45 if (
os_) *
os_ <<
"testIdentifiable()\n";
53 if (
diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
60 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
73 if (
os_) *os_ << diff_string<TextWriter>(diff0) << endl;
79 if (
os_) *os_ << diff_string<TextWriter>(diff1) << endl;
85 if (
os_) *os_ << diff_string<TextWriter>(diff2) << endl;
92 if (
os_) *
os_ <<
"testFragmentArray()\n";
102 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
125 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
130 if (
os_) *
os_ <<
"testIonType()\n";
133 a.
index.push_back(1);
142 if (
os_ &&
diff) *os_ << diff_string<TextWriter>(
diff) << endl;
153 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
166 unit_assert(
diff.b_a.fragmentArray.back()->measurePtr->id ==
"Graduated_cylinder");
172 if (
os_) *
os_ <<
"testMeasure()\n";
184 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
197 if (
os_) *
os_ <<
"testSearchModification()\n";
216 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
235 if (
os_) *
os_ <<
"testPeptideEvidence()\n";
240 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
268 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
279 unit_assert(
diff.a_b.translationTablePtr->id ==
"TranslationTable_ref");
281 unit_assert(
diff.b_a.translationTablePtr->id ==
"fer_elbaTnoitalsnarT");
303 if (
os_) *
os_ <<
"testProteinAmbiguityGroup()\n";
319 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
327 unit_assert(
diff.a_b.proteinDetectionHypothesis.back()->dbSequencePtr->id ==
"DBSequence_ref");
337 if (
os_) *
os_ <<
"testPeptideHypothesis()\n";
349 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
360 unit_assert(
diff.a_b.spectrumIdentificationItemPtr.back()->id ==
"sii_a");
362 unit_assert(
diff.b_a.spectrumIdentificationItemPtr.back()->id ==
"sii_b");
368 if (
os_) *
os_ <<
"testProteinDetectionHypothesis()\n";
389 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
403 unit_assert(
diff.a_b.peptideHypothesis.back().peptideEvidencePtr->id ==
"pe_a");
404 unit_assert(
diff.b_a.peptideHypothesis.back().peptideEvidencePtr->id ==
"pe_b");
405 unit_assert(
diff.a_b.peptideHypothesis.back().spectrumIdentificationItemPtr.size() == 1);
406 unit_assert(
diff.a_b.peptideHypothesis.back().spectrumIdentificationItemPtr.back()->id ==
"sii_a");
407 unit_assert(
diff.b_a.peptideHypothesis.back().spectrumIdentificationItemPtr.size() == 1);
408 unit_assert(
diff.b_a.peptideHypothesis.back().spectrumIdentificationItemPtr.back()->id ==
"sii_b");
417 if (
os_) *
os_ <<
"testSpectrumIdentificationList()\n";
435 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
455 if (
os_) *
os_ <<
"testProteinDetectionList()\n";
467 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
486 if (
os_) *
os_ <<
"testAnalysisData()\n";
501 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
521 if (
os_) *
os_ <<
"testSearchDatabase()" << endl;
543 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
569 if (
os_) *
os_ <<
"testSpectraData()\n" << endl;
582 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
592 unit_assert(
diff.a_b.externalFormatDocumentation.back() ==
"wikipedia");
603 if (
os_) *
os_ <<
"testSourceFile()\n" << endl;
618 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
631 unit_assert(
diff.a_b.externalFormatDocumentation.back() ==
"The Idiot's Guide to External Formats");
632 unit_assert(
diff.b_a.externalFormatDocumentation.back() ==
"External Formats for Dummies");
644 if (
os_) *
os_ <<
"testInputs()\n";
660 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
681 if (
os_) *
os_ <<
"testEnzyme()\n";
685 if (
diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
688 a.
id =
"Donald Trump";
689 b.
id =
"Donald Duck";
705 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
717 unit_assert(
diff.b_a.terminalSpecificity == proteome::Digestion::FullySpecific);
734 if (
os_) *
os_ <<
"testEnzymes()\n";
738 if (
diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
747 if (
os_) *
os_ <<
"testMassTable()\n";
787 if (
os_) *
os_ <<
"testResidue()\n";
802 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
815 if (
os_) *
os_ <<
"testAmbiguousResidue()\n";
830 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
843 if (
os_) *
os_ <<
"testFilter()\n";
863 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
878 if (
os_) *
os_ <<
"testDatabaseTranslation()\n";
897 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
910 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
923 if (
os_) *
os_ <<
"testSpectrumIdentificationProtocol()\n";
932 smp->fixedMod =
true;
933 a.modificationParams.push_back(smp);
934 a.enzymes.enzymes.push_back(EnzymePtr(
new Enzyme(
"a_enzyme")));
935 a.massTable.push_back(MassTablePtr(
new MassTable(
"mt_id")));
941 a.databaseFilters.push_back(
filter);
952 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
970 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
978 if (
os_) *
os_ <<
"testProteinDetectionProtocol()\n";
996 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1004 if (
os_) *
os_ <<
"testAnalysisProtocolCollection()\n";
1010 if (
os_) *
os_ <<
"testContact()\n";
1012 Contact a(
"a_id",
"a_name"), b;
1029 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1041 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1049 if (
os_) *
os_ <<
"testPerson()\n";
1086 if (
os_) *
os_ <<
"testOrganization()\n";
1092 if (
os_) *
os_ <<
"testBibliographicReference()\n";
1098 if (
os_) *
os_ <<
"testProteinDetection()\n";
1104 if (
os_) *
os_ <<
"testSpectrumIdentification()\n";
1110 if (
os_) *
os_ <<
"testAnalysisCollection()\n";
1117 if (
os_) *
os_ <<
"testDBSequence()\n";
1123 if (
os_) *
os_ <<
"testModification()\n";
1129 if (
os_) *
os_ <<
"testSubstitutionModification()\n";
1135 if (
os_) *
os_ <<
"testPeptide()\n";
1141 if (
os_) *
os_ <<
"testSequenceCollection()\n";
1147 if (
os_) *
os_ <<
"testSampleComponent()\n";
1153 if (
os_) *
os_ <<
"testSample()\n";
1161 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1168 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1182 unit_assert(
diff.a_b.contactRole.back()->contactPtr->id ==
"contactPtr");
1183 unit_assert(
diff.b_a.contactRole.back()->contactPtr->id ==
"fer_rehto");
1190 if (
os_) *
os_ <<
"testSpectrumIdentificationItem()\n";
1196 if (
os_) *
os_ <<
"testSpectrumIdentificationResult()\n";
1202 if (
os_) *
os_ <<
"testAnalysisSampleCollection()\n";
1208 if (
os_) *
os_ <<
"testProvider()\n";
1214 if (
os_) *
os_ <<
"testContactRole()\n";
1224 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1231 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1245 if (
os_) *
os_ <<
"testAnalysisSoftware()\n";
1267 if (
os_) *
os_ <<
"testDataCollection()\n";
1282 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1289 if (
os_) *
os_ <<
"testIdentData()\n";
1299 a.
cvs.push_back(
CV());
1311 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1377 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
1380 catch (exception& e)