File: CGraph.h

package info (click to toggle)
kissplice 2.4.0-p1-4
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 25,584 kB
  • sloc: cpp: 10,576; ansic: 3,446; python: 843; sh: 297; makefile: 11
file content (349 lines) | stat: -rw-r--r-- 12,349 bytes parent folder | download | duplicates (4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
/* ***************************************************************************
 *
 *                              KisSplice
 *      de-novo calling alternative splicing events from RNA-seq data.
 *
 * ***************************************************************************
 *
 * Copyright INRIA
 *  contributors :  Vincent Lacroix
 *                  Pierre Peterlongo
 *                  Gustavo Sacomoto
 *                  Vincent Miele
 *                  Alice Julien-Laferriere
 *                  David Parsons
 *
 * pierre.peterlongo@inria.fr
 * vincent.lacroix@univ-lyon1.fr
 *
 * This software is a computer program whose purpose is to detect alternative
 * splicing events from RNA-seq data.
 *
 * This software is governed by the CeCILL license under French law and
 * abiding by the rules of distribution of free software. You can  use,
 * modify and/ or redistribute the software under the terms of the CeCILL
 * license as circulated by CEA, CNRS and INRIA at the following URL
 * "http://www.cecill.info".

 * As a counterpart to the access to the source code and  rights to copy,
 * modify and redistribute granted by the license, users are provided only
 * with a limited warranty  and the software's author,  the holder of the
 * economic rights,  and the successive licensors  have only  limited
 * liability.

 * In this respect, the user's attention is drawn to the risks associated
 * with loading,  using,  modifying and/or developing or reproducing the
 * software by the user in light of its specific status of free software,
 * that may mean  that it is complicated to manipulate,  and  that  also
 * therefore means  that it is reserved for developers  and  experienced
 * professionals having in-depth computer knowledge. Users are therefore
 * encouraged to load and test the software's suitability as regards their
 * requirements in conditions enabling the security of their systems and/or
 * data to be ensured and,  more generally, to use and operate it in the
 * same conditions as regards security.
 *
 * The fact that you are presently reading this means that you have had
 * knowledge of the CeCILL license and that you accept its terms.
 */




#ifndef COMPRESSED_GRAPH_H
#define COMPRESSED_GRAPH_H

// ===========================================================================
//                               Include Libraries
// ===========================================================================
#include <stdio.h>
#include <string.h>
#include <vector>
#include <stack>
#include <algorithm>
#include <utility>




// ===========================================================================
//                             Include Project Files
// ===========================================================================
#include "CEdge.h"
#include "LabelledCEdge.h"




// ===========================================================================
//                              Class declarations
// ===========================================================================



// ===========================================================================
//                             Declare Used Namespaces
// ===========================================================================
using namespace std;





//! A class representing the compacted De-Bruijn graphs
/*!\
 * \brief Its light structure is used for the detection of bi-connected
 *  component in the graph.
 */

#define MAX 1024


class CGraph
{
  public:
    // =======================================================================
    //                               Constructors
    // =======================================================================

  /*!
   * \brief CGraph constructor.
   * Initializes the attributes according to the node numbers
   * Creates directly the CGraph object with its edges from allEdges
  */
    CGraph( int nbNodes, vector<LabelledCEdge> & allEdges, int kValue );

    // =======================================================================
    //                               Destructors
    // =======================================================================
    ~CGraph(void);


    // =======================================================================
    //                              Public Attributes
    // =======================================================================
    int k_value;

    // =======================================================================
    //                              Public Methods
    // =======================================================================
    inline int *get_adj_list(int node) const;
    inline int get_adj_list_sz(int node) const;
    inline int get_n_nodes(void) const;

    void insert_unique_edge_dir(int u, int v);
    void insert_unique_edge(int u, int v);
    void destroy_adj_list(void);
    void destroy(void);

  protected:
    // =======================================================================
    //                            Forbidden Constructors
    // =======================================================================

   CGraph(const CGraph &model)
    {
      printf("%s:%d: error: call to forbidden constructor of CGraph.\n",
          __FILE__, __LINE__);
      exit(EXIT_FAILURE);
    };

   CGraph( void )
   {
         printf("%s:%d: error: call to forbidden constructor of CGraph.\n",
             __FILE__, __LINE__);
         exit(EXIT_FAILURE);
       };

    // =======================================================================
    //                              Protected Methods
    // =======================================================================

    // =======================================================================
    //                             Protected Attributes
    // =======================================================================
    // NOTA: The neighborhood size is always <= 8

    //! Adjacency list
    /*!
     * adj_list is a vector of int tables containing the IDs of "outgoing neighbours"
     * i.e. neighbours v having a u -> v edge (u being the present node).
     * adj_list_sz contains the corresponding sizes
     */
    vector<int*>  adj_list;
    vector<int>   adj_list_sz;
};

// ===========================================================================
//                          Inline functions' definition
// ===========================================================================
int *CGraph::get_adj_list(int node) const
{
	return adj_list[node];
}

int CGraph::get_adj_list_sz(int node) const
{
	return adj_list_sz[node];
}

int CGraph::get_n_nodes(void) const
{
	return (int) adj_list.size();
}


// ===========================================================================
//                          Other functions
// ===========================================================================

void read_node_file(FILE *node_file, vector<char *>& seqs, int k_val);
void read_edge_file(FILE *edge_file, vector<LabelledCEdge>& edges);

