libpappsomspp
Library for mass spectrometry
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pappso::FastaFileIndexer Class Reference

#include <fastafileindexer.h>

Inheritance diagram for pappso::FastaFileIndexer:
pappso::FastaFileIndexerInterface

Public Member Functions

 FastaFileIndexer (const QFileInfo &fastaFile)
 
 FastaFileIndexer (const FastaFileIndexer &other)
 
virtual ~FastaFileIndexer ()
 
void getSequenceByIndex (FastaHandlerInterface &fasta_handler, std::size_t index) override
 
void open () override
 
void close () override
 
FastaFileIndexerSPtr makeFastaFileIndexerSPtr () const
 
std::size_t size () const
 

Private Member Functions

void parseFastaFile ()
 

Private Attributes

QFile m_fasta_file
 
std::vector< qint64 > m_indexArray
 
QTextStream * mpa_sequenceTxtIn = nullptr
 

Detailed Description

Definition at line 51 of file fastafileindexer.h.

Constructor & Destructor Documentation

◆ FastaFileIndexer() [1/2]

pappso::FastaFileIndexer::FastaFileIndexer ( const QFileInfo &  fastaFile)

Definition at line 39 of file fastafileindexer.cpp.

40 : m_fasta_file(fastaFile.absoluteFilePath())
41{
42
43 if(m_fasta_file.fileName().isEmpty())
44 {
45 throw PappsoException(QObject::tr("No FASTA file name specified"));
46 }
47 if(m_fasta_file.open(QIODevice::ReadOnly))
48 {
50 m_fasta_file.close();
51 }
52 else
53 {
54 throw PappsoException(QObject::tr("ERROR opening FASTA file %1 for read")
55 .arg(fastaFile.fileName()));
56 }
57}

References m_fasta_file, and parseFastaFile().

◆ FastaFileIndexer() [2/2]

pappso::FastaFileIndexer::FastaFileIndexer ( const FastaFileIndexer other)

Definition at line 59 of file fastafileindexer.cpp.

60 : m_fasta_file(other.m_fasta_file.fileName())
61{
62
63 m_indexArray = other.m_indexArray;
64 mpa_sequenceTxtIn = nullptr;
65}
std::vector< qint64 > m_indexArray

References m_indexArray, and mpa_sequenceTxtIn.

◆ ~FastaFileIndexer()

pappso::FastaFileIndexer::~FastaFileIndexer ( )
virtual

Definition at line 66 of file fastafileindexer.cpp.

67{
68 close();
69}

References close().

Member Function Documentation

◆ close()

void pappso::FastaFileIndexer::close ( )
overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 138 of file fastafileindexer.cpp.

139{
140 if(mpa_sequenceTxtIn != nullptr)
141 {
142 delete mpa_sequenceTxtIn;
143 mpa_sequenceTxtIn = nullptr;
144 m_fasta_file.close();
145 }
146}

References m_fasta_file, and mpa_sequenceTxtIn.

Referenced by ~FastaFileIndexer().

◆ getSequenceByIndex()

void pappso::FastaFileIndexer::getSequenceByIndex ( FastaHandlerInterface fasta_handler,
std::size_t  index 
)
overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 149 of file fastafileindexer.cpp.

151{
152 open();
153
154 qDebug() << " goto=" << index << " pos=" << m_indexArray[index];
155 bool seek_ok;
156 if((index < m_indexArray.size()) &&
157 (seek_ok = mpa_sequenceTxtIn->seek(m_indexArray[index])))
158 {
159
160 qDebug() << " realpos=" << mpa_sequenceTxtIn->pos();
161 ;
162 if(!seek_ok)
163 {
164
165 throw PappsoException(QObject::tr("ERROR FastaFileIndexer : seek to "
166 "sequence %1, position %2 failed")
167 .arg(index)
168 .arg(m_indexArray[index]));
169 }
170 FastaReader reader(fasta_handler);
171 reader.parseOnlyOne(*mpa_sequenceTxtIn);
172 }
173 else
174 {
175 throw ExceptionOutOfRange(
176 QObject::tr("ERROR reading FASTA file %1 : sequence index %2 "
177 "unreachable, array size=%3")
178 .arg(m_fasta_file.fileName())
179 .arg(index)
180 .arg(m_indexArray.size()));
181 }
182}

References m_fasta_file, m_indexArray, mpa_sequenceTxtIn, open(), and pappso::FastaReader::parseOnlyOne().

