├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── scripts │ └── mac-create-identity.zsh └── workflows │ ├── distribute.yaml │ └── dockergen.yaml ├── .gitignore ├── .gitlab-ci.yml ├── COPYING.txt ├── LICENSE.txt ├── README.md ├── affinity_selection_ms ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── cmlDesign │ │ │ ├── BuildingBlock.java │ │ │ ├── CLI.java │ │ │ ├── CMLDistribution.java │ │ │ ├── CMLEvaluator.java │ │ │ ├── CMLUtils.java │ │ │ ├── CombinatorialMoleculeLibrary.java │ │ │ ├── EntropyCalculator.java │ │ │ ├── EntropyLikeCalculator.java │ │ │ ├── EquidistantBinDistribution.java │ │ │ ├── GreedySearch.java │ │ │ ├── MassDecomposer.java │ │ │ ├── MassDeviationDependentBinDistribution.java │ │ │ ├── Normalization.java │ │ │ ├── NumCandidatesEvaluator.java │ │ │ └── io │ │ │ │ ├── BuildingBlockReader.java │ │ │ │ └── BuildingBlockWriter.java │ │ │ ├── cmlFragmentation │ │ │ ├── AbstractFragmentationPredictor.java │ │ │ ├── FragStepDependentScoring.java │ │ │ ├── FragmentationPredictor.java │ │ │ ├── FragmentationRules.java │ │ │ ├── PrioritizedIterativeFragmentationPredictor.java │ │ │ ├── RuleBasedFragmentationPredictor.java │ │ │ └── SimpleFragmentationRule.java │ │ │ ├── cmlSpectrumPrediction │ │ │ ├── AbstractMs2SpectrumPredictor.java │ │ │ ├── BarcodeSpectrumPredictor.java │ │ │ ├── ICEBERGSpectrumPredictor.java │ │ │ ├── Main.java │ │ │ └── SpectrumPredictor.java │ │ │ └── evaluation │ │ │ └── SpecPredictionEvaluation.java │ └── resources │ │ ├── iceberg_predictMol.py │ │ └── makeMirrorSpectrumPlot.py │ └── test │ └── java │ ├── MassDecomposerTest.java │ └── TEST.java ├── biotransformations ├── build.gradle └── src │ ├── main │ └── java │ │ ├── biotransformer │ │ └── btransformers │ │ │ └── Biotransformer.java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── ms │ │ └── biotransformer │ │ ├── BioTransformation.java │ │ ├── BioTransformerJJob.java │ │ ├── BioTransformerResult.java │ │ ├── BioTransformerSequenceStep.java │ │ ├── BioTransformerSettings.java │ │ ├── BioTransformerWrapper.java │ │ ├── Cyp450Mode.java │ │ ├── MetabolicTransformation.java │ │ └── P2Mode.java │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── ms │ └── biotransformer │ └── BioTransformerWrapperTest.java ├── blob-storage ├── build.gradle ├── gcs-blob-storage │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── storage │ │ └── blob │ │ └── gcs │ │ ├── GCSBlobStorage.java │ │ └── GCSUtils.java └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── storage │ └── blob │ ├── AbstractCompressible.java │ ├── BlobStorage.java │ ├── BlobStorages.java │ ├── Compressible.java │ ├── CompressibleBlobStorage.java │ ├── ReadCachedBlobStorage.java │ ├── file │ └── FileBlobStorage.java │ ├── memory │ ├── InMemoryBlobStorage.java │ └── InMemoryCacheBlobStorage.java │ └── minio │ ├── MinIoS3BlobStorage.java │ └── MinIoUtils.java ├── canopus_predict_oss ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ ├── canopus │ │ ├── Canopus.java │ │ ├── CanopusResult.java │ │ ├── FormulaFeatureVector.java │ │ └── dnn │ │ │ ├── ActivationFunction.java │ │ │ ├── FullyConnectedLayer.java │ │ │ └── PlattLayer.java │ │ └── projectspace │ │ └── canopus │ │ ├── CanopusCfDataProperty.java │ │ ├── CanopusLocations.java │ │ ├── CanopusNpcDataProperty.java │ │ └── CanopusSerializer.java │ └── resources │ └── LICENSE.txt ├── chemical_db_oss ├── build.gradle ├── chemdb_blob_oss │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── chemdb │ │ │ ├── ChemicalBlobDatabase.java │ │ │ ├── SqlIndex.java │ │ │ └── custom │ │ │ └── BlobCustomDatabase.java │ │ └── resources │ │ └── LICENSE.txt ├── chemdb_nitrite_oss │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── chemdb │ │ │ ├── ChemicalNoSQLDBs.java │ │ │ ├── ChemicalNoSQLDatabase.java │ │ │ ├── custom │ │ │ │ └── NoSQLCustomDatabase.java │ │ │ └── nitrite │ │ │ │ ├── ChemicalNitriteDatabase.java │ │ │ │ ├── serializers │ │ │ │ ├── FingerprintCandidateWrapperDeserializer.java │ │ │ │ ├── FingerprintCandidateWrapperSerializer.java │ │ │ │ └── NitriteCompoundSerializers.java │ │ │ │ └── wrappers │ │ │ │ └── FingerprintCandidateWrapper.java │ │ │ └── spectraldb │ │ │ └── SpectralNoSQLDatabase.java │ │ └── test │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── chemdb │ │ │ └── ChemicalNoSQLDatabaseTest.java │ │ └── resources │ │ └── test-blob-db │ │ ├── .tags │ │ ├── C10H18O3.json.gz │ │ ├── C14H22O2.json.gz │ │ ├── C15H10O6.json.gz │ │ ├── C15H14O6.json.gz │ │ ├── C15H22O3.json.gz │ │ ├── C15H24O2.json.gz │ │ ├── C15H26O2.json.gz │ │ ├── C15H26O3.json.gz │ │ ├── C16H20O6.json.gz │ │ ├── C17H18O6.json.gz │ │ ├── C17H22ClN9O2.json.gz │ │ ├── C17H24O3.json.gz │ │ ├── C19H26O5.json.gz │ │ ├── C20H17NO6.json.gz │ │ ├── C21H32O3.json.gz │ │ ├── C22H32O5.json.gz │ │ ├── C24H34O6.json.gz │ │ ├── C27H30O14.json.gz │ │ ├── C34H38O6.json.gz │ │ └── SETTINGS ├── chemdb_rest_oss │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── chemdb │ │ │ └── RESTDatabase.java │ │ └── resources │ │ └── LICENSE.txt ├── chemdb_sql_jdbi_json_oss │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── chemdb │ │ └── SpectralSqlJdbiJsonDatabase.java ├── chemdb_sql_oss │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── groovy │ │ │ └── MetaData.groovy │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── chemdb │ │ │ │ └── ChemicalDatabase.java │ │ └── resources │ │ │ └── LICENSE.txt │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── chemdb │ │ └── ChemicalDatabaseTest.java ├── chemdb_utils_oss │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── chemdb │ │ │ │ ├── InChISMILESUtils.java │ │ │ │ ├── LogPEstimator.java │ │ │ │ └── SpectralUtils.java │ │ └── resources │ │ │ └── LICENSE.txt │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── chemdb │ │ └── InChISMILESUtilsTest.java └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ ├── chemdb │ │ ├── AbstractChemicalDatabase.java │ │ ├── AbstractChemicalDatabaseSynchronousExecutor.java │ │ ├── AnnotateStructures.java │ │ ├── CSVReader.java │ │ ├── ChemDBFileCache.java │ │ ├── ChemDBs.java │ │ ├── ChemDbTags.java │ │ ├── ChemicalDatabaseException.java │ │ ├── CompoundCandidate.java │ │ ├── CompoundCandidateChargeLayer.java │ │ ├── CompoundCandidateChargeState.java │ │ ├── CompoundJsonMapper.java │ │ ├── CompoundReader.java │ │ ├── CompoundWithFingerprint.java │ │ ├── DBLink.java │ │ ├── DBVersion.java │ │ ├── DataSource.java │ │ ├── FilterableChemicalDatabase.java │ │ ├── FilteredChemicalDB.java │ │ ├── FingerprintCandidate.java │ │ ├── FormulaCandidate.java │ │ ├── InMemoryChemicalDatabase.java │ │ ├── PubmedLinks.java │ │ ├── SearchStructureByFormula.java │ │ ├── SearchableDatabase.java │ │ ├── SpectraLibraryUpdateManager.java │ │ ├── WriteableChemicalDatabase.java │ │ └── custom │ │ │ ├── CustomDataSources.java │ │ │ ├── CustomDatabase.java │ │ │ ├── CustomDatabaseSettings.java │ │ │ └── OutdatedDBExeption.java │ │ └── spectraldb │ │ ├── LibraryHit.java │ │ ├── SpectralLibrary.java │ │ ├── SpectralLibrarySearchSettings.java │ │ ├── SpectrumType.java │ │ ├── WriteableSpectralLibrary.java │ │ ├── entities │ │ ├── MergedReferenceSpectrum.java │ │ ├── Ms2ReferenceSpectrum.java │ │ ├── ReferenceFragment.java │ │ ├── ReferenceFragmentationTree.java │ │ └── ReferenceSpectrum.java │ │ └── io │ │ ├── ParsingIterator.java │ │ └── SpectralDbMsExperimentParser.java │ └── resources │ └── LICENSE.txt ├── chemistry_base ├── .gitignore ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── ChemistryBase │ │ │ ├── algorithm │ │ │ │ ├── BasicScore.java │ │ │ │ ├── BinarySearch.java │ │ │ │ ├── BitsetOps.java │ │ │ │ ├── BoundedDoubleQueue.java │ │ │ │ ├── BoundedQueue.java │ │ │ │ ├── Called.java │ │ │ │ ├── FastReadWriteLock.java │ │ │ │ ├── Functor0.java │ │ │ │ ├── HasParameters.java │ │ │ │ ├── HierarchicalClustering.java │ │ │ │ ├── ImmutableParameterized.java │ │ │ │ ├── KMeans.java │ │ │ │ ├── Parameter.java │ │ │ │ ├── ParameterHelper.java │ │ │ │ ├── Parameterized.java │ │ │ │ ├── ParameterizedByAnnotation.java │ │ │ │ ├── Quickselect.java │ │ │ │ ├── Sorting.java │ │ │ │ └── scoring │ │ │ │ │ ├── FormulaScore.java │ │ │ │ │ ├── SScored.java │ │ │ │ │ ├── Score.java │ │ │ │ │ └── Scored.java │ │ │ ├── chem │ │ │ │ ├── Charge.java │ │ │ │ ├── ChemicalAlphabet.java │ │ │ │ ├── CompoundWithAbstractFP.java │ │ │ │ ├── ElectronIonization.java │ │ │ │ ├── Element.java │ │ │ │ ├── FeatureGroup.java │ │ │ │ ├── FormulaConstraints.java │ │ │ │ ├── FormulaFilter.java │ │ │ │ ├── ImmutableMolecularFormula.java │ │ │ │ ├── InChI.java │ │ │ │ ├── InChIs.java │ │ │ │ ├── IonMode.java │ │ │ │ ├── Ionization.java │ │ │ │ ├── IonizedMolecularFormula.java │ │ │ │ ├── Isotopes.java │ │ │ │ ├── MolecularFormula.java │ │ │ │ ├── MolecularFormulaMap.java │ │ │ │ ├── MutableMolecularFormula.java │ │ │ │ ├── PeriodicTable.java │ │ │ │ ├── PrecursorIonType.java │ │ │ │ ├── RetentionTime.java │ │ │ │ ├── Smiles.java │ │ │ │ ├── SmilesU.java │ │ │ │ ├── TableSelection.java │ │ │ │ ├── TableSelectionCache.java │ │ │ │ └── utils │ │ │ │ │ ├── Contaminants.java │ │ │ │ │ ├── DistributionReader.java │ │ │ │ │ ├── ElementMap.java │ │ │ │ │ ├── FormulaEncodingError.java │ │ │ │ │ ├── FormulaFilterList.java │ │ │ │ │ ├── FormulaParsingException.java │ │ │ │ │ ├── FormulaVisitor.java │ │ │ │ │ ├── IsotopicDistribution.java │ │ │ │ │ ├── IsotopicDistributionBlueObeliskReader.java │ │ │ │ │ ├── IsotopicDistributionJSONFile.java │ │ │ │ │ ├── MolecularFormulaPacker.java │ │ │ │ │ ├── MolecularFormulaPool.java │ │ │ │ │ ├── MolecularFormulaScorer.java │ │ │ │ │ ├── MolecularFormulaSet.java │ │ │ │ │ ├── PeriodicTableBlueObeliskReader.java │ │ │ │ │ ├── PeriodicTableJSONReader.java │ │ │ │ │ ├── PeriodicTableReader.java │ │ │ │ │ ├── UnknownElementException.java │ │ │ │ │ ├── ValenceFilter.java │ │ │ │ │ ├── biotransformation │ │ │ │ │ ├── BioTransformation.java │ │ │ │ │ └── BioTransformer.java │ │ │ │ │ └── scoring │ │ │ │ │ ├── ChemicalCompoundScorer.java │ │ │ │ │ ├── DNNFormulaScorer.java │ │ │ │ │ ├── FormulaFeatureVector.java │ │ │ │ │ ├── Hetero2CarbonScorer.java │ │ │ │ │ ├── Hydrogen2CarbonScorer.java │ │ │ │ │ ├── ImprovedHetero2CarbonScorer.java │ │ │ │ │ ├── RDBEMassScorer.java │ │ │ │ │ ├── RDBENormalScorer.java │ │ │ │ │ ├── SpecialMoleculeScorer.java │ │ │ │ │ └── SupportVectorMolecularFormulaScorer.java │ │ │ ├── data │ │ │ │ ├── DataDocument.java │ │ │ │ ├── DataSource.java │ │ │ │ ├── DocumentFormatable.java │ │ │ │ ├── DoubleDataMatrix.java │ │ │ │ ├── JDKDocument.java │ │ │ │ ├── JSONDocumentType.java │ │ │ │ ├── JacksonDocument.java │ │ │ │ ├── Tagging.java │ │ │ │ └── TypeError.java │ │ │ ├── exceptions │ │ │ │ ├── InsufficientDataException.java │ │ │ │ ├── InvalidInputData.java │ │ │ │ ├── MultimereException.java │ │ │ │ └── MultipleChargeException.java │ │ │ ├── fp │ │ │ │ ├── AbstractFingerprint.java │ │ │ │ ├── ArrayFingerprint.java │ │ │ │ ├── BinaryFpDeserializer.java │ │ │ │ ├── BinaryFpSerializer.java │ │ │ │ ├── BooleanFingerprint.java │ │ │ │ ├── CdkFingerprintVersion.java │ │ │ │ ├── ClassyFireFingerprintVersion.java │ │ │ │ ├── ClassyfireProperty.java │ │ │ │ ├── CustomFingerprintVersion.java │ │ │ │ ├── ExtendedConnectivityProperty.java │ │ │ │ ├── FPIter.java │ │ │ │ ├── FPIter2.java │ │ │ │ ├── Fingerprint.java │ │ │ │ ├── FingerprintData.java │ │ │ │ ├── FingerprintVersion.java │ │ │ │ ├── FormulaProperty.java │ │ │ │ ├── FpDeserializer.java │ │ │ │ ├── MaskedFingerprintVersion.java │ │ │ │ ├── MolecularProperty.java │ │ │ │ ├── NPCFingerprintVersion.java │ │ │ │ ├── PredictionPerformance.java │ │ │ │ ├── ProbabilityFingerprint.java │ │ │ │ ├── ShortestPathProperty.java │ │ │ │ ├── SpecialMolecularProperty.java │ │ │ │ ├── StandardFingerprintData.java │ │ │ │ ├── SubstructureCountProperty.java │ │ │ │ ├── SubstructureProperty.java │ │ │ │ └── Tanimoto.java │ │ │ ├── jobs │ │ │ │ ├── JobManagerFactory.java │ │ │ │ └── SiriusJobs.java │ │ │ ├── math │ │ │ │ ├── ByMedianEstimatable.java │ │ │ │ ├── DensityFunction.java │ │ │ │ ├── ExponentialDistribution.java │ │ │ │ ├── HighQualityRandom.java │ │ │ │ ├── IsRealDistributed.java │ │ │ │ ├── KernelCentering.java │ │ │ │ ├── LogNormalDistribution.java │ │ │ │ ├── MathUtils.java │ │ │ │ ├── MatrixUtils.java │ │ │ │ ├── NormalDistribution.java │ │ │ │ ├── ParetoDistribution.java │ │ │ │ ├── PartialNormalDistribution.java │ │ │ │ ├── PartialParetoDistribution.java │ │ │ │ ├── Probability.java │ │ │ │ ├── RealDistribution.java │ │ │ │ └── Statistics.java │ │ │ ├── ms │ │ │ │ ├── AdditionalFields.java │ │ │ │ ├── AnnotatedPeak.java │ │ │ │ ├── CollisionEnergy.java │ │ │ │ ├── CompoundQuality.java │ │ │ │ ├── DetectedAdducts.java │ │ │ │ ├── Deviation.java │ │ │ │ ├── FunctionalMetabolomics.java │ │ │ │ ├── IsolationWindow.java │ │ │ │ ├── MS1MassDeviation.java │ │ │ │ ├── MS2MassDeviation.java │ │ │ │ ├── MassDeviation.java │ │ │ │ ├── MedianNoiseIntensity.java │ │ │ │ ├── MergedMs1Spectrum.java │ │ │ │ ├── MergedMs2Spectrum.java │ │ │ │ ├── Ms2Experiment.java │ │ │ │ ├── Ms2Spectrum.java │ │ │ │ ├── MsFileSource.java │ │ │ │ ├── MsInstrumentation.java │ │ │ │ ├── MultipleSources.java │ │ │ │ ├── MutableMs2Experiment.java │ │ │ │ ├── MutableMs2Spectrum.java │ │ │ │ ├── MutableSpectrum.java │ │ │ │ ├── NoiseInformation.java │ │ │ │ ├── Normalization.java │ │ │ │ ├── NormalizationMode.java │ │ │ │ ├── NumberOfCandidates.java │ │ │ │ ├── NumberOfCandidatesPerIonization.java │ │ │ │ ├── Peak.java │ │ │ │ ├── PossibleAdductSwitches.java │ │ │ │ ├── PossibleAdducts.java │ │ │ │ ├── Quantification.java │ │ │ │ ├── RecalibrationFunction.java │ │ │ │ ├── SimplePeak.java │ │ │ │ ├── SourceLocation.java │ │ │ │ ├── Spectrum.java │ │ │ │ ├── SpectrumFileSource.java │ │ │ │ ├── Splash.java │ │ │ │ ├── ft │ │ │ │ │ ├── AbstractFragmentationGraph.java │ │ │ │ │ ├── Beautified.java │ │ │ │ │ ├── FGraph.java │ │ │ │ │ ├── FTree.java │ │ │ │ │ ├── Fragment.java │ │ │ │ │ ├── FragmentAnnotation.java │ │ │ │ │ ├── ImplicitAdduct.java │ │ │ │ │ ├── IntergraphMapping.java │ │ │ │ │ ├── IonTreeUtils.java │ │ │ │ │ ├── IsotopicMarker.java │ │ │ │ │ ├── Loss.java │ │ │ │ │ ├── LossAnnotation.java │ │ │ │ │ ├── LossType.java │ │ │ │ │ ├── Ms1IsotopePattern.java │ │ │ │ │ ├── Ms2IsotopePattern.java │ │ │ │ │ ├── Recalibrated.java │ │ │ │ │ ├── Score.java │ │ │ │ │ ├── TreeStatistics.java │ │ │ │ │ ├── UnconsideredCandidatesUpperBound.java │ │ │ │ │ └── model │ │ │ │ │ │ ├── AdductSettings.java │ │ │ │ │ │ ├── CandidateFormulas.java │ │ │ │ │ │ ├── Decomposition.java │ │ │ │ │ │ ├── ForbidRecalibration.java │ │ │ │ │ │ ├── FormulaSearchSettings.java │ │ │ │ │ │ ├── FormulaSettings.java │ │ │ │ │ │ ├── IsotopeMs2Settings.java │ │ │ │ │ │ ├── IsotopeSettings.java │ │ │ │ │ │ ├── Timeout.java │ │ │ │ │ │ └── Whiteset.java │ │ │ │ ├── inputValidators │ │ │ │ │ ├── EmptySpectraValidator.java │ │ │ │ │ ├── InvalidException.java │ │ │ │ │ ├── MissingMergedSpectrumValidator.java │ │ │ │ │ ├── Ms2ExperimentValidator.java │ │ │ │ │ └── Warning.java │ │ │ │ ├── lcms │ │ │ │ │ ├── CoelutingTraceSet.java │ │ │ │ │ ├── CompoundReport.java │ │ │ │ │ ├── CompoundTrace.java │ │ │ │ │ ├── IonTrace.java │ │ │ │ │ ├── LCMSPeakInformation.java │ │ │ │ │ ├── MsDataSourceReference.java │ │ │ │ │ ├── QuantificationMeasure.java │ │ │ │ │ ├── QuantificationTable.java │ │ │ │ │ ├── Trace.java │ │ │ │ │ ├── info │ │ │ │ │ │ ├── JoinedSegmentDuetoCosine.java │ │ │ │ │ │ ├── RejectedMsMs.java │ │ │ │ │ │ ├── RejectedMsMsDueToChimeric.java │ │ │ │ │ │ ├── RejectedMsMsDueToLowCosine.java │ │ │ │ │ │ ├── SimilarMsMsButLargeGap.java │ │ │ │ │ │ ├── SplittedSegment.java │ │ │ │ │ │ └── SplittedSegmentDueToLowCosine.java │ │ │ │ │ └── workflows │ │ │ │ │ │ ├── LCMSWorkflow.java │ │ │ │ │ │ ├── MixedWorkflow.java │ │ │ │ │ │ ├── PooledMs2Workflow.java │ │ │ │ │ │ └── RemappingWorkflow.java │ │ │ │ ├── properties │ │ │ │ │ ├── ConfigAnnotation.java │ │ │ │ │ └── FinalConfig.java │ │ │ │ └── utils │ │ │ │ │ ├── AbstractSpectrum.java │ │ │ │ │ ├── AnnotatedSpectrum.java │ │ │ │ │ ├── AnnotatedWrapperSpectrum.java │ │ │ │ │ ├── ArrayWrapperSpectrum.java │ │ │ │ │ ├── BasicMutableSpectrum.java │ │ │ │ │ ├── BasicSpectrum.java │ │ │ │ │ ├── ChargedPeak.java │ │ │ │ │ ├── ChargedSpectrum.java │ │ │ │ │ ├── MassMap.java │ │ │ │ │ ├── MsExperiments.java │ │ │ │ │ ├── MutableMs2SpectrumWithAdditionalFields.java │ │ │ │ │ ├── OrderedSpectrum.java │ │ │ │ │ ├── OrderedSpectrumDelegate.java │ │ │ │ │ ├── PeakComment.java │ │ │ │ │ ├── PeaklistSpectrum.java │ │ │ │ │ ├── SimpleMutableSpectrum.java │ │ │ │ │ ├── SimpleSpectrum.java │ │ │ │ │ ├── SimpleSpectrumWithAdditionalFields.java │ │ │ │ │ ├── SpectrumWithAdditionalFields.java │ │ │ │ │ ├── Spectrums.java │ │ │ │ │ └── WrapperSpectrum.java │ │ │ └── utils │ │ │ │ ├── AlphanumComparator.java │ │ │ │ ├── DataQuality.java │ │ │ │ ├── DebouncedExecutionJJob.java │ │ │ │ ├── DescriptiveOptions.java │ │ │ │ ├── ExFunctions.java │ │ │ │ ├── FastUtilJson.java │ │ │ │ ├── FileUtils.java │ │ │ │ ├── IOFunctions.java │ │ │ │ ├── IterableWithSize.java │ │ │ │ ├── RangeUtils.java │ │ │ │ ├── SimpleSerializers.java │ │ │ │ ├── TaskTimer.java │ │ │ │ ├── Utils.java │ │ │ │ └── ZipCompressionMethod.java │ │ │ ├── ms │ │ │ └── annotations │ │ │ │ ├── Annotated.java │ │ │ │ ├── AnnotatedWithDefaults.java │ │ │ │ ├── AnnotationJJob.java │ │ │ │ ├── DataAnnotation.java │ │ │ │ ├── Ms2ExperimentAnnotation.java │ │ │ │ ├── ProcessedInputAnnotation.java │ │ │ │ ├── Provides.java │ │ │ │ ├── Requires.java │ │ │ │ ├── ResultAnnotation.java │ │ │ │ ├── SpectrumAnnotation.java │ │ │ │ └── TreeAnnotation.java │ │ │ ├── projectspace │ │ │ └── ProjectSpaceProperty.java │ │ │ └── recal │ │ │ ├── ChebychevPolynomialFunction.java │ │ │ ├── MzRecalibration.java │ │ │ └── OrdinaryLeastSquares.