
+
+  if ( f&PROBLEM_OCC3 ){
+    MALIST_alloc (&P->occ, siz, siz2+2); // element=>
+if ( ERROR_MES ) goto ERR;
+    if ( f&PROBLEM_OCC2 ){
+      FLOOP (i, 0, siz) MALIST_ins_tail (&P->occ, (f&PROBLEM_OCC1)?siz2: 0, i, 0);
+    }
+  }
+#endif
+
+    // set outperm
+  if ( P->outperm_fname ){
+    ARY_LOAD (p, int, j, P->outperm_fname, 1, EXIT);
+    if ( perm ){
+      FLOOP (j, 0, siz) perm[j] = p[perm[j]];
+      free2 (p);
+    } else perm = p;
+  }
+  ITEMSET_alloc (&P->II, P->output_fname, perm, siz, siz3);
+  if ( P->II.target<siz && P->II.perm )
+      FLOOP (j, 0, P->II.item_max){ if ( P->II.target == P->II.perm[j] ){ P->II.target = j; break; } }
+
+#ifdef _undo_h_
+  ALISTundo_init ();
+#endif
+
+  return;
+  ERR:;
+  PROBLEM_end (P);
+  EXIT;
+}
+
+#endif
+
+