libpappsomspp
Library for mass spectrometry
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
pappso::cbor::psm::PsmCbor2Json Class Reference

#include <psmcbor2json.h>

Inheritance diagram for pappso::cbor::psm::PsmCbor2Json:
pappso::cbor::psm::PsmFileReaderBase pappso::cbor::CborStreamReaderInterface

Public Member Functions

 PsmCbor2Json (pappso::cbor::JsonStreamWriter *json_output_p)
 
virtual ~PsmCbor2Json ()
 
void close () override
 convenient function to clean pointer before leaving
 
- Public Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
 PsmFileReaderBase ()
 
virtual ~PsmFileReaderBase () override
 
void readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
 
void readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
 
- Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
 CborStreamReaderInterface ()
 
virtual ~CborStreamReaderInterface ()
 

Protected Member Functions

void informationsReady (pappso::UiMonitorInterface &monitor) override
 
void logReady (pappso::UiMonitorInterface &monitor) override
 
void parameterMapReady (pappso::UiMonitorInterface &monitor) override
 
void fastaFilesReady (pappso::UiMonitorInterface &monitor) override
 
void sampleStarted (pappso::UiMonitorInterface &monitor) override
 
void sampleFinished (pappso::UiMonitorInterface &monitor) override
 
void sampleListStarted (pappso::UiMonitorInterface &monitor) override
 
void sampleListFinished (pappso::UiMonitorInterface &monitor) override
 
void scanStarted (pappso::UiMonitorInterface &monitor) override
 
void scanFinished (pappso::UiMonitorInterface &monitor) override
 
void psmReady (pappso::UiMonitorInterface &monitor) override
 
void readProteinMap (pappso::UiMonitorInterface &monitor) override
 
- Protected Member Functions inherited from pappso::cbor::psm::PsmFileReaderBase
void readRoot (pappso::UiMonitorInterface &monitor)
 
virtual void readInformations (pappso::UiMonitorInterface &monitor)
 
virtual void readLog (pappso::UiMonitorInterface &monitor)
 
virtual void readParameterMap (pappso::UiMonitorInterface &monitor)
 
virtual void readSample (pappso::UiMonitorInterface &monitor)
 
virtual void readScan (pappso::UiMonitorInterface &monitor)
 
virtual void readPsm (pappso::UiMonitorInterface &monitor)
 
virtual void proteinMapReady (pappso::UiMonitorInterface &monitor)
 
PsmFile readPsmFile (bool &is_ok)
 
void writePsmFile (CborStreamWriter &writer, const PsmFile &psm_file)
 
void writePsmFileList (CborStreamWriter &writer, const std::vector< PsmFile > &file_list)
 
PsmProteinRef readPsmProteinRef (bool &is_ok)
 
pappso::PeptideSp getCurrentPsmPeptideSp () const
 
pappso::QualifiedMassSpectrumSPtr getCurrentQualifiedMassSpectrumSPtr () const
 get the qualified Spectrum for the current PSM
 
bool currentProteinRefListContainsDecoy () const
 tells if the current PSM has a decoy accession
 
bool currentProteinRefListContainsTarget () const
 tells if the current PSM has a target accession
 
double getPrecursorMass (double mz_prec, uint charge) const
 convenient function do compute precusor ion mass
 
- Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool getExpectedString ()
 
void initCborReader (QFile *pcborfile)
 
void initCborReader (QIODevice *pcborfile)
 

Protected Attributes

pappso::cbor::JsonStreamWriter * mp_jsonOutput
 
- Protected Attributes inherited from pappso::cbor::psm::PsmFileReaderBase
QStringList m_targetFastaFiles
 
