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
|
/*
Ray
Copyright (C) 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 _SearchDirectory_h
#define _SearchDirectory_h
#include "VirtualKmerColor.h"
#include <code/KmerAcademyBuilder/Kmer.h>
#include <code/GeneOntology/KeyEncoder.h>
#include <set>
#include <string>
#include <fstream>
#include <vector>
using namespace std;
#define DUMMY_IDENTIFIER 999999999999ULL
#define CONFIG_COLORED_LINE_MAX_LENGTH 10000
/**
* This class represents a directory
* with fasta files
* to be used for coloring
*/
class SearchDirectory{
KeyEncoder m_encoder;
bool m_hasBufferedLine;
/** this is to avoid using tellg() and seekg() **/
char m_bufferedLine[CONFIG_COLORED_LINE_MAX_LENGTH];
bool m_hasN;
string m_path;
vector<string> m_files;
vector<int> m_counts;
set<int> m_createdDirectories;
/** sequence lazy loader */
bool m_hasFile;
int m_currentSequencePosition;
char m_currentSequenceHeader[CONFIG_COLORED_LINE_MAX_LENGTH];
char m_currentSequenceBuffer[CONFIG_COLORED_LINE_MAX_LENGTH];
int m_currentSequenceNumberOfAvailableKmers;
int m_currentFile;
int m_currentSequence;
bool m_noMoreSequence;
FILE* m_currentFileStream;
void readDirectory();
/** lazy load some sequences */
void loadSomeSequence();
void readLineFromFile(char*line,int length);
bool lineIsSequenceHeader(char*line);
string filterName(string a);
public:
void constructor(string path);
/** get the number of sequences in the file */
int getCount(int i);
string*getFileName(int i);
string*getDirectoryName();
void countEntriesInFile(int j);
/** get the number of files in the directory */
int getSize();
void setCount(int file,int count);
// sequence reader
void createSequenceReader(int file,int sequence,int kmerLength);
int getCurrentSequenceLengthInKmers();
bool hasNextKmer(int kmerLength);
void iterateToNextKmer();
void getNextKmer(int kmerLength,Kmer*kmer);
bool kmerContainsN();
string getCurrentSequenceName();
bool hasCurrentSequenceIdentifier();
LargeIndex getCurrentSequenceIdentifier();
bool hasIdentifier_EMBL_CDS();
PhysicalKmerColor getIdentifier_EMBL_CDS();
bool hasDirectory(int file);
void setCreatedDirectory(int file);
};
#endif
|
