BGI/SOAPdenovo2/standardPregraph/connect.c

   1 /*
   2  * connect.c
   3  *
   4  * Copyright (c) 2008-2012 BGI-Shenzhen <soap at genomics dot org dot cn>.
   5  *
   6  * This file is part of SOAPdenovo.
   7  *
   8  * SOAPdenovo is free software: you can redistribute it and/or modify
   9  * it under the terms of the GNU General Public License as published by
  10  * the Free Software Foundation, either version 3 of the License, or
  11  * (at your option) any later version.
  12  *
  13  * SOAPdenovo is distributed in the hope that it will be useful,
  14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16  * GNU General Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License
  19  * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
  20  *
  21  */
  22
  23 #include "stdinc.h"
  24 #include "newhash.h"
  25 #include "kmerhash.h"
  26 #include "extfunc.h"
  27 #include "extvab.h"
  28
  29 #define CNBLOCKSIZE 100000
  30
  31 void createCntMemManager ()
  32 {
  33         if ( !cn_mem_manager )
  34         {
  35                 cn_mem_manager = createMem_manager ( CNBLOCKSIZE, sizeof ( CONNECT ) );
  36         }
  37         else
  38         {
  39                 fprintf ( stderr, "The cn_mem_manger created.\n" );
  40         }
  41 }
  42
  43 void destroyConnectMem ()
  44 {
  45         freeMem_manager ( cn_mem_manager );
  46         cn_mem_manager = NULL;
  47 }
  48
  49 CONNECT * allocateCN ( unsigned int contigId, int gap )
  50 {
  51         CONNECT * newCN;
  52         newCN = ( CONNECT * ) getItem ( cn_mem_manager );
  53         newCN->contigID = contigId;
  54         newCN->gapLen = gap;
  55         newCN->minGap = 0;
  56         newCN->maxGap = 0;
  57         newCN->bySmall = 0;
  58         newCN->smallIns = 0;
  59         newCN->weakPoint = 0;
  60         newCN->weight = 1;
  61         newCN->weightNotInherit = 0;
  62         newCN->mask = 0;
  63         newCN->used = 0;
  64         newCN->checking = 0;
  65         newCN->deleted = 0;
  66         newCN->prevInScaf = 0;
  67         newCN->inherit = 0;
  68         newCN->singleInScaf = 0;
  69         newCN->nextInScaf = NULL;
  70         return newCN;
  71 }
  72
  73 void output_cntGVZ ( char * outfile )
  74 {
  75         char name[256];
  76         FILE * fp;
  77         unsigned int i;
  78         CONNECT * connect;
  79         boolean flag;
  80         sprintf ( name, "%s.scaffold.gvz", outfile );
  81         fp = ckopen ( name, "w" );
  82         fprintf ( fp, "digraph G{\n" );
  83         fprintf ( fp, "\tsize=\"512,512\";\n" );
  84
  85         for ( i = num_ctg; i > 0; i-- )
  86         {
  87                 if ( !contig_array[i].downwardConnect )
  88                 {
  89                         continue;
  90                 }
  91
  92                 connect = contig_array[i].downwardConnect;
  93
  94                 while ( connect )
  95                 {
  96                         if ( connect->deleted )
  97                         {
  98                                 connect = connect->next;
  99                                 continue;
 100                         }
 101
 102                         if ( connect->prevInScaf || connect->nextInScaf )
 103                         {
 104                                 flag = 1;
 105                         }
 106                         else
 107                         {
 108                                 flag = 0;
 109                         }
 110
 111                         if ( !connect->mask )
 112                                 fprintf ( fp, "\tC%d_%d -> C%d_%d [label = \"%d(%d_%d)\"];\n", i, contig_array[i].length, connect->contigID, contig_array[connect->contigID].length,
 113                                           connect->gapLen, flag, connect->weight );
 114                         else
 115                                 fprintf ( fp, "\tC%d_%d -> C%d_%d [label = \"%d(%d_%d)\", color = red];\n", i, contig_array[i].length, connect->contigID, contig_array[connect->contigID].length,
 116                                           connect->gapLen, flag, connect->weight );
 117
 118                         connect = connect->next;
 119                 }
 120         }
 121
 122         fprintf ( fp, "}\n" );
 123         fclose ( fp );
 124 }
 125
 126 /***************** below this line all codes are about lookup table *****************/
 127
 128 void createCntLookupTable ()
 129 {
 130         if ( !cntLookupTable )
 131         {
 132                 cntLookupTable = ( CONNECT ** ) ckalloc ( ( 3 * num_ctg + 1 ) * sizeof ( CONNECT * ) );
 133         }
 134 }
 135
 136 void deleteCntLookupTable ()
 137 {
 138         if ( cntLookupTable )
 139         {
 140                 free ( ( void * ) cntLookupTable );
 141                 cntLookupTable = NULL;
 142         }
 143 }
 144
 145 void putCnt2LookupTable ( unsigned int from_c, CONNECT * cnt )
 146 {
 147         if ( !cnt || !cntLookupTable )
 148         {
 149                 return;
 150         }
 151
 152         unsigned int index = 2 * from_c + cnt->contigID;
 153         cnt->nextInLookupTable = cntLookupTable[index];
 154         cntLookupTable[index] = cnt;
 155 }
 156
 157 static CONNECT * getCntInLookupTable ( unsigned int from_c, unsigned int to_c )
 158 {
 159         unsigned int index = 2 * from_c + to_c;
 160         CONNECT * ite_cnt = cntLookupTable[index];
 161
 162         while ( ite_cnt )
 163         {
 164                 if ( ite_cnt->contigID == to_c )
 165                 {
 166                         return ite_cnt;
 167                 }
 168
 169                 ite_cnt = ite_cnt->nextInLookupTable;
 170         }
 171
 172         return NULL;
 173 }
 174
 175 CONNECT * getCntBetween ( unsigned int from_c, unsigned int to_c )
 176 {
 177         CONNECT * pcnt;
 178
 179         if ( cntLookupTable )
 180         {
 181                 pcnt = getCntInLookupTable ( from_c, to_c );
 182                 return pcnt;
 183         }
 184
 185         pcnt = contig_array[from_c].downwardConnect;
 186
 187         while ( pcnt )
 188         {
 189                 if ( pcnt->contigID == to_c )
 190                 {
 191                         return pcnt;
 192                 }
 193
 194                 pcnt = pcnt->next;
 195         }
 196
 197         return pcnt;
 198 }
 199
 200 /*
 201 void removeCntInLookupTable(unsigned int from_c,unsigned int to_c)
 202 {
 203     unsigned int index = 2*from_c + to_c;
 204     CONNECT *ite_cnt = cntLookupTable[index];
 205     CONNECT *cnt;
 206
 207     if(!ite_cnt){
 208         printf("removeCntInLookupTable: not found A\n");
 209         return;
 210     }
 211     if(ite_cnt->contigID==to_c){
 212         cntLookupTable[index] = ite_cnt->nextInLookupTable;
 213         return;
 214     }
 215
 216     while(ite_cnt->nextInLookupTable&&ite_cnt->nextInLookupTable->contigID!=to_c)
 217         ite_cnt = ite_cnt->nextInLookupTable;
 218
 219     if(ite_cnt->nextInLookupTable){
 220         cnt = ite_cnt->nextInLookupTable;
 221         ite_cnt->nextInLookupTable = cnt->nextInLookupTable;
 222         return;
 223     }
 224     printf("removeCntInLookupTable: not found B\n");
 225     return;
 226 }
 227 */