35 specificity.
cut =
"theCake";
36 specificity.
noCut =
"notTheCake";
37 specificity.
sense =
"non";
47 sampleEnzyme.
name =
"oxiclean";
48 sampleEnzyme.
description =
"makes your whites whiter.";
62 searchDatabase.
localPath =
"http://www.eharmony.com";
67 searchDatabase.
type =
"online dating service";
69 return searchDatabase;
96 peptideProphetResult.
allNttProb.push_back(0.0000);
97 peptideProphetResult.
allNttProb.push_back(0.0000);
98 peptideProphetResult.
allNttProb.push_back(0.780);
100 return peptideProphetResult;
107 analysisResult.
analysis =
"peptideprophet";
112 return analysisResult;
119 alternativeProtein.
protein =
"Dos Pinos";
123 return alternativeProtein;
131 modAminoAcidMass.
mass = 12.345;
133 return modAminoAcidMass;
143 return modificationInfo;
150 searchHit.
peptide =
"RAGMALLICK";
179 enzymaticSearchConstraint.
enzyme =
"emyzne";
183 return enzymaticSearchConstraint;
192 aminoAcidModification.
massDiff = 9.63333;
193 aminoAcidModification.
mass = 82.65;
194 aminoAcidModification.
variable =
"c";
195 aminoAcidModification.
symbol =
"r";
197 return aminoAcidModification;
204 searchSummary.
baseName =
"mseharmony";
220 return searchSummary;
238 spectrumQuery.
spectrum =
"ultraviolet";
240 spectrumQuery.
endScan = 19120415;
243 spectrumQuery.
index = 3547;
250 return spectrumQuery;
269 return msmsRunSummary;
277 match->feature->mz = 1.234;
278 match->feature->retentionTime = 5.678;
286 if (
os_) *
os_ <<
"\ntestSpecificity() ... \n";
292 specificity.
write(writer);
295 istringstream iss(oss.str());
296 readSpecificity.
read(iss);
300 if (
os_) *
os_ << oss.str() << endl;
306 if (
os_) *
os_ <<
"\ntestSampleEnzyme() ... \n";
312 sampleEnzyme.
write(writer);
315 istringstream iss(oss.str());
316 readSampleEnzyme.
read(iss);
320 if (
os_) *
os_ << oss.str() << endl;
326 if (
os_) *
os_ <<
"\ntestSearchDatabase() ... \n";
332 searchDatabase.
write(writer);
335 istringstream iss(oss.str());
336 readSearchDatabase.
read(iss);
340 if (
os_) *
os_ << oss.str() << endl;
346 if (
os_) *
os_ <<
"\ntestQ3RatioResult() ... \n";
355 istringstream iss(oss.str());
359 if (
os_) *
os_ << oss.str() << endl;
365 if (
os_) *
os_ <<
"\ntestPeptideProphetResult() ... \n";
374 istringstream iss(oss.str());
375 readPeptideProphetResult.
read(iss);
379 if (
os_) *
os_ << oss.str() << endl;
385 if (
os_) *
os_ <<
"\ntestAnalysisResult() ...\n";
391 analysisResult.
write(writer);
394 istringstream iss(oss.str());
395 readAnalysisResult.
read(iss);
399 if(
os_) *
os_ << oss.str() << endl;
407 analysisResult2.
write(writer2);
410 istringstream iss2(oss2.str());
411 readAnalysisResult2.
read(iss2);
413 unit_assert(analysisResult2 == readAnalysisResult2);
415 if(
os_) *
os_ << oss2.str() << endl;
422 if (
os_) *
os_ <<
"\ntestAlternativeProtein() ...\n";
428 alternativeProtein.
write(writer);
431 istringstream iss(oss.str());
432 readAlternativeProtein.
read(iss);
434 unit_assert(alternativeProtein == readAlternativeProtein);
436 if(
os_) *
os_ << oss.str() << endl;
442 if (
os_) *
os_ <<
"\ntestModAminoAcidMass() ...\n";
448 modAminoAcidMass.
write(writer);
451 istringstream iss(oss.str());
452 readModAminoAcidMass.
read(iss);
454 unit_assert(modAminoAcidMass == readModAminoAcidMass);
456 if(
os_) *
os_ << oss.str() << endl;
461 if (
os_) *
os_ <<
"\ntestModificationInfo() ...\n";
467 modificationInfo.
write(writer);
470 istringstream iss(oss.str());
471 readModificationInfo.
read(iss);
473 unit_assert(modificationInfo == readModificationInfo);
475 if(
os_) *
os_ << oss.str() << endl;
481 if (
os_) *
os_ <<
"\ntestSearchHit() ...\n";
487 searchHit.