// Functor that load the bcc nodes in memory
class NodeLoader 
{
 private:
  vector<char *>& _seqs;
  vector<int>& _label;
 public:
  NodeLoader(vector<char *>& seqs, vector<int>& label)
    : _seqs(seqs), _label(label) {}
  void operator()(FILE* node_file, int written_lines){
    char* buffer = new char[100 * MAX];      
    for (int i = 0; i < written_lines ; i++) {
      char* p;
      fgets(buffer, 100 * MAX, node_file);      
      if (strlen(buffer) == 100 * MAX)
	{  
	  p = strtok(buffer, "\t\n");
	  fprintf(stdout, "ERROR: node %s with sequence larger than %d!", p, 100 * MAX);
	  exit(0);
	}      
      // Node label
      p = strtok( buffer, "\t\n" );
      _label.push_back(atoi(p));      
      // Node seq
      p = strtok( NULL, "\t\n"  );
      char* seq = new char[strlen(p) + 1];
      strcpy( seq, p );      
      // Node seq_r
      p = strtok( NULL, "\t\n" );      
      _seqs.push_back( seq );
    }
    delete [] buffer;
  }
};

// return false if nbnodes<4
// required a functor to acts on the file lines
template<class TFunctor>
bool read_node_noncontigous_file_withoptimIO( FILE *contents_file_node, FILE* node_file, 
					      int *required_sequence, int *file_index,
					      TFunctor& functor )
{  
  char* buffer = new char[100 * MAX];
  ////////////////////////////
  ////////////////////////////
  ////////////////////////////
  // IO optimization (start)
  ////////////////////////////
  int written_lines_before, written_lines_for_record, written_lines;
  //normally would skip directly to the record, but for the time being use the formatted file
  for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_node);
  fscanf(contents_file_node, "%d \n",&written_lines_before );
  fscanf(contents_file_node, "%d \n",&written_lines_for_record );
  // if a graph node was not written to disk   
  if ( written_lines_before == written_lines_for_record) 
    { fprintf(stderr, "The required record %d does not exist in the bcc graph !\n", *required_sequence); exit(0); }  
  // where to search the record
  written_lines =  written_lines_for_record - written_lines_before;

  bool atleast4nodes = false;
  if (written_lines>=4){ //Less than 4 nodes, cannot contain a bubble!
    atleast4nodes = true;
    //normally would skip directly to the record, but for the time being use the formatted file
    for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, node_file);  
    ////////////////////////////
    // IO optimization (end)
    ////////////////////////////
    ////////////////////////////
    ////////////////////////////  
    functor(node_file, written_lines);
  }
  delete [] buffer;
  return atleast4nodes;
}

// Functor that load the bcc edges in memory
class EdgeLoader
{
 private:
  vector<LabelledCEdge>& _edges;
 public:
 EdgeLoader(vector<LabelledCEdge>& edges) 
   : _edges(edges) {}
  void operator()(FILE* edge_file, int written_lines){
    if (written_lines>0){
      char* buffer = new char[100 * MAX];
      char* u = new char[MAX];
      char* v = new char[MAX];
      char* label = new char[MAX];
      _edges.reserve(written_lines);//count_nb_lines(edge_file));
      for (int i = 0; i < written_lines ; i++) {
	char* p;
	fgets(buffer, 100 * MAX, edge_file);	
	// outgoing node
	p = strtok( buffer, "\t\n" );
	strcpy( u, p );	
	// incoming node
	p = strtok( NULL, "\t\n" );
	strcpy( v, p );	
	// edge label
	p = strtok( NULL, "\t\n" );
	strcpy(label, p);	
	_edges.push_back( LabelledCEdge( atoi(u), atoi(v), label ) );
      }      
      sort( _edges.begin(), _edges.end() );
      delete [] u;
      delete [] v;
      delete [] label; 
      delete [] buffer;      
    }
  }
};

// required a functor to acts on the file lines
template<class TFunctor>
void read_edge_file_withoptimIO( FILE *contents_file_edge, FILE *edge_file,
				 int *required_sequence, int *file_index,
				 TFunctor& functor )
{
  char* buffer = new char[100 * MAX];
  ////////////////////////////
  ////////////////////////////
  ////////////////////////////
  // IO optimization (start) 
  // [replicate as above]
  ////////////////////////////
  int written_lines_before, written_lines_for_record, written_lines;
  //normally would skip directly to the record, but for the time being use the formatted file
  for (int i = 0; i < *required_sequence+*file_index-2 ; i++) fgets(buffer, 100 * MAX, contents_file_edge);
  fscanf(contents_file_edge, "%d \n",&written_lines_before );
  fscanf(contents_file_edge, "%d \n",&written_lines_for_record );
  // if a graph edge  was not written to disk   
  if ( written_lines_before == written_lines_for_record) 
    { fprintf(stderr, "The required record %d does not exist in the bcc graph !\n", *required_sequence); exit(0); }  
  // where to search the record
  written_lines =  written_lines_for_record - written_lines_before;
  //normally would skip directly to the record, but for the time being use the formatted file
  for (int i = 0; i < written_lines_before ; i++) fgets(buffer, 100 * MAX, edge_file);  
  ////////////////////////////
  // IO optimization (end)
  ////////////////////////////
  ////////////////////////////
  ////////////////////////////
  functor(edge_file, written_lines);       
  delete [] buffer;
}

#endif // COMPRESSED_GRAPH_H