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
|
/*
* Ray -- Parallel genome assemblies for parallel DNA sequencing
* Copyright (C) 2013 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/>
*/
#include "AttributeFetcher.h"
bool AttributeFetcher::fetchObjectMetaData(Kmer * object){
if(!m_initializedFetcher){
m_queryWasSent=false;
m_initializedFetcher=true;
}else if(!m_queryWasSent){
MessageTag tag = RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
Rank destination = m_parameters->vertexRank(object);
MessageUnit*message=(MessageUnit*)m_outboxAllocator->allocate(1*sizeof(MessageUnit));
int bufferPosition=0;
object->pack(message,&bufferPosition);
Message aMessage(message,m_virtualCommunicator->getElementsPerQuery(tag),
destination, tag, m_rank);
m_virtualCommunicator->pushMessage(m_identifier, &aMessage);
m_queryWasSent = true;
}else if(m_virtualCommunicator->isMessageProcessed(m_identifier)){
vector<MessageUnit> elements;
m_virtualCommunicator->getMessageResponseElements(m_identifier, &elements);
int bufferPosition=0;
uint8_t edges = elements[bufferPosition++];
m_depth=elements[bufferPosition++];
#ifdef CONFIG_ASSERT
assert(m_depth>= 1);
#endif
m_parents = object->getIngoingEdges(edges, m_parameters->getWordSize());
m_children = object->getOutgoingEdges(edges, m_parameters->getWordSize());
m_queryWasSent = false;
return true;
}
return false;
}
void AttributeFetcher::initialize(Parameters*parameters, VirtualCommunicator*virtualCommunicator,
WorkerHandle identifier, RingAllocator * outboxAllocator,
MessageTag RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT){
m_virtualCommunicator = virtualCommunicator;
m_parameters = parameters;
m_identifier = identifier;
m_outboxAllocator = outboxAllocator;
m_rank = m_parameters->getRank();
this->RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT = RAY_MPI_TAG_GET_VERTEX_EDGES_COMPACT;
reset();
}
void AttributeFetcher::reset(){
m_initializedFetcher = false;
}
CoverageDepth AttributeFetcher::getDepth(){
return m_depth;
}
vector<Kmer>* AttributeFetcher::getParents(){
return &m_parents;
}
vector<Kmer>* AttributeFetcher::getChildren(){
return &m_children;
}
|