QStringList m_decoyFastaFiles
 
PsmProteinMap m_proteinMap
 
QString m_currentSampleName
 
PsmFile m_currentPeaklistFile
 
std::vector< PsmFile > m_currentIdentificationFileList
 
QCborMap m_cborInformations
 
QCborArray m_cborLog
 
QCborMap m_cborParameterMap
 
QCborMap m_cborScanId
 
QCborMap m_cborScanPrecursor
 
QCborMap m_cborScanMs2
 
QCborMap m_cborScanProps
 
QCborMap m_cborScanPsmEval
 
QCborMap m_cborScanPsmProps
 
QString m_currentPsmProforma
 
std::vector< PsmProteinRef > m_currentPsmProteinRefList
 
- Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader * mpa_cborReader = nullptr
 
QString m_expectedString
 
QByteArray m_data
 

Detailed Description

Todo:
write docs

Definition at line 41 of file psmcbor2json.h.

Constructor & Destructor Documentation

◆ PsmCbor2Json()

pappso::cbor::psm::PsmCbor2Json::PsmCbor2Json ( pappso::cbor::JsonStreamWriter *  json_output_p)

Default constructor

Definition at line 35 of file psmcbor2json.cpp.

36{
37 mp_jsonOutput = json_output_p;
38
39 *mp_jsonOutput << "{" << Qt::endl;
40}
pappso::cbor::psm::PsmCbor2Json::mp_jsonOutput
pappso::cbor::JsonStreamWriter * mp_jsonOutput
Definition psmcbor2json.h:78

References mp_jsonOutput.

◆ ~PsmCbor2Json()

pappso::cbor::psm::PsmCbor2Json::~PsmCbor2Json ( )
virtual

Destructor

Definition at line 43 of file psmcbor2json.cpp.

44{
45}

Member Function Documentation

◆ close()

void pappso::cbor::psm::PsmCbor2Json::close ( )
overridevirtual

convenient function to clean pointer before leaving

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 48 of file psmcbor2json.cpp.

49{
50
51 mp_jsonOutput->endMap();
52}
pappso::cbor::JsonStreamWriter::endMap
void endMap()
ends an object in JSON output simply print "}"
Definition jsonstreamwriter.cpp:52

References pappso::cbor::JsonStreamWriter::endMap().

◆ fastaFilesReady()

void pappso::cbor::psm::PsmCbor2Json::fastaFilesReady ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 55 of file psmcbor2json.cpp.

57{
58 if(!m_targetFastaFiles.isEmpty())
59 {
60 mp_jsonOutput->appendKey("target_fasta_files");
61 mp_jsonOutput->writeArray(m_targetFastaFiles);
62 }
63 if(!m_decoyFastaFiles.isEmpty())
64 {
65 mp_jsonOutput->appendKey("decoy_fasta_files");
66 mp_jsonOutput->writeArray(m_decoyFastaFiles);
67 }
68}
pappso::cbor::JsonStreamWriter::writeArray
void writeArray(QStringList &str_list)
convert a string list to a JSON array
Definition jsonstreamwriter.cpp:121
pappso::cbor::JsonStreamWriter::appendKey
void appendKey(const QString &key)
writes a key (dictionary entry) to JSON text
Definition jsonstreamwriter.cpp:96

◆ informationsReady()

void pappso::cbor::psm::PsmCbor2Json::informationsReady ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 71 of file psmcbor2json.cpp.

73{
74
75 mp_jsonOutput->appendKey("informations");
76 mp_jsonOutput->writeCborMap(m_cborInformations);
77}
pappso::cbor::JsonStreamWriter::writeCborMap
void writeCborMap(const QCborMap &cbor_map)
converts a CBOR map (object) into JSON text in output
Definition jsonstreamwriter.cpp:77

◆ logReady()

void pappso::cbor::psm::PsmCbor2Json::logReady ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 80 of file psmcbor2json.cpp.

81{
82 mp_jsonOutput->appendKey("log");
83 mp_jsonOutput->writeCborArray(m_cborLog);
84}
pappso::cbor::JsonStreamWriter::writeCborArray
void writeCborArray(const QCborArray &cbor_array)
converts a CBOR array (list) into JSON text in output
Definition jsonstreamwriter.cpp:86

◆ parameterMapReady()

void pappso::cbor::psm::PsmCbor2Json::parameterMapReady ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 88 of file psmcbor2json.cpp.

