39 if (
os_) *
os_ <<
"testContact()\n";
55 if (
os_) *
os_ << diff << endl;
62 if (
os_) *
os_ <<
"testInstrument()\n";
78 if (
os_) *
os_ << diff << endl;
85 if (
os_) *
os_ <<
"testConfiguration()\n";
103 if (
os_) *
os_ << diff << endl;
110 if (
os_) *
os_ <<
"testPrediction()\n";
126 if (
os_) *
os_ << diff << endl;
133 if (
os_) *
os_ <<
"testValidation()\n";
147 if (
os_) *
os_ << diff << endl;
154 if (
os_) *
os_ <<
"testEvidence()\n";
168 if (
os_) *
os_ << diff << endl;
175 if (
os_) *
os_ <<
"testRetentionTime()\n";
189 if (
os_) *
os_ << diff << endl;
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);
212 if (
os_) *
os_ << diff << endl;
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;
232 if (
os_) *
os_ << diff << endl;
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);
257 if (
os_) *
os_ << diff << endl;
264 if (
os_) *
os_ <<
"testCompound()\n";
279 if (
os_) *
os_ << diff << endl;
286 if (
os_) *
os_ <<
"testTransition()\n";
307 if (
os_) *
os_ << diff << endl;
313 if (
os_) *
os_ <<
"testTarget()\n";
332 if (
os_) *
os_ << diff << endl;
339 if (
os_) *
os_ <<
"testSoftware()\n";
354 if (
os_) *
os_ << diff << endl;
413 if (
os_) *
os_ <<
"testTraData()\n";
420 a.
cvs.push_back(
CV());
430 if (
os_) *
os_ << diff << endl;
466 int main(
int argc,
char* argv[])
472 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
int main(int argc, char *argv[])
boost::shared_ptr< Software > SoftwarePtr
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.
std::string id
Identifier for the compound to be used for referencing within a document.
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Instrument on which transitions are validated.
Information about a prediction for a suitable transition using some software.
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.
std::string id
String label for this transition.
std::string version
Version of the software program described.
std::vector< SoftwarePtr > softwarePtrs
List of software packages used in the generation of one of more transitions described in the document...
Information about empirical mass spectrometer observations of the peptide.
std::string id
Identifier for the software to be used for referencing within a document.
PeptidePtr peptidePtr
Reference to a peptide for which this target is the trigger.
std::string id
String label for this target.
represents a post-translational modification (PTM) modification formula or masses must be provided at...
std::string id
Identifier for the instrument to be used for referencing within a document.
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...
SoftwarePtr softwarePtr
Reference to a software package from which this prediction is derived.
void diff(const string &filename1, const string &filename2)
Chemical compound other than a peptide for which one or more transitions.
represents a peptide or polypeptide (a sequence of amino acids)
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.
InstrumentPtr instrumentPtr
Reference to an instrument for which this configuration information is appropriate.
std::vector< UserParam > userParams
a collection of uncontrolled user terms
std::vector< Publication > publications
List of publications from which the transitions were collected or wherein they are published...
MS_m_z
m/z: Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion ...
MS_ionization_type
ionization type: The method by which gas phase ions are generated from the sample.
boost::shared_ptr< Contact > ContactPtr
ContactPtr contactPtr
Reference to a contact person originating this information.
std::vector< CV > cvs
List of controlled vocabularies used in a TraML document note: one of the <cv> elements in this list ...
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
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
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
std::vector< Configuration > configurationList
List of insutrument configurations used in the validation or optimization of the transitions.
#define TEST_PROLOG_EX(argc, argv, suffix)
boost::shared_ptr< Instrument > InstrumentPtr
std::vector< Configuration > configurationList
List of instrument configurations used in the validation or optimization of the target.
std::vector< RetentionTime > retentionTimes
List of retention time information entries.
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)
std::string id
Identifier for the publication to be used for referencing within a document.
const std::string & sequence() const
returns the sequence of amino acids making up the peptide