write(writer);
490 istringstream iss(oss.str());
491 readSearchHit.
read(iss);
495 if(
os_) *
os_ << oss.str() << endl;
500 if(
os_) *
os_ <<
"\ntestSearchResult() ... \n";
506 searchResult.
write(writer);
509 istringstream iss(oss.str());
510 readSearchResult.
read(iss);
514 if(
os_) *
os_ << oss.str() << endl;
521 if (
os_) *
os_ <<
"\ntestEnzymaticSearchConstraint() ... \n";
527 enzymaticSearchConstraint.
write(writer);
530 istringstream iss(oss.str());
531 readEnzymaticSearchConstraint.
read(iss);
533 unit_assert(enzymaticSearchConstraint == readEnzymaticSearchConstraint);
535 if(
os_) *
os_ << oss.str() << endl;
541 if (
os_) *
os_ <<
"\ntestAminoAcidModification() ... \n";
547 aminoAcidModification.
write(writer);
550 istringstream iss(oss.str());
551 readAminoAcidModification.
read(iss);
553 unit_assert(aminoAcidModification == readAminoAcidModification);
555 if(
os_) *
os_ << oss.str() << endl;
561 if(
os_) *
os_ <<
"\ntestSearchSummary() ... \n";
567 searchSummary.
write(writer);
570 istringstream iss(oss.str());
571 readSearchSummary.
read(iss);
575 if(
os_) *
os_ << oss.str() << endl;
581 if(
os_) *
os_ <<
"\ntestSpectrumQuery() ... \n";
587 spectrumQuery.
write(writer);
589 if(
os_) *
os_ << oss.str() << endl;
592 istringstream iss(oss.str());
593 readSpectrumQuery.
read(iss);
595 readSpectrumQuery.
write(writer);
596 if(
os_) *
os_ << oss.str() << endl;
599 if(
os_) *
os_ << oss.str() << endl;
605 if(
os_) *
os_ <<
"\ntestMSMSRunSummary() ... \n";
611 msmsRunSummary.
write(writer);
614 istringstream iss(oss.str());
615 readMSMSRunSummary.
read(iss);
619 if(
os_) *
os_ << oss.str() << endl;
625 if(
os_) *
os_ <<
"\ntestMSMSPipelineAnalysis() ... \n";
628 msmsPipelineAnalysis.
date =
"20000101";
629 msmsPipelineAnalysis.
summaryXML =
"/2000/01/20000101/20000101.xml";
630 msmsPipelineAnalysis.
xmlns =
"http://regis-web.systemsbiology.net/pepXML";
631 msmsPipelineAnalysis.
xmlnsXSI =
"aruba";
639 msmsPipelineAnalysis.
write(writer);
642 istringstream iss(oss.str());
643 readMSMSPipelineAnalysis.
read(iss);
645 unit_assert(msmsPipelineAnalysis == readMSMSPipelineAnalysis);
647 if(
os_) *
os_ << oss.str() << endl;
653 if(
os_) *
os_ <<
"\ntestMatch() ... \n";
659 match->write(writer);
662 istringstream iss(oss.str());
665 ostringstream checkstream;
667 readMatch.
write(check);
670 if(
os_) *
os_ << oss.str() << endl;
671 if(
os_) *
os_ << checkstream.str() << endl;
679 if(
os_) *
os_ <<
"\ntestMatchData() ... \n";
689 matchData.
write(writer);
692 istringstream iss(oss.str());
693 readMatchData.
read(iss);
696 ostringstream checkstream;
698 readMatchData.
write(check);
701 if(
os_) *
os_ << oss.str() << endl;
702 if(
os_) *
os_ << checkstream.str() << endl;
708 if(
os_) *
os_ << oss.str() << endl;
714 ifstream ifs(
"20080619-A-6mixtestRG_Data10_msprefix.pep.xml");
717 throw runtime_error(
"bad ifs");
722 msmsPipelineAnalysis.
read(ifs);
724 ofstream ofs(
"test.pep.xml", ios::app);
726 msmsPipelineAnalysis.
write(writer);
730 int main(
int argc,
char* argv[])
737 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
738 if (
os_) *
os_ <<
"MinimumPepXMLTest ... \n";
std::string searchEngine
SEQUEST, Mascot, COMET, etc.
int index
Search constraint applied specifically to this query.
void testAlternativeProtein()
boost::shared_ptr< Match > MatchPtr
EnzymaticSearchConstraint enzymaticSearchConstraint
The XMLWriter class provides simple, tag-level XML syntax writing.
std::string fidelity
Semispecific means that at least one end of a pepide must conform to the cleavage specificity...