◆ makeFastaFileIndexerSPtr()

FastaFileIndexerSPtr pappso::FastaFileIndexer::makeFastaFileIndexerSPtr ( ) const

Definition at line 186 of file fastafileindexer.cpp.

187{
188
189 return std::make_shared<FastaFileIndexer>(*this);
190}

◆ open()

void pappso::FastaFileIndexer::open ( )
overridevirtual

Implements pappso::FastaFileIndexerInterface.

Definition at line 122 of file fastafileindexer.cpp.

123{
124 if(mpa_sequenceTxtIn != nullptr)
125 return;
126 if(m_fasta_file.open(QIODevice::ReadOnly))
127 {
128 mpa_sequenceTxtIn = new QTextStream(&m_fasta_file);
129 }
130 else
131 {
132 throw PappsoException(QObject::tr("ERROR opening FASTA file %1 for read")
133 .arg(m_fasta_file.fileName()));
134 }
135}

References m_fasta_file, and mpa_sequenceTxtIn.

Referenced by getSequenceByIndex().

◆ parseFastaFile()

void pappso::FastaFileIndexer::parseFastaFile ( )
private

Definition at line 73 of file fastafileindexer.cpp.

74{
75
76 qDebug();
77 QDataStream bin_in(&m_fasta_file);
78 qint64 position = 0;
79
80 // QChar first_char;
81 // txt_in >> first_char;
82 qint8 char_in;
83 bin_in >> char_in;
84 while(!bin_in.atEnd() && (char_in < (qint8)21))
85 { // eat Windows \r\n
86 position++;
87 bin_in >> char_in;
88 }
89 while(!bin_in.atEnd())
90 {
91 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
92 // << " first_char=" << first_char;
93 if(char_in == (qint8)'>')
94 {
95
96 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
97 // << " index=" << m_indexArray.size()
98 // << " position=" << position;
99 m_indexArray.push_back(position);
100 }
101 // eat line
102 position++;
103 bin_in >> char_in;
104 while(!bin_in.atEnd() && (char_in > (qint8)20))
105 {
106 position++;
107 bin_in >> char_in;
108 }
109 position++;
110 bin_in >> char_in;
111
112 if(!bin_in.atEnd() && (char_in < (qint8)21))
113 { // eat Windows \r\n
114 position++;
115 bin_in >> char_in;
116 }
117 }
118 qDebug();
119}

References m_fasta_file, and m_indexArray.

Referenced by FastaFileIndexer().

◆ size()

std::size_t pappso::FastaFileIndexer::size ( ) const

Definition at line 194 of file fastafileindexer.cpp.

195{
196 return m_indexArray.size();
197}

References m_indexArray.

Member Data Documentation

◆ m_fasta_file

QFile pappso::FastaFileIndexer::m_fasta_file
private

Definition at line 73 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), close(), getSequenceByIndex(), open(), and parseFastaFile().

◆ m_indexArray

std::vector<qint64> pappso::FastaFileIndexer::m_indexArray
private

Definition at line 74 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), getSequenceByIndex(), parseFastaFile(), and size().

◆ mpa_sequenceTxtIn

QTextStream* pappso::FastaFileIndexer::mpa_sequenceTxtIn = nullptr
private

Definition at line 75 of file fastafileindexer.h.

Referenced by FastaFileIndexer(), close(), getSequenceByIndex(), and open().


The documentation for this class was generated from the following files: