Go to the source code of this file.
§ testContact()
Definition at line 37 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), pwiz::tradata::Contact::id, MS_m_z, os_, unit_assert, and pwiz::data::ParamContainer::userParams.
39 if (
os_) *
os_ <<
"testContact()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
§ testInstrument()
Definition at line 60 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), pwiz::tradata::Instrument::id, MS_m_z, os_, unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
62 if (
os_) *
os_ <<
"testInstrument()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Instrument on which transitions are validated.
std::string id
Identifier for the instrument to be used for referencing within a document.
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
§ testConfiguration()
void testConfiguration |
( |
| ) |
|
Definition at line 83 of file DiffTest.cpp.
References pwiz::tradata::Configuration::contactPtr, pwiz::data::ParamContainer::cvParams, diff(), pwiz::tradata::Configuration::instrumentPtr, MS_m_z, os_, unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
85 if (
os_) *
os_ <<
"testConfiguration()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Instrument on which transitions are validated.
Instrument configuration used in the validation or optimization of the transitions.
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
InstrumentPtr instrumentPtr
Reference to an instrument for which this configuration information is appropriate.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
boost::shared_ptr< Contact > ContactPtr
ContactPtr contactPtr
Reference to a contact person originating this information.
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
boost::shared_ptr< Instrument > InstrumentPtr
§ testPrediction()
Definition at line 108 of file DiffTest.cpp.
References pwiz::tradata::Prediction::contactPtr, pwiz::data::ParamContainer::cvParams, diff(), MS_m_z, os_, pwiz::tradata::Prediction::softwarePtr, unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
110 if (
os_) *
os_ <<
"testPrediction()\n";
boost::shared_ptr< Software > SoftwarePtr
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about a prediction for a suitable transition using some software.
SoftwarePtr softwarePtr
Reference to a software package from which this prediction is derived.
void diff(const string &filename1, const string &filename2)
ContactPtr contactPtr
Reference to a contact person that generated this prediction.
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
boost::shared_ptr< Contact > ContactPtr
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
§ testValidation()
Definition at line 131 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), MS_m_z, MS_peak_intensity, os_, pwiz::data::ParamContainer::set(), unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
133 if (
os_) *
os_ <<
"testValidation()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about the state of validation of a transition on a given instrument model.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
§ testEvidence()
Definition at line 152 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), MS_m_z, MS_peak_intensity, os_, pwiz::data::ParamContainer::set(), unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
154 if (
os_) *
os_ <<
"testEvidence()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about empirical mass spectrometer observations of the peptide.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
§ testRetentionTime()
void testRetentionTime |
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| ) |
|
Definition at line 173 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), MS_m_z, MS_peak_intensity, os_, pwiz::data::ParamContainer::set(), unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
175 if (
os_) *
os_ <<
"testRetentionTime()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
§ testProtein()
Definition at line 194 of file DiffTest.cpp.
References diff(), pwiz::proteome::Protein::id, MS_m_z, os_, pwiz::proteome::Peptide::sequence(), and unit_assert.
Referenced by test().
196 if (
os_) *
os_ <<
"testProtein()\n";
199 a.userParams.push_back(
UserParam(
"common"));
200 b.userParams.push_back(
UserParam(
"common"));
201 a.cvParams.push_back(
MS_m_z);
202 b.cvParams.push_back(
MS_m_z);
Calculate diffs of objects in a ProteoWizard data model hierarchy.
void diff(const string &filename1, const string &filename2)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
const std::string & sequence() const
returns the sequence of amino acids making up the peptide
§ testModification()
void testModification |
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| ) |
|
Definition at line 217 of file DiffTest.cpp.
References diff(), os_, and unit_assert.
219 if (
os_) *
os_ <<
"testModification()\n";
222 a.location = b.location = 7;
223 a.monoisotopicMassDelta = b.monoisotopicMassDelta = 42;
224 a.averageMassDelta = b.averageMassDelta = 42;
229 a.monoisotopicMassDelta = 84;
Calculate diffs of objects in a ProteoWizard data model hierarchy.
represents a post-translational modification (PTM) modification formula or masses must be provided at...
void diff(const string &filename1, const string &filename2)
§ testPeptide()
Definition at line 237 of file DiffTest.cpp.
References diff(), MS_m_z, MS_peak_intensity, os_, pwiz::proteome::Peptide::sequence(), and unit_assert.
239 if (
os_) *
os_ <<
"testPeptide()\n";
242 a.userParams.push_back(
UserParam(
"common"));
243 b.userParams.push_back(
UserParam(
"common"));
244 a.cvParams.push_back(
MS_m_z);
245 b.cvParams.push_back(
MS_m_z);
Calculate diffs of objects in a ProteoWizard data model hierarchy.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
represents a peptide or polypeptide (a sequence of amino acids)
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
const std::string & sequence() const
returns the sequence of amino acids making up the peptide
§ testCompound()
Definition at line 262 of file DiffTest.cpp.
References pwiz::data::ParamContainer::cvParams, diff(), pwiz::tradata::Compound::id, MS_m_z, os_, pwiz::tradata::Compound::retentionTimes, unit_assert, and pwiz::data::ParamContainer::userParams.
Referenced by test().
264 if (
os_) *
os_ <<
"testCompound()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
std::string id
Identifier for the compound to be used for referencing within a document.
void diff(const string &filename1, const string &filename2)
Chemical compound other than a peptide for which one or more transitions.
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
§ testTransition()
Definition at line 284 of file DiffTest.cpp.
References pwiz::tradata::Transition::configurationList, diff(), pwiz::tradata::Transition::id, MS_peak_intensity, MS_selected_ion_m_z, os_, pwiz::tradata::Transition::peptidePtr, pwiz::tradata::Transition::precursor, pwiz::tradata::Transition::product, pwiz::data::ParamContainer::set(), unit_assert, and pwiz::tradata::Configuration::validations.
Referenced by test().
286 if (
os_) *
os_ <<
"testTransition()\n";
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about the state of validation of a transition on a given instrument model.
Instrument configuration used in the validation or optimization of the transitions.
std::string id
String label for this transition.
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
represents a peptide or polypeptide (a sequence of amino acids)
Product product
Product (Q3) of the transition.
PeptidePtr peptidePtr
Reference to a peptide which this transition is intended to identify.
boost::shared_ptr< Peptide > PeptidePtr
std::vector< Validation > validations
std::vector< Configuration > configurationList
List of insutrument configurations used in the validation or optimization of the transitions.
Precursor precursor
Precursor (Q1) of the transition.
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
§ testTarget()
Definition at line 311 of file DiffTest.cpp.
References pwiz::tradata::Target::configurationList, diff(), pwiz::tradata::Target::id, MS_peak_intensity, MS_selected_ion_m_z, os_, pwiz::tradata::Target::peptidePtr, pwiz::tradata::Target::precursor, pwiz::data::ParamContainer::set(), unit_assert, and pwiz::tradata::Configuration::validations.
Referenced by test().
313 if (
os_) *
os_ <<
"testTarget()\n";
Precursor precursor
Precursor (Q1) of the target.
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about the state of validation of a transition on a given instrument model.
A peptide or compound that is to be included or excluded from a target list of precursor m/z values...
Instrument configuration used in the validation or optimization of the transitions.
PeptidePtr peptidePtr
Reference to a peptide for which this target is the trigger.
std::string id
String label for this target.
MS_selected_ion_m_z
selected ion m/z: Mass-to-charge ratio of an selected ion.
MS_peak_intensity
peak intensity: Intensity of ions as measured by the height or area of a peak in a mass spectrum...
void diff(const string &filename1, const string &filename2)
represents a peptide or polypeptide (a sequence of amino acids)
boost::shared_ptr< Peptide > PeptidePtr
std::vector< Validation > validations
std::vector< Configuration > configurationList
List of instrument configurations used in the validation or optimization of the target.
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
§ testSoftware()
§ testTraData()
Definition at line 411 of file DiffTest.cpp.
References pwiz::data::Diff< object_type, config_type, object_result_type >::a_b, pwiz::data::Diff< object_type, config_type, object_result_type >::b_a, pwiz::tradata::TraData::cvs, diff(), pwiz::tradata::Publication::id, os_, pwiz::tradata::TraData::publications, pwiz::data::ParamContainer::set(), pwiz::tradata::TraData::softwarePtrs, unit_assert, and UO_dalton.
Referenced by test().
413 if (
os_) *
os_ <<
"testTraData()\n";
420 a.
cvs.push_back(
CV());
boost::shared_ptr< Software > SoftwarePtr
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Information about an ontology or CV source and a short 'lookup' tag to refer to.
std::vector< SoftwarePtr > softwarePtrs
List of software packages used in the generation of one of more transitions described in the document...
void diff(const string &filename1, const string &filename2)
std::vector< Publication > publications
List of publications from which the transitions were collected or wherein they are published...
std::vector< CV > cvs
List of controlled vocabularies used in a TraML document note: one of the <cv> elements in this list ...
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
std::string id
Identifier for the publication to be used for referencing within a document.
§ test()
Definition at line 444 of file DiffTest.cpp.
References testCompound(), testConfiguration(), testContact(), testEvidence(), testInstrument(), testModification(), testPeptide(), testPrediction(), testProtein(), testRetentionTime(), testSoftware(), testTarget(), testTraData(), testTransition(), and testValidation().
§ main()
int main |
( |
int |
argc, |
|
|
char * |
argv[] |
|
) |
| |
§ os_