std::string peptideNextAA
void read(std::istream &is)
int startScan
first scan number integrated into MS/MS spectrum
void testSearchDatabase()
void read(std::istream &is)
void write(XMLWriter &writer) const
std::string precursorMassType
average or monoisotopic
std::vector< SearchResultPtr > searchResult
void testModificationInfo()
std::string sense
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut ...
void read(std::istream &is)
void read(std::istream &is)
AnalysisResult analysisResult
std::string noCut
Zero or more 1-letter residue codes.
std::string peptidePrevAA
std::string searchNbhdCalculator
void write(XMLWriter &writer) const
SearchHit makeSearchHit()
int main(int argc, char *argv[])
void write(XMLWriter &writer) const
std::vector< AminoAcidModification > aminoAcidModifications
double retentionTimeSec
Unique identifier.
EnzymaticSearchConstraint makeEnzymaticSearchConstraint()
double calcNeutralPepMass
PeptideProphetResult makePeptideProphetResult()
std::vector< SearchSummaryPtr > searchSummary
void write(XMLWriter &writer) const
void write(minimxml::XMLWriter &writer) const
int assumedCharge
Precursor ion charge used for search.
std::string searchID
Format of file storing the runner up peptides (if not present in pepXML)
std::vector< AlternativeProtein > alternativeProteins
ModAminoAcidMass modAminoAcidMass
void write(XMLWriter &writer) const
size_t minSpace
minimum separation between adjacent cleavages. default 1.
Specificity makeSpecificity()
boost::shared_ptr< SearchResult > SearchResultPtr
std::vector< SearchHitPtr > searchHit
void testEnzymaticSearchConstraint()
boost::shared_ptr< SearchSummary > SearchSummaryPtr
boost::shared_ptr< SearchHit > SearchHitPtr
void testAnalysisResult()
void write(minimxml::XMLWriter &writer) const
std::string fragmentMassType
average or monoisotopic
void read(std::istream &is)
AnalysisResult makeAnalysisResult()
std::string XSISchemaLocation
void read(std::istream &is)
void read(std::istream &is)
Database search settings.
void read(std::istream &is)
std::string cut
One or more 1-letter residue codes.
std::string databaseReleaseIdentifier
void write(XMLWriter &writer) const
PeptideProphetResult peptideProphetResult
void write(XMLWriter &writer) const
MSMSRunSummary msmsRunSummary
void read(std::istream &is)
std::string modifiedPeptide
void write(XMLWriter &writer) const
std::vector< double > allNttProb
void write(XMLWriter &writer) const
void testModAminoAcidMass()
SearchDatabase makeSearchDatabase()
AlternativeProtein makeAlternativeProtein()
void write(XMLWriter &writer) const
void read(std::istream &is)
void read(std::istream &is)
void read(std::istream &is)
void write(XMLWriter &writer) const
void testMSMSPipelineAnalysis()
void read(std::istream &is)
void read(std::istream &is)
void write(XMLWriter &writer) const
std::string baseName
Full path location of mzXML file for this search run (without the .mzXML extension) ...
SampleEnzyme makeSampleEnzyme()
void testInvarianceUnderProteinProphet()
std::string name
Controlled code name for the enzyme that can be referred to by applications.
SearchResult makeSearchResult()
void read(std::istream &is)
void testAminoAcidModification()
std::vector< MatchPtr > matches
SearchSummary makeSearchSummary()
void write(XMLWriter &writer) const
SearchDatabase searchDatabase
runner up search hit data type extension (e.g. .tgz)
std::string warpFunctionCalculator
ModificationInfo modificationInfo
std::vector< SpectrumQueryPtr > spectrumQueries
MSMSRunSummary makeMSMSRunSummary()
AminoAcidModification makeAminoAcidModification()
Q3RatioResult q3RatioResult
Q3RatioResult makeQ3RatioResult()
void write(XMLWriter &writer) const
int endScan
last scan number integrated into MS/MS spectrum
boost::tribool independent
If there are multiple specificities and independent is true, then a single peptide cannot exhibit one...
void testPeptideProphetResult()
double precursorNeutralMass
void testMSMSRunSummary()
void read(std::istream &is)
#define TEST_PROLOG(argc, argv)
boost::shared_ptr< SpectrumQuery > SpectrumQueryPtr
void read(std::istream &is)
std::string description
Free text to describe alternative names, special conditions, etc.
void write(XMLWriter &writer) const
void write(XMLWriter &writer) const
ModificationInfo makeModificationInfo()
int maxNumInternalCleavages
void write(XMLWriter &writer) const
void read(std::istream &is)
SpectrumQuery makeSpectrumQuery()
void read(std::istream &is)
ModAminoAcidMass makeModAminoAcidMass()
SampleEnzyme sampleEnzyme