libpappsomspp
Library for mass spectrometry
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pappso::cbor::psm::PsmCborUtils Class Reference

utilities to help managing data in PSM CBOR data file More...

#include <psmcborutils.h>

Classes

struct  PsmProteinRef

Static Public Member Functions

static void prepareCborScanWithSpectrum (QCborMap &cbor_scan, const pappso::QualifiedMassSpectrum &ms2_qualified_mass_spectrum, const std::vector< pappso::PrecursorIonData > &alternative_precursors)
static void prepareCborScanWithSpectrumAndPeakList (QCborMap &cbor_scan, const pappso::QualifiedMassSpectrum &ms2_qualified_mass_spectrum, const std::vector< pappso::PrecursorIonData > &alternative_precursors)
static std::vector< PsmProteinRef > getPsmProteinRefList (const QCborMap &cbor_psm)
static void setPsmProteinRefList (QCborMap &cbor_psm, const std::vector< PsmProteinRef > &protein_ref_list)
static void mergePsmProteinRefList (QCborMap &cbor_psm_destination, const QCborMap &cbor_psm_source)

Detailed Description

utilities to help managing data in PSM CBOR data file

Definition at line 44 of file psmcborutils.h.

Member Function Documentation

◆ getPsmProteinRefList()

std::vector< PsmCborUtils::PsmProteinRef > pappso::cbor::psm::PsmCborUtils::getPsmProteinRefList ( const QCborMap & cbor_psm)
static

Definition at line 124 of file psmcborutils.cpp.

125{
126 std::vector<PsmCborUtils::PsmProteinRef> protein_ref_list;
127
128 if(cbor_psm.contains(QString("protein_list")))
129 {
130 for(auto it : cbor_psm.value("protein_list").toArray())
131 {
132 QCborMap cbor_protein_ref = it.toMap();
133 PsmCborUtils::PsmProteinRef protein_ref;
134 protein_ref.accession = cbor_protein_ref.value("accession").toString();
135
136 for(auto ref_position : cbor_protein_ref.value("positions").toArray())
137 {
138 protein_ref.positions.push_back(ref_position.toInteger());
139 }
140 protein_ref_list.push_back(protein_ref);
141 }
142 }
143
144 return protein_ref_list;
145}

References pappso::cbor::psm::PsmCborUtils::PsmProteinRef::accession, and pappso::cbor::psm::PsmCborUtils::PsmProteinRef::positions.

Referenced by mergePsmProteinRefList().

◆ mergePsmProteinRefList()

void pappso::cbor::psm::PsmCborUtils::mergePsmProteinRefList ( QCborMap & cbor_psm_destination,
const QCborMap & cbor_psm_source )
static

Definition at line 173 of file psmcborutils.cpp.

175{
176 std::vector<PsmCborUtils::PsmProteinRef> protein_ref_list =
177 getPsmProteinRefList(cbor_psm_destination);
178 std::vector<PsmCborUtils::PsmProteinRef> protein_ref_list_source =
179 getPsmProteinRefList(cbor_psm_source);
180
181 protein_ref_list.insert(
182 protein_ref_list.end(), protein_ref_list_source.begin(), protein_ref_list_source.end());
183
184
185 std::sort(protein_ref_list.begin(),
186 protein_ref_list.end(),
187 [](PsmCborUtils::PsmProteinRef &a, PsmCborUtils::PsmProteinRef &b) {
188 return a.accession > b.accession;
189 });
190
191 std::vector<PsmCborUtils::PsmProteinRef> unique_protein_ref_list;
192
193 for(auto it = protein_ref_list.begin(); it != protein_ref_list.end(); it++)
194 {
195 // qDebug() << it->proforma;
196 if(unique_protein_ref_list.size() > 0)
197 {
198 if(unique_protein_ref_list.back().accession == it->accession)
199 {
200 // merge positions
201 unique_protein_ref_list.back().positions.insert(
202 unique_protein_ref_list.back().positions.end(),
203 it->positions.begin(),
204 it->positions.end());
205
206 std::sort(unique_protein_ref_list.back().positions.begin(),
207 unique_protein_ref_list.back().positions.end());
208
209 auto last = std::unique(unique_protein_ref_list.back().positions.begin(),
210 unique_protein_ref_list.back().positions.end());
211 // v now holds {1 2 3 4 5 x x}, where 'x' is indeterminate
212 unique_protein_ref_list.back().positions.erase(
213 last, unique_protein_ref_list.back().positions.end());
214 }
215 else
216 {
217 unique_protein_ref_list.push_back(*it);
218 }
219 }
220 else
221 {
222 unique_protein_ref_list.push_back(*it);
223 }
224
225 qDebug();
226 }
227
228 setPsmProteinRefList(cbor_psm_destination, unique_protein_ref_list);
229}
pappso::cbor::psm::PsmCborUtils::setPsmProteinRefList
static void setPsmProteinRefList(QCborMap &cbor_psm, const std::vector< PsmProteinRef > &protein_ref_list)
Definition psmcborutils.cpp:149
pappso::cbor::psm::PsmCborUtils::getPsmProteinRefList
static std::vector< PsmProteinRef > getPsmProteinRefList(const QCborMap &cbor_psm)
Definition psmcborutils.cpp:124