90{
91 mp_jsonOutput->appendKey("parameter_map");
92 mp_jsonOutput->writeCborMap(m_cborParameterMap);
93}

◆ psmReady()

void pappso::cbor::psm::PsmCbor2Json::psmReady ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 206 of file psmcbor2json.cpp.

207{
208 mp_jsonOutput->startMap(); // psm
209 mp_jsonOutput->appendKey("proforma");
210 mp_jsonOutput->appendValue(m_currentPsmProforma);
211 mp_jsonOutput->appendKey("protein_list");
212 mp_jsonOutput->startArray();
213 for(auto &protein_ref : m_currentPsmProteinRefList)
214 {
215 mp_jsonOutput->startMap();
216 mp_jsonOutput->appendKey("accession");
217 mp_jsonOutput->appendValue(protein_ref.accession);
218 mp_jsonOutput->appendKey("positions");
219 mp_jsonOutput->startArray();
220 for(auto position : protein_ref.positions)
221 {
222 mp_jsonOutput->appendValue(position);
223 }
224 mp_jsonOutput->endArray();
225 mp_jsonOutput->endMap();
226 }
227 mp_jsonOutput->endArray();
228 if(!m_cborScanPsmProps.isEmpty())
229 {
230 mp_jsonOutput->appendKey("props");
231 mp_jsonOutput->writeCborMap(m_cborScanPsmProps);
232 }
233 mp_jsonOutput->appendKey("eval");
234 mp_jsonOutput->writeCborMap(m_cborScanPsmEval);
235
236 mp_jsonOutput->endMap(); // psm
237}
pappso::cbor::JsonStreamWriter::appendValue
void appendValue(const QString &value)
writes String value to JSON text
Definition jsonstreamwriter.cpp:106
pappso::cbor::JsonStreamWriter::endArray
void endArray()
ends an array in JSON output simply print "]"
Definition jsonstreamwriter.cpp:44
pappso::cbor::JsonStreamWriter::startMap
void startMap()
start an object in JSON output simply print "{"
Definition jsonstreamwriter.cpp:68
pappso::cbor::JsonStreamWriter::startArray
void startArray()
starts an array in JSON output simply print "["
Definition jsonstreamwriter.cpp:60
pappso::cbor::psm::PsmFileReaderBase::m_currentPsmProteinRefList
std::vector< PsmProteinRef > m_currentPsmProteinRefList
Definition psmfilereaderbase.h:143

◆ readProteinMap()

void pappso::cbor::psm::PsmCbor2Json::readProteinMap ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 113 of file psmcbor2json.cpp.

115{
116 mp_jsonOutput->appendKey("protein_map");
117 mp_jsonOutput->startMap();
118 if(!mpa_cborReader->enterContainer())
119 {
120 throw pappso::PappsoException(QObject::tr("enterContainer in protein map failed"));
121 }
122 QString accession;
123 while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
124 {
125 mpa_cborReader->decodeString(accession);
126 mp_jsonOutput->appendKey(accession);
127
128 QCborMap cbor_protein;
129 mpa_cborReader->readCborMap(cbor_protein);
130 mp_jsonOutput->writeCborMap(cbor_protein);
131 }
132
133 mpa_cborReader->leaveContainer();
134 mp_jsonOutput->endMap();
135}
pappso::cbor::CborStreamReader::readCborMap
bool readCborMap(QCborMap &cbor_map)
transfer the entire current CBOR map to a QCborMap object
Definition cborstreamreader.cpp:217
pappso::cbor::CborStreamReader::decodeString
bool decodeString(QString &the_str)
decode the current cbor value as a string the point to the next value the current value is decoded as...
Definition cborstreamreader.cpp:48

◆ sampleFinished()

void pappso::cbor::psm::PsmCbor2Json::sampleFinished ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 198 of file psmcbor2json.cpp.

