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
|
/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2010, 2011, 2012, 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 "ExtensionElement.h"
#include <code/SequencesLoader/Read.h>
#include <string.h>
/** set the sequence */
void ExtensionElement::setSequence(const char*b,MyAllocator*allocator){
m_read.constructor(b,allocator,false);
m_hasPairedRead=false;
}
void ExtensionElement::getSequence(char*sequence,Parameters*parameters){
m_read.getSeq(sequence,parameters->getColorSpaceMode(),false);
}
int ExtensionElement::getPosition(){
return m_position;
}
char ExtensionElement::getStrand(){
return m_strand;
}
bool ExtensionElement::hasPairedRead(){
return m_hasPairedRead;
}
PairedRead*ExtensionElement::getPairedRead(){
return &m_pairedRead;
}
void ExtensionElement::setStartingPosition(int a){
m_position=a;
}
void ExtensionElement::setStrand(char a){
m_strand=a;
}
void ExtensionElement::setType(int a){
m_type=a;
}
bool ExtensionElement::isLeftEnd(){
return m_type==TYPE_LEFT_END;
}
bool ExtensionElement::isRightEnd(){
return m_type==TYPE_RIGHT_END;
}
int ExtensionElement::getType(){
return m_type;
}
void ExtensionElement::setPairedRead(PairedRead a){
m_pairedRead=a;
m_hasPairedRead=true;
}
void ExtensionElement::setStrandPosition(int a){
m_strandPosition=a;
}
int ExtensionElement::getStrandPosition(){
return m_strandPosition;
}
void ExtensionElement::removeSequence(){
/* TODO: not implemented */
}
void ExtensionElement::constructor(){
m_canMove=true;
m_numberOfTries=0;
m_activated=false;
m_agreement=0;
}
void ExtensionElement::increaseNumberOfTries(){
m_numberOfTries++;
#if 0
cout<<"Number of tries is "<<(int)m_numberOfTries<<endl;
#endif
}
int ExtensionElement::getNumberOfTries()const{
return m_numberOfTries;
}
bool ExtensionElement::canMove(){
return m_canMove;
}
void ExtensionElement::freezePlacement(){
m_canMove=false;
}
void ExtensionElement::increaseAgreement(){
m_agreement ++ ;
}
int ExtensionElement::getAgreement(){
return m_agreement;
}
int ExtensionElement::getReadLength(){
return m_read.length();
}
void ExtensionElement::deactivate(){
m_activated=false;
}
void ExtensionElement::activate(){
m_activated=true;
}
bool ExtensionElement::isActive()const{
return m_activated;
}
|