References pappso::a, pappso::b, getPsmProteinRefList(), pappso::last, and setPsmProteinRefList().

Referenced by pappso::cbor::psm::CborScanMapBase::filterPsmListUniqueUniqueProforma().

◆ prepareCborScanWithSpectrum()

void pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum ( QCborMap & cbor_scan,
const pappso::QualifiedMassSpectrum & ms2_qualified_mass_spectrum,
const std::vector< pappso::PrecursorIonData > & alternative_precursors )
static

Definition at line 42 of file psmcborutils.cpp.

46{
47 // id
48 QCborMap cbor_scan_id;
49 cbor_scan_id.insert(QString("index"),
50 (qint64)ms2_qualified_mass_spectrum.getMassSpectrumId().getSpectrumIndex());
51 cbor_scan_id.insert(QString("native_id"),
52 ms2_qualified_mass_spectrum.getMassSpectrumId().getNativeId());
53 bool is_ok;
54 std::size_t scan =
55 ms2_qualified_mass_spectrum.getMassSpectrumId().extractScanNumberFromNativeId(&is_ok);
56 if(is_ok)
57 {
58 cbor_scan_id.insert(QString("scan"), (qint64)scan);
59 }
60 cbor_scan.insert(QString("id"), cbor_scan_id.toCborValue());
61
62
63 // precursor
64 QCborMap cbor_scan_precursor;
65 cbor_scan_precursor.insert(QString("z"), ms2_qualified_mass_spectrum.getPrecursorCharge());
66 cbor_scan_precursor.insert(QString("mz"), ms2_qualified_mass_spectrum.getPrecursorMz());
67 cbor_scan_precursor.insert(QString("mh"),
68 ms2_qualified_mass_spectrum.getPrecursorMass() + MHPLUS);
69 cbor_scan_precursor.insert(QString("mass"), ms2_qualified_mass_spectrum.getPrecursorMass());
70 cbor_scan_precursor.insert(QString("intensity"),
71 ms2_qualified_mass_spectrum.getPrecursorIntensity());
72 if(alternative_precursors.size() > 0)
73 {
74 QCborArray alternatives_cbor;
75 for(const pappso::PrecursorIonData &precursor : alternative_precursors)
76 {
77 QCborMap cbor_alt_item;
78 cbor_alt_item.insert(QString("z"), precursor.charge);
79 cbor_alt_item.insert(QString("mz"), precursor.mz);
80 cbor_alt_item.insert(QString("intensity"), precursor.intensity);
81 alternatives_cbor.append(cbor_alt_item);
82 }
83
84 cbor_scan_precursor.insert(QString("alternatives"), alternatives_cbor);
85 }
86
87 cbor_scan.insert(QString("precursor"), cbor_scan_precursor.toCborValue());
88
89
90 // ms2
91 QCborMap cbor_scan_ms2;
92 cbor_scan_ms2.insert(QString("rt"), ms2_qualified_mass_spectrum.getRtInSeconds());
93 cbor_scan.insert(QString("ms2"), cbor_scan_ms2.toCborValue());
94}
pappso::MassSpectrumId::getSpectrumIndex
std::size_t getSpectrumIndex() const
Definition massspectrumid.cpp:113
pappso::MassSpectrumId::getNativeId
const QString & getNativeId() const
Definition massspectrumid.cpp:99
pappso::MassSpectrumId::extractScanNumberFromNativeId
std::size_t extractScanNumberFromNativeId(bool *is_ok) const
try to find scan id in the native id string
Definition massspectrumid.cpp:145
pappso::QualifiedMassSpectrum::getPrecursorCharge
uint getPrecursorCharge(bool *ok=nullptr) const
get precursor charge
Definition qualifiedmassspectrum.cpp:336
pappso::QualifiedMassSpectrum::getPrecursorIntensity
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
get precursor intensity
Definition qualifiedmassspectrum.cpp:396
pappso::QualifiedMassSpectrum::getPrecursorMass
double getPrecursorMass(bool *ok_p=nullptr) const
get precursor mass given the charge stats and precursor mz
Definition qualifiedmassspectrum.cpp:260
pappso::QualifiedMassSpectrum::getMassSpectrumId
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
Definition qualifiedmassspectrum.cpp:154
pappso::QualifiedMassSpectrum::getPrecursorMz
pappso_double getPrecursorMz(bool *ok=nullptr) const
get precursor mz
Definition qualifiedmassspectrum.cpp:240
pappso::QualifiedMassSpectrum::getRtInSeconds
pappso_double getRtInSeconds() const
Get the retention time in seconds.
Definition qualifiedmassspectrum.cpp:205
pappso::MHPLUS
const pappso_double MHPLUS(1.007276466879)

