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
|
/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
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, version 3 of the License.
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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _LibraryWorker
#define _LibraryWorker
#include <code/SequencesLoader/ReadHandle.h>
#include <code/SeedingData/PathHandle.h>
#include <code/SeedingData/SeedingData.h>
#include <code/SeedExtender/ExtensionData.h>
#include <RayPlatform/communication/VirtualCommunicator.h>
#include <RayPlatform/memory/RingAllocator.h>
#include <RayPlatform/scheduling/Worker.h>
#include <map>
#include <stdint.h>
using namespace std;
class LibraryElement{
public:
int m_readPosition;
uint16_t m_strandPosition;
char m_readStrand;
} ATTRIBUTE_PACKED;
/*
* Computes average outer distances
* \author Sébastien Boisvert
*/
class LibraryWorker : public Worker {
MessageTag RAY_MPI_TAG_GET_READ_MATE;
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS;
bool m_done;
ReadFetcher m_readFetcher;
map<int,map<int,int> >*m_libraryDistances;
ExtensionData*m_ed;
SplayTree<ReadHandle,LibraryElement> m_database;
MyAllocator*m_allocator;
VirtualCommunicator*m_virtualCommunicator;
WorkerHandle m_SEEDING_i;
RingAllocator*m_outboxAllocator;
Parameters*m_parameters;
int m_EXTENSION_currentPosition;
bool m_EXTENSION_reads_requested;
SeedingData*m_seedingData;
int m_EXTENSION_edgeIterator;
StaticVector*m_inbox;
StaticVector*m_outbox;
bool m_EXTENSION_hasPairedReadRequested;
int*m_detectedDistances;
public:
void constructor(WorkerHandle id,SeedingData*seedingData,VirtualCommunicator*virtualCommunicator,RingAllocator*outboxAllocator,
Parameters*parameters,StaticVector*inbox,StaticVector*outbox,map<int,map<int,int> >*libraryDistances,int*detectedDistances,
MyAllocator*allocator,
MessageTag RAY_MPI_TAG_GET_READ_MATE,
MessageTag RAY_MPI_TAG_REQUEST_VERTEX_READS
);
/** work a little bit
* the class Worker provides no implementation for that
*/
void work();
/** is the worker done doing its things */
bool isDone();
/** get the worker number */
WorkerHandle getWorkerIdentifier();
};
#endif
|