200{
201 mp_jsonOutput->endArray(); // scan_list
202 mp_jsonOutput->endMap(); // sample
203}

◆ sampleListFinished()

void pappso::cbor::psm::PsmCbor2Json::sampleListFinished ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 105 of file psmcbor2json.cpp.

107{
108
109 mp_jsonOutput->endArray();
110}

◆ sampleListStarted()

void pappso::cbor::psm::PsmCbor2Json::sampleListStarted ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 96 of file psmcbor2json.cpp.

98{
99
100 mp_jsonOutput->appendKey("sample_list");
101 mp_jsonOutput->startArray();
102}

◆ sampleStarted()

void pappso::cbor::psm::PsmCbor2Json::sampleStarted ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 166 of file psmcbor2json.cpp.

167{
168 //"name": "tandem2017_nopatch_20120906_balliau_extract_1_A01_urnb-1",
169 qDebug();
170 mp_jsonOutput->startMap(); // sample
171 mp_jsonOutput->appendKey("name");
172 mp_jsonOutput->appendValue(m_currentSampleName);
173
174
175 mp_jsonOutput->appendKey("identification_file_list");
176 mp_jsonOutput->startArray();
177 for(auto &identification_file : m_currentIdentificationFileList)
178 {
179 mp_jsonOutput->startMap();
180 mp_jsonOutput->appendKey("name");
181 mp_jsonOutput->appendValue(identification_file.name);
182 mp_jsonOutput->endMap();
183 }
184 mp_jsonOutput->endArray();
185
186
187 mp_jsonOutput->appendKey("peaklist_file");
188 mp_jsonOutput->startMap();
189 mp_jsonOutput->appendKey("name");
190 mp_jsonOutput->appendValue(m_currentPeaklistFile.name);
191 mp_jsonOutput->endMap();
192
193 mp_jsonOutput->appendKey("scan_list");
194 mp_jsonOutput->startArray();
195}
pappso::cbor::psm::PsmFileReaderBase::m_currentIdentificationFileList
std::vector< PsmFile > m_currentIdentificationFileList
Definition psmfilereaderbase.h:132

◆ scanFinished()

void pappso::cbor::psm::PsmCbor2Json::scanFinished ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 158 of file psmcbor2json.cpp.

159{
160 mp_jsonOutput->endArray(); // psm_list
161 mp_jsonOutput->endMap(); // scan
162}

◆ scanStarted()

void pappso::cbor::psm::PsmCbor2Json::scanStarted ( pappso::UiMonitorInterface &  monitor)
overrideprotectedvirtual

Reimplemented from pappso::cbor::psm::PsmFileReaderBase.

Definition at line 138 of file psmcbor2json.cpp.

139{
140
141 mp_jsonOutput->startMap();
142 mp_jsonOutput->appendKey("id");
143 mp_jsonOutput->writeCborMap(m_cborScanId);
144 mp_jsonOutput->appendKey("precursor");
145 mp_jsonOutput->writeCborMap(m_cborScanPrecursor);
146 mp_jsonOutput->appendKey("ms2");
147 mp_jsonOutput->writeCborMap(m_cborScanMs2);
148 if(!m_cborScanProps.isEmpty())
149 {
150 mp_jsonOutput->appendKey("props");
151 mp_jsonOutput->writeCborMap(m_cborScanProps);
152 };
153 mp_jsonOutput->appendKey("psm_list");
154 mp_jsonOutput->startArray();
155}

Member Data Documentation

◆ mp_jsonOutput

pappso::cbor::JsonStreamWriter* pappso::cbor::psm::PsmCbor2Json::mp_jsonOutput
protected

Definition at line 78 of file psmcbor2json.h.

Referenced by PsmCbor2Json().

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