References pappso::MassSpectrumId::extractScanNumberFromNativeId(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getPrecursorMass(), pappso::QualifiedMassSpectrum::getPrecursorMz(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MassSpectrumId::getSpectrumIndex(), and pappso::MHPLUS().

Referenced by prepareCborScanWithSpectrumAndPeakList().

◆ prepareCborScanWithSpectrumAndPeakList()

void pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrumAndPeakList ( QCborMap & cbor_scan,
const pappso::QualifiedMassSpectrum & ms2_qualified_mass_spectrum,
const std::vector< pappso::PrecursorIonData > & alternative_precursors )
static

Definition at line 97 of file psmcborutils.cpp.

101{
102 prepareCborScanWithSpectrum(cbor_scan, ms2_qualified_mass_spectrum, alternative_precursors);
103 QCborMap spectrum_cbor;
104
105 QCborArray mz_cbor;
106 QCborArray intensity_cbor;
107 for(const pappso::DataPoint &data_point :
108 *(ms2_qualified_mass_spectrum.getMassSpectrumCstSPtr().get()))
109 {
110 mz_cbor.append(data_point.x);
111 intensity_cbor.append(data_point.y);
112 }
113 spectrum_cbor.insert(QString("mz"), mz_cbor);
114 spectrum_cbor.insert(QString("intensity"), intensity_cbor);
115
116 QCborMap new_ms2_map = cbor_scan.value("ms2").toMap();
117 new_ms2_map.insert(QString("spectrum"), spectrum_cbor.toCborValue());
118
119 cbor_scan.insert(QString("ms2"), new_ms2_map);
120}
pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr
MassSpectrumCstSPtr getMassSpectrumCstSPtr() const
Get the MassSpectrumCstSPtr.
Definition qualifiedmassspectrum.cpp:138
pappso::cbor::psm::PsmCborUtils::prepareCborScanWithSpectrum
static void prepareCborScanWithSpectrum(QCborMap &cbor_scan, const pappso::QualifiedMassSpectrum &ms2_qualified_mass_spectrum, const std::vector< pappso::PrecursorIonData > &alternative_precursors)
Definition psmcborutils.cpp:42

References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), and prepareCborScanWithSpectrum().

◆ setPsmProteinRefList()

void pappso::cbor::psm::PsmCborUtils::setPsmProteinRefList ( QCborMap & cbor_psm,
const std::vector< PsmProteinRef > & protein_ref_list )
static

Definition at line 149 of file psmcborutils.cpp.

151{
152 QCborArray protein_list;
153
154 for(auto it : protein_ref_list)
155 {
156 QCborMap protein_ref;
157 protein_ref.insert(QString("accession"), it.accession);
158 QCborArray positions_arr;
159 for(auto position : it.positions)
160 {
161 positions_arr.append((qint64)position);
162 }
163 protein_ref.insert(QString("positions"), positions_arr);
164 protein_list.append(protein_ref);
165 }
166
167 cbor_psm.remove(QString("protein_list"));
168 cbor_psm.insert(QString("protein_list"), protein_list);
169}

Referenced by mergePsmProteinRefList().

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