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── additional_elements.json │ │ ├── adduct-switch.profile │ │ ├── bioformulas.bin.gz │ │ ├── blueobelisk_elements.xml │ │ ├── blueobelisk_isotopes.xml │ │ ├── chemcalc_distribution.json │ │ ├── de.unijena.bioinf.ms.defaults │ │ ├── chemistry_base.auto.config │ │ └── chemistry_base.class.map │ │ ├── elements.json │ │ ├── fingerprints │ │ ├── biosmarts.txt │ │ ├── chemont.csv.gz │ │ ├── ecfp.txt │ │ ├── fingerprint_selection_indizes.txt │ │ ├── insilico.txt │ │ ├── npc │ │ │ ├── classes.csv │ │ │ ├── pathways.csv │ │ │ └── superclasses.csv │ │ ├── ringsystems.txt │ │ └── shortest_paths.txt │ │ ├── index_fingerprints.txt │ │ ├── isotopic_distributions.json │ │ ├── merged.json │ │ ├── merged_distribution.json │ │ ├── molecules.txt │ │ ├── obsidian.xml │ │ ├── orbitrap.profile │ │ ├── qtof.profile │ │ └── sirius.build.properties │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── ChemistryBase │ ├── chem │ ├── FormulaConstraintsTest.java │ ├── FormulaPackerTest.java │ ├── FormulaTest.java │ ├── IonTest.java │ ├── ParserTest.java │ ├── QuicksortTest.java │ ├── RetentionTimeTest.java │ └── TanimotoTest.java │ ├── data │ └── TableTest.java │ ├── ms │ ├── FPTest.java │ ├── TreeTest.java │ ├── ft │ │ └── model │ │ │ └── WhitesetTest.java │ └── utils │ │ ├── OrderedSpectrumDelegateTest.java │ │ └── SpectrumsTest.java │ ├── transfomation │ └── TransformerTest.java │ └── utils │ ├── FileUtilsTest.java │ ├── SpectrumsExtractMostIntenseTest.java │ ├── SpectrumsExtractMostIntenseWindowTest.java │ └── UtilsTest.java ├── combinatorial_fragmenter ├── build.gradle └── src │ ├── main │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── fragmenter │ │ ├── AbstractFragmentationTreeAnnotator.java │ │ ├── AnnotateFragmentationTree.java │ │ ├── BondTypeScoring.java │ │ ├── CircularFingerprinterMod.java │ │ ├── CombinatorialEdge.java │ │ ├── CombinatorialFragment.java │ │ ├── CombinatorialFragment2.java │ │ ├── CombinatorialFragmenter.java │ │ ├── CombinatorialFragmenterScoring.java │ │ ├── CombinatorialGraph.java │ │ ├── CombinatorialGraphManipulator.java │ │ ├── CombinatorialNode.java │ │ ├── CombinatorialSubtree.java │ │ ├── CombinatorialSubtreeCalculator.java │ │ ├── CombinatorialSubtreeCalculatorJsonReader.java │ │ ├── CombinatorialSubtreeCalculatorJsonWriter.java │ │ ├── CombinatorialSubtreeJsonReader.java │ │ ├── CombinatorialSubtreeJsonWriter.java │ │ ├── CombinatorialSubtreeManipulator.java │ │ ├── CriticalPathInsertionSubtreeCalculator.java │ │ ├── CriticalPathSubtreeCalculator.java │ │ ├── CriticalPathSubtreeCalculatorWithInsertion.java │ │ ├── DataProcessor.java │ │ ├── DataProcessorExecutor.java │ │ ├── DirectedBondTypeScoring.java │ │ ├── EMFragmenterScoring.java │ │ ├── EMFragmenterScoring2.java │ │ ├── InsertionSubtreeCalculator.java │ │ ├── InsilicoFragmentationPeakAnnotator.java │ │ ├── InsilicoFragmentationResult.java │ │ ├── IterateThroughMolecule.java │ │ ├── MolecularGraph.java │ │ ├── PCSTFragmentationTreeAnnotator.java │ │ ├── PrimSubtreeCalculator.java │ │ ├── PriorizedFragmenter.java │ │ ├── ScoringParameterEstimator.java │ │ ├── SmartsGen.java │ │ └── SubtreeComputationMethod.java │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── fragmenter │ ├── CombinatorialFragmenterTest.java │ ├── CombinatorialGraphManipulatorTest.java │ ├── CombinatorialSubtreeManipulatorTest.java │ ├── CriticalPathInsertionSubtreeCalculatorTest.java │ ├── CriticalPathSubtreeCalculatorTest.java │ ├── InsertionSubtreeCalculatorTest.java │ ├── PCSTFragmentationTreeAnnotatorTest.java │ └── PrimSubtreeCalculatorTest.java ├── confidence_score_predict_oss ├── README.md ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── confidence_score │ │ ├── CSICovarianceConfidenceScorer.java │ │ ├── CombinedFeatureCreator.java │ │ ├── CombinedFeatureCreatorALL.java │ │ ├── CombinedFeatureCreatorALL6TO10.java │ │ ├── CombinedFeatureCreatorBIODISTANCE.java │ │ ├── CombinedFeatureCreatorBIODISTANCE2TO5.java │ │ ├── CombinedFeatureCreatorBIODISTANCE6TO10.java │ │ ├── CombinedFeatureCreatorBIONODISTANCE.java │ │ ├── ConfidenceScoreApproximateDistance.java │ │ ├── ConfidenceScorer.java │ │ ├── ExpansiveSearchConfidenceMode.java │ │ ├── FeatureCreator.java │ │ ├── Utils.java │ │ ├── features │ │ ├── AllConfidenceScoreDiffHitFeatures.java │ │ ├── AllConfidenceScoreSameHitFeatures.java │ │ ├── CandlistSizeFeatures.java │ │ ├── CanopusDiffFeatures.java │ │ ├── DistanceFeatures.java │ │ ├── EpiExplIntFeatures.java │ │ ├── EpiFragmenterScoreFeatures.java │ │ ├── EpiPeakSetFeatures.java │ │ ├── EpiPeakSetIntFeatures.java │ │ ├── EpiRatioExplPeaksFeatures.java │ │ ├── EpiUnexplainedPeaksFeatures.java │ │ ├── ExplIntFeatures.java │ │ ├── FptLengthDiffFeatures.java │ │ ├── FptLengthFeature.java │ │ ├── FptLengthFeatureHit.java │ │ ├── LogDistanceFeatures.java │ │ ├── LogPvalueDistanceFeatures.java │ │ ├── LogPvalueFeatures.java │ │ ├── LogPvalueKDEFeatures.java │ │ ├── MassFeatures.java │ │ ├── PlattFeatures.java │ │ ├── PredictionQualityFeatures.java │ │ ├── PredictorQualityFeatures.java │ │ ├── PvalueDistanceFeatures.java │ │ ├── PvalueFeatures.java │ │ ├── PvalueKDEFeatures.java │ │ ├── PvalueScoreDiffScorerFeatures.java │ │ ├── PvalueScoreUtils.java │ │ ├── SIRIUSTreeScoreFeatures.java │ │ ├── ScoreDiffScorerFeatures.java │ │ ├── ScoreFeatures.java │ │ ├── ScoreFeaturesNonBio.java │ │ ├── SiriusScoreFeatures.java │ │ ├── Sqrt3PvalueKDEFeatures.java │ │ ├── SqrtPvalueKDEFeatures.java │ │ ├── TanimotoDistanceFeatures.java │ │ ├── TanimotoToPredFeatures.java │ │ └── TopHItInBioFeatures.java │ │ └── svm │ │ ├── FptFptInchiSmilesFormulaName.java │ │ ├── FptFptSMILESFormulaName.java │ │ ├── LibLinearImpl.java │ │ ├── LinearSVMPredictor.java │ │ ├── Predictor.java │ │ ├── SVMInterface.java │ │ ├── SVMPredict.java │ │ ├── SVMScales.java │ │ ├── SVMUtils.java │ │ └── TrainedSVM.java │ └── resources │ ├── LICENSE.txt │ └── de.unijena.bioinf.ms.defaults │ ├── confidence_score_predict_oss.auto.config │ └── confidence_score_predict_oss.class.map ├── data └── demo-data.zip ├── default_properties ├── .gitignore ├── annotations │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ └── properties │ │ │ ├── ConfigType.java │ │ │ ├── DefaultConfigProvider.java │ │ │ ├── DefaultInstanceProvider.java │ │ │ ├── DefaultProperty.java │ │ │ ├── IllegalDefaultPropertyKeyException.java │ │ │ ├── ParameterConfig.java │ │ │ ├── PersistentProperties.java │ │ │ ├── PropertyFileListener.java │ │ │ ├── PropertyFileWatcher.java │ │ │ ├── PropertyManager.java │ │ │ ├── ReflectionConfigCrawler.java │ │ │ └── SiriusConfigUtils.java │ │ └── test │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ └── properties │ │ │ └── ParameterConfigTest.java │ │ └── resources │ │ ├── test.annotation.properties │ │ └── test.build.properties ├── build.gradle ├── processor │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── PropertyAnnotationProcessor.java │ │ └── resources │ │ ├── LICENSE.txt │ │ └── META-INF │ │ └── services │ │ └── javax.annotation.processing.Processor └── src │ └── main │ └── resources │ └── LICENSE.txt ├── dist ├── ExplorerLicTester │ ├── Agilent.Licensing.Client.v2.dll │ ├── ExplorerLicTester.application │ ├── ExplorerLicTester.exe │ ├── ExplorerLicTester.exe.config │ ├── ExplorerLicTester.exe.manifest │ ├── ExplorerLicTester.pdb │ ├── Licensing.dll │ └── Newtonsoft.Json.dll └── macos.entitlements ├── document-storage ├── build.gradle └── src │ ├── main │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── storage │ │ └── db │ │ └── nosql │ │ ├── Database.java │ │ ├── Filter.java │ │ ├── Index.java │ │ ├── IndexType.java │ │ ├── Metadata.java │ │ ├── nitrite │ │ ├── CustomDocumentStream.java │ │ ├── CustomObjectCursor.java │ │ ├── NitriteDatabase.java │ │ ├── filters │ │ │ └── RangeFilter.java │ │ ├── joining │ │ │ ├── JoinedDocumentStream.java │ │ │ └── JoinedReflectionIterable.java │ │ └── projection │ │ │ ├── InjectedDocumentStream.java │ │ │ ├── InjectedObjectStream.java │ │ │ └── OptFieldDocumentStream.java │ │ └── utils │ │ ├── ExtFieldUtils.java │ │ └── PKSuppliers.java │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── storage │ └── db │ └── nosql │ └── nitrite │ └── NitriteDatabaseTest.java ├── elgordo ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── elgordo │ │ ├── AnnotatedLipidSpectrum.java │ │ ├── ChainAnnotation.java │ │ ├── ChainFragmentAnnotation.java │ │ ├── EnforceElGordoFormula.java │ │ ├── FragmentLib.java │ │ ├── HeadGroup.java │ │ ├── HeadGroupFragmentAnnotation.java │ │ ├── LipidAnnotation.java │ │ ├── LipidChain.java │ │ ├── LipidClass.java │ │ ├── LipidDetectionLevel.java │ │ ├── LipidSpecies.java │ │ ├── LipidStructureMatcher.java │ │ ├── MassToLipid.java │ │ ├── PrecursorAnnotation.java │ │ └── TagStructuresByElGordo.java │ └── resources │ ├── de.unijena.bioinf.ms.defaults │ ├── elgordo.auto.config │ └── elgordo.class.map │ └── elgordo │ ├── headgroups.txt │ ├── models.csv │ └── models_species.csv ├── fingerblast_oss ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── fingerid │ │ │ └── blast │ │ │ ├── AbstractFBCandidateFingerprints.java │ │ │ ├── AbstractFBCandidates.java │ │ │ ├── AbstractFingerblastResult.java │ │ │ ├── BayesianNetworkFactory.java │ │ │ ├── BayesianNetworkFromDatabaseProvider.java │ │ │ ├── BayesianNetworkFromDirectoryProvider.java │ │ │ ├── BayesianNetworkScoringProvider.java │ │ │ ├── BayesianNetworkScoringStorage.java │ │ │ ├── BayesianScoringUtils.java │ │ │ ├── BayesnetScoring.java │ │ │ ├── BayesnetScoringBuilder.java │ │ │ ├── BayesnetScoringCorrelation.java │ │ │ ├── BayesnetScoringCorrelationBuilder.java │ │ │ ├── BayesnetScoringCorrelationFormulaSpecificBuilder.java │ │ │ ├── BayesnetScoringFormulaSpecificBuilder.java │ │ │ ├── BayesnetScoringTrainingData.java │ │ │ ├── BayesnetScoringWithDynamicComputation.java │ │ │ ├── BayesnetScoringWithDynamicComputationPersistent.java │ │ │ ├── BayesnetScoringWithTwoParents.java │ │ │ ├── CSIFingerIdScoring.java │ │ │ ├── FBCandidateFingerprints.java │ │ │ ├── FBCandidates.java │ │ │ ├── Fingerblast.java │ │ │ ├── FingerblastResult.java │ │ │ ├── FingerblastScoring.java │ │ │ ├── FingerblastScoringMethod.java │ │ │ ├── FingerprintStatistics.java │ │ │ ├── MixedScoring.java │ │ │ ├── MsNovelistCompoundCandidate.java │ │ │ ├── MsNovelistFBCandidateFingerprints.java │ │ │ ├── MsNovelistFBCandidates.java │ │ │ ├── ProbabilityEstimateScoring.java │ │ │ ├── ScoringMethodFactory.java │ │ │ ├── SimpleMaximumLikelihoodScoring.java │ │ │ ├── TopCSIScore.java │ │ │ ├── TopMsNovelistScore.java │ │ │ └── parameters │ │ │ ├── MFandFpParameters.java │ │ │ ├── ParameterStore.java │ │ │ └── Statistics.java │ └── resources │ │ └── LICENSE.txt │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── fingerid │ └── blast │ └── BayesScoringUtilsTest.java ├── fingerid_base_oss ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── fingerid │ │ ├── InputFeatures.java │ │ ├── SpectralPreprocessor.java │ │ ├── connection_pooling │ │ ├── ConnectionPool.java │ │ ├── PoolFunction.java │ │ ├── PooledConnection.java │ │ ├── PooledDB.java │ │ └── PooledDBReconnector.java │ │ ├── predictor_types │ │ ├── PredictorType.java │ │ └── UserDefineablePredictorType.java │ │ └── utils │ │ └── FingerIDProperties.java │ └── resources │ ├── LICENSE.txt │ └── csi_fingerid.build.properties ├── fingerid_project_space_oss ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── projectspace │ │ └── fingerid │ │ ├── FBCandidateFingerprintSerializer.java │ │ ├── FBCandidateFingerprintSerializerTopK.java │ │ ├── FBCandidateFingerprintsTopK.java │ │ ├── FBCandidateNumber.java │ │ ├── FBCandidatesSerializer.java │ │ ├── FBCandidatesSerializerTopK.java │ │ ├── FBCandidatesTopK.java │ │ ├── FingerIdDataProperty.java │ │ ├── FingerIdDataSerializer.java │ │ ├── FingerIdLocations.java │ │ ├── FingerprintSerializer.java │ │ ├── MsNovelistFBCandidatesSerializer.java │ │ └── StructureSearchResultSerializer.java │ └── resources │ └── LICENSE.txt ├── fingerprint_pvalues_oss ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── fingerid │ │ └── pvalues │ │ ├── ConditionalProbabilitiesEstimator.java │ │ ├── DotParser.java │ │ ├── Edge.java │ │ ├── FPVariable.java │ │ ├── FingerprintTree.java │ │ ├── Main.java │ │ ├── Probability.java │ │ ├── TreeDP.java │ │ └── TreeDPSparse.java │ └── resources │ └── LICENSE.txt ├── fingerprinter_oss ├── README.md ├── build.gradle ├── fingerprinter_cli │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── fingerid │ │ │ └── SimpleFingerprinterCLI.java │ │ └── resources │ │ └── fingerprints.mask └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── fingerid │ │ ├── Fingerprinter.java │ │ ├── FormulaBits.java │ │ ├── Mask.java │ │ ├── TableUtils.java │ │ └── fingerprints │ │ ├── BiosmartsFingerprinter.java │ │ ├── CFMFingerprinter.java │ │ ├── ECFPFingerprinter.java │ │ ├── ExtendedFingerprintVersion.java │ │ ├── FPKernel.java │ │ ├── FastCdkFingerprinter.java │ │ ├── FixedFingerprinter.java │ │ ├── FixedMACCSFingerprinter.java │ │ ├── InsilicoFingerprinter.java │ │ ├── MarcusPathFingerprinter.java │ │ ├── NeighbourSetFingerprinter.java │ │ ├── NeighbourhoodFingerprinter.java │ │ ├── OpenBabelFingerprinter.java │ │ ├── RingsystemFingerprinter.java │ │ ├── ShortestPathFingerprinter.java │ │ ├── SmartsBuilder.java │ │ ├── SphericalFingerprint.java │ │ └── cache │ │ ├── IFingerprinterCache.java │ │ └── NonBlockingIFingerprinterCache.java │ └── resources │ ├── LICENSE.txt │ ├── neighbourhood.txt │ └── nsmarts.txt ├── fragmentation_tree ├── .gitignore ├── FastFragmentationTreeAlign │ ├── .gitignore │ ├── AlignmentViewer │ │ ├── build.gradle │ │ └── src │ │ │ └── main │ │ │ ├── java │ │ │ ├── de │ │ │ │ └── unijena │ │ │ │ │ └── bioinf │ │ │ │ │ └── ftalign │ │ │ │ │ └── view │ │ │ │ │ ├── AlignmentWindow.java │ │ │ │ │ ├── ApplicationState.java │ │ │ │ │ ├── ApplicationWindow.java │ │ │ │ │ ├── DataElement.java │ │ │ │ │ ├── LoadWindow.java │ │ │ │ │ ├── Main.java │ │ │ │ │ ├── MakeStatistics.java │ │ │ │ │ ├── Pair.java │ │ │ │ │ ├── PlotWindow.java │ │ │ │ │ ├── Progress.java │ │ │ │ │ └── StandardScoringWithWhiteList.java │ │ │ └── net │ │ │ │ └── iharder │ │ │ │ └── FileDrop.java │ │ │ └── resources │ │ │ └── LICENSE.txt │ ├── ClassicTreeAlign │ │ ├── build.gradle │ │ └── src │ │ │ └── main │ │ │ ├── java │ │ │ ├── fragtreealigner │ │ │ │ ├── CmlUtil.java │ │ │ │ ├── FragmentationTreeAligner.java │ │ │ │ ├── algorithm │ │ │ │ │ ├── ScoringFunction.java │ │ │ │ │ ├── ScoringFunctionNeutralLosses.java │ │ │ │ │ ├── ScoringFunctionSimple.java │ │ │ │ │ └── TreeAligner.java │ │ │ │ ├── domainobjects │ │ │ │ │ ├── Alignment.java │ │ │ │ │ ├── AlignmentComparator.java │ │ │ │ │ ├── chem │ │ │ │ │ │ ├── basics │ │ │ │ │ │ │ ├── ChemInfo.java │ │ │ │ │ │ │ ├── Element.java │ │ │ │ │ │ │ ├── ElementTable.java │ │ │ │ │ │ │ └── MolecularFormula.java │ │ │ │ │ │ ├── components │ │ │ │ │ │ │ ├── ChemicalComponent.java │ │ │ │ │ │ │ ├── Compound.java │ │ │ │ │ │ │ ├── FunctionalGroup.java │ │ │ │ │ │ │ ├── FunctionalGroupSubstitution.java │ │ │ │ │ │ │ └── NeutralLoss.java │ │ │ │ │ │ └── structure │ │ │ │ │ │ │ ├── BondType.java │ │ │ │ │ │ │ ├── MolecularStructure.java │ │ │ │ │ │ │ ├── MolecularStructureAtom.java │ │ │ │ │ │ │ └── MolecularStructureBond.java │ │ │ │ │ ├── db │ │ │ │ │ │ ├── DatabaseStatistics.java │ │ │ │ │ │ ├── FragmentationTreeDatabase.java │ │ │ │ │ │ └── FragmentationTreeDatabaseEntry.java │ │ │ │ │ ├── graphs │ │ │ │ │ │ ├── AlignmentResTree.java │ │ │ │ │ │ ├── AlignmentResTreeEdge.java │ │ │ │ │ │ ├── AlignmentResTreeNode.java │ │ │ │ │ │ ├── AlignmentTree.java │ │ │ │ │ │ ├── AlignmentTreeEdge.java │ │ │ │ │ │ ├── AlignmentTreeNode.java │ │ │ │ │ │ ├── Edge.java │ │ │ │ │ │ ├── FragmentationTree.java │ │ │ │ │ │ ├── FragmentationTreeEdge.java │ │ │ │ │ │ ├── FragmentationTreeNode.java │ │ │ │ │ │ ├── Graph.java │ │ │ │ │ │ ├── Node.java │ │ │ │ │ │ ├── Tree.java │ │ │ │ │ │ ├── TreeEdge.java │ │ │ │ │ │ └── TreeNode.java │ │ │ │ │ └── util │ │ │ │ │ │ └── Coordinate.java │ │ │ │ ├── ui │ │ │ │ │ ├── GraphPanelListener.java │ │ │ │ │ └── MainFrame.java │ │ │ │ └── util │ │ │ │ │ ├── Classifier.java │ │ │ │ │ ├── Macros.java │ │ │ │ │ ├── Normalizer.java │ │ │ │ │ ├── PValue.java │ │ │ │ │ ├── Parameters.java │ │ │ │ │ ├── ParseToAlignmentInstance.java │ │ │ │ │ ├── ParseToAlignmentTree.java │ │ │ │ │ ├── Session.java │ │ │ │ │ ├── Sim2Dist.java │ │ │ │ │ ├── StructureScore2Distance.java │ │ │ │ │ └── VertexMatcher.java │ │ │ └── ml │ │ │ │ └── options │ │ │ │ ├── OptionData.java │ │ │ │ ├── OptionSet.java │ │ │ │ └── Options.java │ │ │ └── resources │ │ │ └── LICENSE.txt │ ├── FTAlignmentTool │ │ ├── build.gradle │ │ └── src │ │ │ └── main │ │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── ftalign │ │ │ │ ├── Benchmarker.java │ │ │ │ ├── CIDBase.java │ │ │ │ ├── CSVHandler.java │ │ │ │ ├── CSVMatrix.java │ │ │ │ ├── CSVReader.java │ │ │ │ ├── CommonLossScoring.java │ │ │ │ ├── DecoyDatabase.java │ │ │ │ ├── Main.java │ │ │ │ ├── ScoreFormula.java │ │ │ │ ├── StandardScoring.java │ │ │ │ ├── StandardScoring2.java │ │ │ │ ├── TestScoring.java │ │ │ │ ├── TraceLog2.java │ │ │ │ ├── WeightingReader.java │ │ │ │ ├── analyse │ │ │ │ ├── FTDataElement.java │ │ │ │ ├── FTDataset.java │ │ │ │ ├── Normalizer.java │ │ │ │ ├── Pearson.java │ │ │ │ └── TreeSizeNormalizer.java │ │ │ │ ├── graphics │ │ │ │ ├── GraphicalBacktrace.java │ │ │ │ └── GraphicalBacktrace2.java │ │ │ │ └── parallelograms │ │ │ │ ├── ParaCount.java │ │ │ │ ├── ParaNodes.java │ │ │ │ └── ParallelogramIterator.java │ │ │ └── resources │ │ │ ├── LICENSE.txt │ │ │ └── lossweights.csv │ ├── FTBlast │ │ ├── build.gradle │ │ └── src │ │ │ └── main │ │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── ftblast │ │ │ │ ├── CLI.java │ │ │ │ ├── Dataset.java │ │ │ │ ├── Query.java │ │ │ │ └── ScoreTable.java │ │ │ └── resources │ │ │ └── LICENSE.txt │ ├── FastTreeAlign │ │ ├── build.gradle │ │ └── src │ │ │ ├── main │ │ │ ├── java │ │ │ │ └── de │ │ │ │ │ └── unijena │ │ │ │ │ └── bioinf │ │ │ │ │ ├── counting │ │ │ │ │ ├── AlignmentWrapper.java │ │ │ │ │ ├── CompleteTreeDecorator.java │ │ │ │ │ ├── DPPathCounting.java │ │ │ │ │ ├── DPSubtreeCounter.java │ │ │ │ │ ├── WeightedPathCounting.java │ │ │ │ │ └── Weighting.java │ │ │ │ │ ├── treealign │ │ │ │ │ ├── AbstractBacktrace.java │ │ │ │ │ ├── AlignmentTree.java │ │ │ │ │ ├── AlignmentTreeBacktrace.java │ │ │ │ │ ├── Backtrace.java │ │ │ │ │ ├── Set.java │ │ │ │ │ ├── StackedBacktrace.java │ │ │ │ │ ├── TraceItem.java │ │ │ │ │ ├── TraceLog.java │ │ │ │ │ ├── Tree.java │ │ │ │ │ ├── TreeAlignmentAlgorithm.java │ │ │ │ │ ├── TreeDecorator.java │ │ │ │ │ ├── dp │ │ │ │ │ │ ├── DPTreeAlign.java │ │ │ │ │ │ ├── Table.java │ │ │ │ │ │ └── TreeMap.java │ │ │ │ │ ├── map │ │ │ │ │ │ ├── IntFloatArrayMap.java │ │ │ │ │ │ ├── IntFloatHashMap.java │ │ │ │ │ │ ├── IntFloatIterator.java │ │ │ │ │ │ ├── IntFloatMap.java │ │ │ │ │ │ ├── IntPairFloatArrayMap.java │ │ │ │ │ │ ├── IntPairFloatHashMap.java │ │ │ │ │ │ ├── IntPairFloatIterator.java │ │ │ │ │ │ ├── IntPairFloatMap.java │ │ │ │ │ │ ├── MapInspectable.java │ │ │ │ │ │ └── MapInspector.java │ │ │ │ │ ├── multijoin │ │ │ │ │ │ ├── DPMultiJoin.java │ │ │ │ │ │ ├── HashTable.java │ │ │ │ │ │ ├── MultiJoinTraceItem.java │ │ │ │ │ │ └── TreeHashMap.java │ │ │ │ │ ├── scoring │ │ │ │ │ │ ├── AbstractMultijoinScoring.java │ │ │ │ │ │ ├── AbstractScoring.java │ │ │ │ │ │ ├── Scoring.java │ │ │ │ │ │ └── SimpleEqualityScoring.java │ │ │ │ │ └── sparse │ │ │ │ │ │ ├── DPSparseTreeAlign.java │ │ │ │ │ │ ├── HashTable.java │ │ │ │ │ │ ├── Mode.java │ │ │ │ │ │ ├── QueueItem.java │ │ │ │ │ │ └── TreeHashMap.java │ │ │ │ │ └── util │ │ │ │ │ └── Iterators.java │ │ │ └── resources │ │ │ │ └── LICENSE.txt │ │ │ └── test │ │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── counting │ │ │ ├── PathCounterTest.java │ │ │ ├── SubtreeCounterTest.java │ │ │ ├── TestTree.java │ │ │ └── WeightCounterTest.java │ │ │ └── treealign │ │ │ └── map │ │ │ ├── IntFloatHashMapTest.java │ │ │ └── IntPairFloatMapTest.java │ └── build.gradle ├── build.gradle ├── fragmentation_tree_construction │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ ├── FragmentationTreeConstruction │ │ │ │ ├── computation │ │ │ │ │ ├── DoubleEndWeightedQueue2.java │ │ │ │ │ ├── FasterTreeComputationInstance.java │ │ │ │ │ ├── FragmentationPatternAnalysis.java │ │ │ │ │ ├── SiriusPlugin.java │ │ │ │ │ ├── graph │ │ │ │ │ │ ├── GraphBuilder.java │ │ │ │ │ │ ├── GraphReduction.java │ │ │ │ │ │ ├── LossValidator.java │ │ │ │ │ │ ├── SimpleReduction.java │ │ │ │ │ │ └── SubFormulaGraphBuilder.java │ │ │ │ │ ├── recalibration │ │ │ │ │ │ ├── AbstractRecalibrationStrategy.java │ │ │ │ │ │ ├── HypothesenDrivenRecalibration.java │ │ │ │ │ │ ├── LeastSquare.java │ │ │ │ │ │ ├── MedianSlope.java │ │ │ │ │ │ └── RecalibrationStrategy.java │ │ │ │ │ ├── scoring │ │ │ │ │ │ ├── AdductSwitchLossScorer.java │ │ │ │ │ │ ├── BeautificationScorer.java │ │ │ │ │ │ ├── CarbohydrogenScorer.java │ │ │ │ │ │ ├── ChemicalPriorEdgeScorer.java │ │ │ │ │ │ ├── ChemicalPriorScorer.java │ │ │ │ │ │ ├── ClippedPeakIsNoiseScorer.java │ │ │ │ │ │ ├── CollisionEnergyEdgeScorer.java │ │ │ │ │ │ ├── CommonFragmentsScore.java │ │ │ │ │ │ ├── CommonLossEdgeScorer.java │ │ │ │ │ │ ├── CommonRootLossScorer.java │ │ │ │ │ │ ├── DBELossScorer.java │ │ │ │ │ │ ├── DBPairedScorer.java │ │ │ │ │ │ ├── DecompositionScorer.java │ │ │ │ │ │ ├── FragmentScorer.java │ │ │ │ │ │ ├── FragmentSizeScorer.java │ │ │ │ │ │ ├── FreeRadicalEdgeScorer.java │ │ │ │ │ │ ├── GeneralGraphScorer.java │ │ │ │ │ │ ├── IntrinsicallyChargedScorer.java │ │ │ │ │ │ ├── LossScorer.java │ │ │ │ │ │ ├── LossSizeScorer.java │ │ │ │ │ │ ├── MassDeviationEdgeScorer.java │ │ │ │ │ │ ├── MassDeviationVertexScorer.java │ │ │ │ │ │ ├── MultimereLossScorer.java │ │ │ │ │ │ ├── PeakIsNoiseScorer.java │ │ │ │ │ │ ├── PeakPairScorer.java │ │ │ │ │ │ ├── PeakScorer.java │ │ │ │ │ │ ├── PenalizeLowIntensiveParentsScore.java │ │ │ │ │ │ ├── PhosphorScorer.java │ │ │ │ │ │ ├── PureCarbonNitrogenLossScorer.java │ │ │ │ │ │ ├── RelativeLossSizeScorer.java │ │ │ │ │ │ ├── StrangeElementFragmentScorer.java │ │ │ │ │ │ ├── StrangeElementLossScorer.java │ │ │ │ │ │ ├── StrangeElementRootScorer.java │ │ │ │ │ │ ├── StrangeElementScorer.java │ │ │ │ │ │ ├── StrangeElementSmallFragmentScorer.java │ │ │ │ │ │ └── TreeSizeScorer.java │ │ │ │ │ └── tree │ │ │ │ │ │ ├── TreeBuilder.java │ │ │ │ │ │ ├── TreeBuilderFactory.java │ │ │ │ │ │ └── ilp │ │ │ │ │ │ ├── AbstractSolver.java │ │ │ │ │ │ ├── AbstractTreeBuilder.java │ │ │ │ │ │ ├── ILPSolverException.java │ │ │ │ │ │ └── IlpFactory.java │ │ │ │ ├── ftheuristics │ │ │ │ │ ├── AbstractHeuristic.java │ │ │ │ │ ├── CriticalPathInsertionHeuristic.java │ │ │ │ │ ├── CriticalPathInsertionHeuristic2.java │ │ │ │ │ ├── CriticalPathInsertionWithIsotopePeaksHeuristic.java │ │ │ │ │ ├── DeepSearchHeuristic.java │ │ │ │ │ ├── ExtendedCriticalPathHeuristic.java │ │ │ │ │ ├── FastInsertionHeuristic.java │ │ │ │ │ ├── GreedyHeuristic.java │ │ │ │ │ ├── LegacyInsertionHeuristic.java │ │ │ │ │ ├── PrimStarHeuristic.java │ │ │ │ │ ├── TopDownHeuristic.java │ │ │ │ │ └── treebuilder │ │ │ │ │ │ ├── ExtendedCriticalPathHeuristicTreeBuilder.java │ │ │ │ │ │ └── GreedyBuilder.java │ │ │ │ ├── inspection │ │ │ │ │ └── GraphOutput.java │ │ │ │ └── model │ │ │ │ │ ├── Ms2IsotopePatternMatch.java │ │ │ │ │ ├── PredefinedPeak.java │ │ │ │ │ ├── Scoring.java │ │ │ │ │ └── UseHeuristic.java │ │ │ │ └── sirius │ │ │ │ └── plugins │ │ │ │ ├── AdductNeutralizationPlugin.java │ │ │ │ ├── AdductSwitchPlugin.java │ │ │ │ ├── AminoAcidPlugin.java │ │ │ │ ├── BottomUpSearch.java │ │ │ │ ├── DefaultPlugin.java │ │ │ │ ├── ElGordoPlugin.java │ │ │ │ ├── PredefinedPeakPlugin.java │ │ │ │ ├── TreeStatisticPlugin.java │ │ │ │ └── UseLossMassDeviationScoringPlugin.java │ │ └── resources │ │ │ ├── LICENSE.txt │ │ │ ├── de.unijena.bioinf.ms.defaults │ │ │ ├── fragmentation_tree_construction.auto.config │ │ │ └── fragmentation_tree_construction.class.map │ │ │ └── profiles │ │ │ ├── adduct-switch.json │ │ │ ├── default.json │ │ │ ├── old_profiles │ │ │ ├── bruker_tof.json │ │ │ ├── default.json │ │ │ ├── orbitrap.json │ │ │ ├── qtof.json │ │ │ ├── torbitrap.json │ │ │ └── tqtof.json │ │ │ ├── orbitrap.json │ │ │ └── qtof.json │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── FragmentationTreeConstruction │ │ └── computation │ │ └── PreprocessingTest.java ├── ft_cbc │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── FragmentationTreeConstruction │ │ └── computation │ │ └── tree │ │ └── ilp │ │ └── CLPSolver.java ├── ft_cplex │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── FragmentationTreeConstruction │ │ │ └── computation │ │ │ └── tree │ │ │ └── ilp │ │ │ └── CPLEXSolver.java │ │ └── resources │ │ └── LICENSE.txt ├── ft_glpk │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── FragmentationTreeConstruction │ │ └── computation │ │ └── tree │ │ └── ilp │ │ └── GLPKSolver.java └── ft_gurobi │ ├── build.gradle │ └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── FragmentationTreeConstruction │ │ └── computation │ │ └── tree │ │ └── ilp │ │ └── GrbSolver.java │ └── resources │ └── LICENSE.txt ├── gibbs_sampling ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── GibbsSampling │ │ │ ├── LibraryHitQuality.java │ │ │ ├── Zodiac.java │ │ │ ├── ZodiacScore.java │ │ │ ├── ZodiacUtils.java │ │ │ ├── model │ │ │ ├── AbstractEdgeFilter.java │ │ │ ├── AllOrNothingLibraryHitsScorer.java │ │ │ ├── Candidate.java │ │ │ ├── CombinedReaction.java │ │ │ ├── CompoundResult.java │ │ │ ├── Connectivity.java │ │ │ ├── DummyFragmentCandidate.java │ │ │ ├── EdgeFilter.java │ │ │ ├── EdgeScorer.java │ │ │ ├── EdgeThresholdFilter.java │ │ │ ├── EdgeThresholdMinConnectionsFilter.java │ │ │ ├── FormulaFactory.java │ │ │ ├── FragmentWithIndex.java │ │ │ ├── FragmentsAndLosses.java │ │ │ ├── FragmentsCandidate.java │ │ │ ├── GibbsMFCorrectionNetwork.java │ │ │ ├── GibbsParallel.java │ │ │ ├── Graph.java │ │ │ ├── GraphBuilder.java │ │ │ ├── GraphValidationMessage.java │ │ │ ├── HasFormula.java │ │ │ ├── HasLibraryHit.java │ │ │ ├── LibraryHit.java │ │ │ ├── LibraryHitScorer.java │ │ │ ├── LocalEdgeFilter.java │ │ │ ├── NoEdgeFilter.java │ │ │ ├── NodeScorer.java │ │ │ ├── RankNodeScorer.java │ │ │ ├── Reaction.java │ │ │ ├── ReactionStepSizeScorer.java │ │ │ ├── SimpleReaction.java │ │ │ ├── StandardCandidate.java │ │ │ ├── StandardNodeScorer.java │ │ │ ├── ThreePhaseGibbsSampling.java │ │ │ ├── Transformation.java │ │ │ ├── TwoPhaseGibbsSampling.java │ │ │ ├── ZodiacResult.java │ │ │ ├── ZodiacResultsWithClusters.java │ │ │ ├── distributions │ │ │ │ ├── DummyScoreProbabilityDistribution.java │ │ │ │ ├── EmpiricalScoreProbabilityDistribution.java │ │ │ │ ├── ExponentialDistribution.java │ │ │ │ ├── LogNormalDistribution.java │ │ │ │ ├── ParetoDistribution.java │ │ │ │ ├── ScoreProbabilityDistribution.java │ │ │ │ ├── ScoreProbabilityDistributionEstimator.java │ │ │ │ └── ScoreProbabilityDistributionFix.java │ │ │ └── scorer │ │ │ │ ├── CommonFragmentAndLossScorer.java │ │ │ │ ├── CommonFragmentAndLossScorerNoiseIntensityWeighted.java │ │ │ │ ├── CommonFragmentAndLossWithTreeScoresScorer.java │ │ │ │ ├── CommonFragmentScorer.java │ │ │ │ ├── CommonRootLossScorer.java │ │ │ │ ├── EdgeScorings.java │ │ │ │ ├── FTAlignScorer.java │ │ │ │ ├── ReactionScorer.java │ │ │ │ └── SameIonizationScorer.java │ │ │ └── properties │ │ │ ├── ZodiacAnalogueNodes.java │ │ │ ├── ZodiacClusterCompounds.java │ │ │ ├── ZodiacEdgeFilterThresholds.java │ │ │ ├── ZodiacEpochs.java │ │ │ ├── ZodiacLibraryScoring.java │ │ │ ├── ZodiacNumberOfConsideredCandidatesAt300Mz.java │ │ │ ├── ZodiacNumberOfConsideredCandidatesAt800Mz.java │ │ │ ├── ZodiacRatioOfConsideredCandidatesPerIonization.java │ │ │ └── ZodiacRunInTwoSteps.java │ └── resources │ │ ├── LICENSE.txt │ │ └── de.unijena.bioinf.ms.defaults │ │ ├── gibbs_sampling.auto.config │ │ └── gibbs_sampling.class.map │ └── test │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── GibbsSampling │ │ └── model │ │ ├── ExamplePreparationUtils.java │ │ ├── FragmentCandidateTest.java │ │ ├── GraphBuilderTest.java │ │ └── scorer │ │ ├── CommonFragmentAndLossScorerNoiseIntensityWeightedTest.java │ │ └── CommonFragmentAndLossScorerTest.java │ └── resources │ └── tiny-example │ ├── A_1_C33H40O10_M+H+.json │ ├── A_2_C29H36N6O8_M+H+.json │ ├── A_4_C32H38N4O6_M+Na+.json │ ├── A_7_C28H46O11_M+K+.json │ ├── A_spectrum.ms │ ├── B_1_C35H42N4O4_M+Na+.json │ ├── B_2_C34H46O8_M+Na+.json │ ├── B_spectrum.ms │ ├── C_1_C31H46O12_M+Na+.json │ ├── C_2_C28H50O13_M+K+.json │ ├── C_4_C33H44O12_M+H+.json │ └── C_spectrum.ms ├── gradle.properties ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── graph_utils_oss ├── build.gradle └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── graphUtils │ └── tree │ ├── BackrefTreeAdapter.java │ ├── BackrefTreeType.java │ ├── GraphException.java │ ├── PostOrderTraversal.java │ ├── PreOrderTraversal.java │ ├── StackedTreeCursor.java │ ├── Tree.java │ ├── TreeAdapter.java │ ├── TreeCursor.java │ ├── TreeCursorBackref.java │ ├── TreeException.java │ └── TreeType.java ├── icons ├── sirius-icon.icns ├── sirius-icon.ico └── sirius-icon.png ├── io ├── .gitignore ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── babelms │ │ │ ├── CloseableIterator.java │ │ │ ├── ConsistencyValidator.java │ │ │ ├── DataWriter.java │ │ │ ├── GenericParser.java │ │ │ ├── GenericWriter.java │ │ │ ├── MsExperimentParser.java │ │ │ ├── MsIO.java │ │ │ ├── Parser.java │ │ │ ├── ReportingInputStream.java │ │ │ ├── SpectralParser.java │ │ │ ├── ZippedSpectraParser.java │ │ │ ├── annotations │ │ │ └── CompoundMetaData.java │ │ │ ├── binary │ │ │ ├── MassTraceIo.java │ │ │ ├── SpectrumBinaryReader.java │ │ │ └── SpectrumBinaryWriter.java │ │ │ ├── cef │ │ │ ├── AgilentCefExperimentParser.java │ │ │ ├── CEF.java │ │ │ ├── CEFUtils.java │ │ │ ├── CalStep.java │ │ │ ├── ChromPeaks.java │ │ │ ├── Chromatogram.java │ │ │ ├── Compound.java │ │ │ ├── CompoundList.java │ │ │ ├── CompoundScores.java │ │ │ ├── CpdScore.java │ │ │ ├── Device.java │ │ │ ├── Location.java │ │ │ ├── MSDetails.java │ │ │ ├── MSPeaks.java │ │ │ ├── MassCalibration.java │ │ │ ├── MzOfInterest.java │ │ │ ├── ObjectFactory.java │ │ │ ├── P.java │ │ │ ├── RTRange.java │ │ │ ├── RTRanges.java │ │ │ └── Spectrum.java │ │ │ ├── chemdb │ │ │ ├── CacheEntry.java │ │ │ ├── CompoundQuery.java │ │ │ ├── DBMolecularFormulaCache.java │ │ │ └── Databases.java │ │ │ ├── chemspider │ │ │ └── ChemSpider.java │ │ │ ├── descriptor │ │ │ ├── DefaultDescriptors.java │ │ │ ├── Descriptor.java │ │ │ └── DescriptorRegistry.java │ │ │ ├── dot │ │ │ ├── DotHandler.java │ │ │ ├── DotParser.java │ │ │ ├── Edge.java │ │ │ ├── FTDotReader.java │ │ │ ├── FTDotWriter.java │ │ │ ├── Graph.java │ │ │ └── Vertex.java │ │ │ ├── gnps │ │ │ ├── GnpsJsonParser.java │ │ │ ├── GnpsRecord.java │ │ │ └── GnpsSpectrumParser.java │ │ │ ├── inputresource │ │ │ ├── ByteInputResource.java │ │ │ ├── InputResource.java │ │ │ ├── InputResourceParsingIterator.java │ │ │ ├── PathInputResource.java │ │ │ └── StringInputResource.java │ │ │ ├── intermediate │ │ │ ├── ExperimentData.java │ │ │ └── ExperimentDataParser.java │ │ │ ├── json │ │ │ ├── FTJsonReader.java │ │ │ ├── FTJsonWriter.java │ │ │ ├── FTreeDeserializer.java │ │ │ ├── FTreeSerializer.java │ │ │ ├── JsonExperimentParser.java │ │ │ └── JsonExperimentParserDispatcher.java │ │ │ ├── massbank │ │ │ ├── MassbankExperimentParser.java │ │ │ ├── MassbankFormat.java │ │ │ └── MassbankSpectralParser.java │ │ │ ├── mgf │ │ │ ├── MgfParser.java │ │ │ └── MgfWriter.java │ │ │ ├── mona │ │ │ └── MonaJsonParser.java │ │ │ ├── ms │ │ │ ├── AnnotatedSpectrumWriter.java │ │ │ ├── CsvParser.java │ │ │ ├── InputFileConfig.java │ │ │ ├── JenaMsParser.java │ │ │ └── JenaMsWriter.java │ │ │ ├── msp │ │ │ ├── MSP.java │ │ │ ├── MSPExperimentParser.java │ │ │ └── MSPSpectralParser.java │ │ │ ├── mzml │ │ │ ├── AbstractMzParser.java │ │ │ ├── MzMlExperimentParser.java │ │ │ └── MzXmlExperimentParser.java │ │ │ ├── pubchem │ │ │ └── Pubchem.java │ │ │ ├── sdf │ │ │ └── SdfExperimentParser.java │ │ │ ├── txt │ │ │ └── TxtExperimentParser.java │ │ │ └── utils │ │ │ ├── Base64.java │ │ │ ├── CSVParser.java │ │ │ ├── FTGraphWriter.java │ │ │ ├── Fingerprint2Base64.java │ │ │ ├── ParserUtils.java │ │ │ └── SmilesUCdk.java │ └── resources │ │ └── LICENSE.txt │ └── test │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── babelms │ │ ├── ParserTestUtils.java │ │ ├── cef │ │ ├── AgilentCefExperimentParserTest.java │ │ └── CEFTestMain.java │ │ ├── gnps │ │ └── GnpsJsonParserTest.java │ │ ├── json │ │ └── FTJsonWriterTest.java │ │ ├── massbank │ │ └── MassbankFormatTest.java │ │ ├── mona │ │ └── MonaJsonParserTest.java │ │ ├── ms │ │ ├── FTioTest.java │ │ └── MsParserTest.java │ │ ├── msp │ │ └── MSPExperimentParserTest.java │ │ ├── sdf │ │ └── SdfExperimentParserTest.java │ │ └── txt │ │ └── TxtExperimentParserTest.java │ └── resources │ ├── Adenosine.ms │ ├── cef │ ├── fbf_known_adducts.cef │ └── fbf_unknown_adduct.cef │ ├── de │ └── unijena │ │ └── bioinf │ │ └── babelms │ │ └── ms │ │ ├── C12H25N7O3_[M+H]+.json │ │ └── casmi2016_084.json │ ├── gnps │ ├── collection_format.json │ ├── only_spectrum.json │ ├── single_format.json │ └── spectrum_array.json │ ├── massbank │ ├── MSBNK-UFZ-UP000040.txt │ ├── empty.txt │ ├── invalid.txt │ └── multirecord.txt │ ├── mona │ ├── MoNA010759.json │ ├── MoNA010759.msp │ ├── MoNA020112.json │ ├── attribution.txt │ ├── invalid_fields.json │ └── missing_fields.json │ └── sdf │ └── UP000538.sdf ├── isotope_pattern ├── .gitignore ├── build.gradle ├── isogen_cli │ ├── .settings │ │ └── org.eclipse.jdt.core.prefs │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── IsotopePatternAnalysis │ │ │ │ └── isogencli │ │ │ │ ├── Main.java │ │ │ │ └── Options.java │ │ └── resources │ │ │ └── LICENSE.txt │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── IsotopePatternAnalysis │ │ └── isogencli │ │ └── TestMain.java ├── isotope_pattern_analysis │ ├── .settings │ │ └── org.eclipse.jdt.core.prefs │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── IsotopePatternAnalysis │ │ │ │ ├── ExtractedIsotopePattern.java │ │ │ │ ├── IsotopePattern.java │ │ │ │ ├── IsotopePatternAnalysis.java │ │ │ │ ├── IsotopicIntensitySettings.java │ │ │ │ ├── Main.java │ │ │ │ ├── PatternGenerator.java │ │ │ │ ├── extraction │ │ │ │ ├── SimpleTargetedPatternExtractor.java │ │ │ │ └── TargetedPatternExtraction.java │ │ │ │ ├── generation │ │ │ │ ├── CachedIsoTable.java │ │ │ │ ├── FastIsotopePatternGenerator.java │ │ │ │ ├── FastTwoPeakSimulator.java │ │ │ │ ├── FineStructureMerger.java │ │ │ │ ├── FinestructureGenerator.java │ │ │ │ ├── FinestructurePatternGenerator.java │ │ │ │ ├── FragmentIsotopeGenerator.java │ │ │ │ ├── IsotopePatternGenerator.java │ │ │ │ ├── Isotopologue.java │ │ │ │ ├── IsotopologueTable.java │ │ │ │ ├── Isotopologues.java │ │ │ │ └── SimpleIsotopologues.java │ │ │ │ ├── scoring │ │ │ │ ├── IsotopePatternScorer.java │ │ │ │ ├── LogNormDistributedIntensityScorer.java │ │ │ │ ├── MassDeviationScorer.java │ │ │ │ ├── MassDifferenceDeviationScorer.java │ │ │ │ ├── MissingPeakScorer.java │ │ │ │ ├── MzMineScorer.java │ │ │ │ ├── NormalDistributedIntensityScorer.java │ │ │ │ └── ScorePerPeak.java │ │ │ │ └── util │ │ │ │ ├── FixedBagIntensityDependency.java │ │ │ │ ├── FixedIntensity.java │ │ │ │ ├── IntensityDependency.java │ │ │ │ ├── LinearIntensityDependency.java │ │ │ │ └── PiecewiseLinearFunctionIntensityDependency.java │ │ └── resources │ │ │ ├── LICENSE.txt │ │ │ └── de.unijena.bioinf.ms.defaults │ │ │ ├── isotope_pattern_analysis.auto.config │ │ │ └── isotope_pattern_analysis.class.map │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── IsotopePatternAnalysis │ │ ├── PatternExtractionTest.java │ │ └── PatternGeneratorTest.java └── sirius_isotopes │ ├── build.gradle │ └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── sirius │ │ └── plugins │ │ ├── IsotopePatternInMs1Plugin.java │ │ └── IsotopePatternInMs2Plugin.java │ └── resources │ └── LICENSE.txt ├── jpackage ├── LICENSE-Full.txt ├── cli-launcher.properties └── wix-resources │ └── main.wxs ├── lcms ├── build.gradle ├── lcms_gui │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── lcms │ │ │ └── debuggui │ │ │ ├── GUI.java │ │ │ ├── GUI2.java │ │ │ └── Gradient.java │ │ └── resources │ │ └── LICENSE.txt ├── mzml-converter │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── cli │ │ │ └── lcms │ │ │ └── LCMSMain.java │ │ └── resources │ │ └── LICENSE.txt ├── readme.md └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ ├── io │ │ └── lcms │ │ │ ├── CVUtils.java │ │ │ ├── LCMSParser.java │ │ │ ├── LCMSParsing.java │ │ │ ├── MzMLParser.java │ │ │ ├── MzXMLParser.java │ │ │ └── MzXMLSaxParser.java │ │ ├── lcms │ │ ├── ChimericDetector.java │ │ ├── ChromatogramBuilder.java │ │ ├── CorrelatedPeakDetector.java │ │ ├── Extrema.java │ │ ├── InMemoryStorage.java │ │ ├── InternalStatistics.java │ │ ├── IonIdentityNetwork.java │ │ ├── LCMSCompoundSummary.java │ │ ├── LCMSProccessingInstance.java │ │ ├── LoessFunction.java │ │ ├── Maxima.java │ │ ├── MemoryFileStorage.java │ │ ├── Ms1Ms2Pairing.java │ │ ├── Ms1Remapping.java │ │ ├── Ms2CosineSegmenter.java │ │ ├── ProcessedSample.java │ │ ├── SavitzkyGolayFilter.java │ │ ├── SpectralMerger.java │ │ ├── SpectrumStorage.java │ │ ├── TraceConverter.java │ │ ├── align │ │ │ ├── AlignedFeatures.java │ │ │ ├── Aligner.java │ │ │ ├── Aligner2.java │ │ │ ├── Cluster.java │ │ │ └── GapFilling.java │ │ ├── ionidentity │ │ │ ├── AdductMassDifference.java │ │ │ ├── AdductResolver.java │ │ │ ├── Assignment.java │ │ │ ├── CorrelationGroupScorer.java │ │ │ ├── CorrelationGroupScorer2.java │ │ │ ├── Edge.java │ │ │ ├── GibbsSampler.java │ │ │ ├── IonAssignment.java │ │ │ ├── IonNetwork.java │ │ │ ├── IonNode.java │ │ │ └── LearnCorrelationScoring.java │ │ ├── noise │ │ │ ├── GlobalNoiseModel.java │ │ │ ├── LocalNoiseModel.java │ │ │ ├── Ms2NoiseStatistics.java │ │ │ ├── NoiseModel.java │ │ │ └── NoiseStatistics.java │ │ ├── peakshape │ │ │ ├── CustomPeakShape.java │ │ │ ├── CustomPeakShapeFitting.java │ │ │ ├── GaussianFitting.java │ │ │ ├── GaussianShape.java │ │ │ ├── LaplaceFitting.java │ │ │ ├── LaplaceShape.java │ │ │ ├── PeakShape.java │ │ │ └── PeakShapeFitting.java │ │ └── quality │ │ │ ├── AlignmentQuality.java │ │ │ ├── LCMSQualityCheck.java │ │ │ ├── LCMSQualityCheckResult.java │ │ │ ├── Quality.java │ │ │ └── QualityAnnotation.java │ │ └── model │ │ └── lcms │ │ ├── AlignedFeatureTable.java │ │ ├── ChromatogramCache.java │ │ ├── ChromatographicPeak.java │ │ ├── ConsensusFeature.java │ │ ├── CorrelatedChromatographicPeak.java │ │ ├── CorrelatedIon.java │ │ ├── CorrelationGroup.java │ │ ├── Feature.java │ │ ├── FragmentedIon.java │ │ ├── GapFilledIon.java │ │ ├── IonAnnotation.java │ │ ├── IonConnection.java │ │ ├── IonGroup.java │ │ ├── LCMSRun.java │ │ ├── MergedPeak.java │ │ ├── MergedSpectrum.java │ │ ├── MergedSpectrumWithCollisionEnergies.java │ │ ├── MsDataProcessing.java │ │ ├── MutableChromatographicPeak.java │ │ ├── Polarity.java │ │ ├── Precursor.java │ │ ├── QuantileShiftingWindowNoiseModel.java │ │ ├── Scan.java │ │ └── ScanPoint.java │ └── resources │ └── LICENSE.txt ├── lcms2 ├── build.gradle ├── src │ ├── main │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── lcms │ │ │ ├── LCMSProcessing.java │ │ │ ├── LCMSStorageFactory.java │ │ │ ├── ScanPointMapping.java │ │ │ ├── adducts │ │ │ ├── AdductEdge.java │ │ │ ├── AdductManager.java │ │ │ ├── AdductNetwork.java │ │ │ ├── AdductNode.java │ │ │ ├── AdductRelationship.java │ │ │ ├── IonType.java │ │ │ ├── KnownMassDelta.java │ │ │ ├── LossRelationship.java │ │ │ ├── MultimereRelationship.java │ │ │ ├── ProjectSpaceTraceProvider.java │ │ │ ├── Scorer.java │ │ │ ├── TraceProvider.java │ │ │ ├── UnknownLossRelationship.java │ │ │ ├── UnrelatedRelationship.java │ │ │ └── assignment │ │ │ │ ├── AdductAssignment.java │ │ │ │ ├── AdductBeamSearch.java │ │ │ │ ├── CompoundGroup.java │ │ │ │ ├── OptimalAssignmentViaBeamSearch.java │ │ │ │ └── SubnetworkResolver.java │ │ │ ├── align │ │ │ ├── AlignWithRecalibration.java │ │ │ ├── AlignedMoI.java │ │ │ ├── AlignmentAlgorithm.java │ │ │ ├── AlignmentBackbone.java │ │ │ ├── AlignmentScorer.java │ │ │ ├── AlignmentStatistics.java │ │ │ ├── AlignmentStorage.java │ │ │ ├── AlignmentStrategy.java │ │ │ ├── AlignmentThresholds.java │ │ │ ├── BeamSearchAlgorithm.java │ │ │ ├── GreedyAlgorithm.java │ │ │ ├── GreedyTwoStageAlignmentStrategy.java │ │ │ ├── MoI.java │ │ │ ├── MvBasedAlignmentStorage.java │ │ │ └── RecalibrationFunction.java │ │ │ ├── centroiding │ │ │ ├── CentroidIndividualSpectraStrategy.java │ │ │ └── CentroidingStrategy.java │ │ │ ├── datatypes │ │ │ ├── CustomDataType.java │ │ │ └── SpectrumDatatype.java │ │ │ ├── features │ │ │ ├── IsotopePatternExtractionStrategy.java │ │ │ ├── MergedApexIsotopePatternExtractor.java │ │ │ ├── MergedFeatureExtractionStrategy.java │ │ │ └── SegmentMergedFeatures.java │ │ │ ├── io │ │ │ ├── CVUtils.java │ │ │ ├── LCMSImporter.java │ │ │ ├── LCMSParser.java │ │ │ ├── MzMLParser.java │ │ │ ├── MzXMLParser.java │ │ │ ├── MzXMLSaxParser.java │ │ │ ├── Polarity.java │ │ │ └── Precursor.java │ │ │ ├── isotopes │ │ │ ├── IsotopeDetectionByCorrelation.java │ │ │ ├── IsotopeDetectionStrategy.java │ │ │ ├── IsotopePattern.java │ │ │ └── IsotopeResult.java │ │ │ ├── merge │ │ │ ├── MergeMvStorage.java │ │ │ ├── MergeStorage.java │ │ │ ├── MergeTracesWithoutGapFilling.java │ │ │ ├── MergedTrace.java │ │ │ ├── MergingStrategy.java │ │ │ ├── PairwiseScanPointMapping.java │ │ │ └── ScanPointInterpolator.java │ │ │ ├── msms │ │ │ ├── MergeGreedyStrategy.java │ │ │ ├── MergedPeak.java │ │ │ ├── MergedSpectrum.java │ │ │ ├── MostIntensivePeakInIsolationWindowAssignmentStrategy.java │ │ │ ├── Ms2MergeStrategy.java │ │ │ ├── Ms2TraceStrategy.java │ │ │ ├── MsMsQuerySpectrum.java │ │ │ ├── MsMsTraceReference.java │ │ │ └── TrackablePeak.java │ │ │ ├── projectspace │ │ │ ├── PickFeaturesAndImportToSirius.java │ │ │ ├── ProjectSpaceImporter.java │ │ │ ├── SiriusDatabaseAdapter.java │ │ │ └── SiriusProjectDocumentDbAdapter.java │ │ │ ├── quality │ │ │ ├── CheckAdductQuality.java │ │ │ ├── CheckAlignmentQuality.java │ │ │ ├── CheckIsotopeQuality.java │ │ │ ├── CheckMs2Quality.java │ │ │ ├── CheckPeakQuality.java │ │ │ ├── FeatureQualityChecker.java │ │ │ └── QualityAssessment.java │ │ │ ├── spectrum │ │ │ ├── Ms1SpectrumHeader.java │ │ │ ├── Ms2SpectrumHeader.java │ │ │ ├── MsSpectrumHeaderDatatype.java │ │ │ └── SpectrumStorage.java │ │ │ ├── statistics │ │ │ ├── AverageOfTop100TracesNormalization.java │ │ │ ├── MappingAlgorithm.java │ │ │ ├── MedianNoiseCollectionStrategy.java │ │ │ ├── NormalizationStrategy.java │ │ │ ├── SampleStats.java │ │ │ ├── SampleStatsDataType.java │ │ │ ├── StatisticsCollectionStrategy.java │ │ │ ├── TraceStats.java │ │ │ └── UserSpecifiedThresholds.java │ │ │ ├── trace │ │ │ ├── ContigousTraceDatatype.java │ │ │ ├── ContiguousTrace.java │ │ │ ├── LCMSStorage.java │ │ │ ├── ProcessedSample.java │ │ │ ├── ProjectedTrace.java │ │ │ ├── Rect.java │ │ │ ├── Trace.java │ │ │ ├── TraceRectangleMap.java │ │ │ ├── TraceRectangleMapByRVMap.java │ │ │ ├── TraceStorage.java │ │ │ ├── filter │ │ │ │ ├── Filter.java │ │ │ │ ├── GaussFilter.java │ │ │ │ ├── NoFilter.java │ │ │ │ ├── SavitzkyGolayFilter.java │ │ │ │ └── WaveletFilter.java │ │ │ └── segmentation │ │ │ │ ├── ApexDetection.java │ │ │ │ ├── Extrema.java │ │ │ │ ├── LegacySegmenter.java │ │ │ │ ├── PersistentHomology.java │ │ │ │ ├── TraceSegment.java │ │ │ │ └── TraceSegmentationStrategy.java │ │ │ ├── traceextractor │ │ │ ├── AdductAndIsotopeBasedDetectionStrategy.java │ │ │ ├── CombinedTraceDetectionStrategy.java │ │ │ ├── ConnectRelatedMoIs.java │ │ │ ├── IntensivePeaksAreConfident.java │ │ │ ├── IsotopesAndAdductsAreConfidentStrategy.java │ │ │ ├── MassOfInterestCombinedStrategy.java │ │ │ ├── MassOfInterestConfidenceEstimatorStrategy.java │ │ │ ├── PickIntensivePeaksDetectionStrategy.java │ │ │ ├── PickIntensivePeaksInConsecutiveSpectraStrategy.java │ │ │ ├── PickMsPrecursorPeakDetectionStrategy.java │ │ │ ├── PrecursorsWithMsMsAreConfidentStrategy.java │ │ │ ├── RectbasedCachingStrategy.java │ │ │ ├── TraceCachingStrategy.java │ │ │ ├── TraceDetectionStrategy.java │ │ │ ├── TracePicker.java │ │ │ └── TracesWithTooManyApexesAreStrange.java │ │ │ └── utils │ │ │ ├── AlignedFeatureUtils.java │ │ │ ├── AlignmentBeamSearch.java │ │ │ ├── MultipleCharges.java │ │ │ ├── TrackFeatureToFile.java │ │ │ ├── TrackFeatureToLog.java │ │ │ └── Tracker.java │ └── test │ │ └── java │ │ └── PersistentHomologyTest.java └── viewer │ ├── index.html │ └── viewer.js ├── lcms_mel ├── build.gradle ├── readme.md └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── lcms │ ├── detection │ ├── ChromatographicPeak.java │ ├── FeatureBuilder.java │ ├── FilteredTrace.java │ ├── GaussFilter.java │ ├── MaxPeakSpectrum.java │ ├── PersistentHomology.java │ ├── Scorer.java │ └── TraceCandidate.java │ └── io │ ├── CVUtils.java │ ├── IOThrowingConsumer.java │ ├── LCMSImporter.java │ ├── LCMSParser.java │ ├── MzMLParser.java │ ├── MzXMLParser.java │ └── MzXMLSaxParser.java ├── licence-groups.json ├── license-overrides.txt ├── lombok.config ├── mass_decomposition ├── .gitignore ├── .settings │ └── org.eclipse.jdt.core.prefs ├── build.gradle ├── mass_decomposer │ ├── build.gradle │ └── src │ │ ├── main │ │ ├── java │ │ │ └── de │ │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ └── MassDecomposer │ │ │ │ ├── Alphabet.java │ │ │ │ ├── ChemicalValidator.java │ │ │ │ ├── Chemistry │ │ │ │ ├── AddDeNovoDecompositionsToWhiteset.java │ │ │ │ ├── ChemicalAlphabetWrapper.java │ │ │ │ ├── DecomposerCache.java │ │ │ │ └── MassToFormulaDecomposer.java │ │ │ │ ├── DecompIterator.java │ │ │ │ ├── DecompositionValidator.java │ │ │ │ ├── Interval.java │ │ │ │ ├── MassDecomposer.java │ │ │ │ ├── NonEmptyFormulaValidator.java │ │ │ │ ├── RangeMassDecomposer.java │ │ │ │ ├── ValenceBoundary.java │ │ │ │ ├── ValenceValidator.java │ │ │ │ ├── ValencyAlphabet.java │ │ │ │ └── Weight.java │ │ └── resources │ │ │ └── LICENSE.txt │ │ └── test │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── MassDecomposer │ │ └── MassDecomposerTest.java └── src │ └── main │ └── resources │ └── LICENSE.txt ├── ml_utils ├── build.gradle └── src │ └── main │ ├── java │ └── org │ │ └── libsvm │ │ └── SVM.java │ └── resources │ └── LICENSE.txt ├── model_store_oss ├── build.gradle └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── ms │ └── stores │ └── model │ ├── AbstractBlobModelStore.java │ ├── CanopusClientDataStore.java │ ├── CanopusDataStore.java │ ├── DefaultBlobModelStore.java │ ├── FingerIdClientDataStore.java │ ├── FingerIdDataStore.java │ ├── ModelStore.java │ ├── ModelStores.java │ └── MsNovelistDataStore.java ├── ms_persistence_oss ├── build.gradle ├── ms_persistence_document_storage_oss │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ └── persistence │ │ │ └── storage │ │ │ ├── ComputeStateEvent.java │ │ │ ├── MetadataUtils.java │ │ │ ├── MsProjectDocumentDatabase.java │ │ │ ├── NetworkingProjectDocumentDatabase.java │ │ │ ├── SiriusProjectDatabaseImpl.java │ │ │ ├── SiriusProjectDocumentDatabase.java │ │ │ ├── StatsAndTaggingSupport.java │ │ │ ├── StorageUtils.java │ │ │ ├── exceptions │ │ │ ├── ProjectStateException.java │ │ │ └── ProjectTypeException.java │ │ │ └── nitrite │ │ │ ├── FpDataDocs.java │ │ │ └── NitriteSirirusProject.java │ │ └── test │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ └── persistence │ │ │ └── storage │ │ │ └── SiriusProjectDatabaseImplTest.java │ │ └── resources │ │ ├── canopus.tsv │ │ ├── canopus_npc.tsv │ │ ├── csi_fingerid.tsv │ │ ├── peaklists │ │ ├── Bicuculline_Unknown.ms │ │ ├── ForTox_TestMix_AMSMS_MFE-MS2Extr.cef │ │ ├── ForTox_TestMix_TMSMS_multi_msms.cef │ │ └── laudanosine.mgf │ │ ├── sirius-project-all-fp-data.sirius │ │ ├── sirius-project-features.sirius │ │ ├── structures │ │ ├── C47H75NO17.json.gz │ │ └── C6H4ClN3.json.gz │ │ └── trees │ │ ├── C15H24ClN3O3_[M+K]+.json │ │ ├── C18H19NO6_[M+Na]+.json │ │ └── C20H17NO6_[M+H]+.json ├── ms_persistence_io_oss │ ├── build.gradle │ └── src │ │ ├── main │ │ └── java │ │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── babelms │ │ │ └── cef │ │ │ └── AgilentCefCompoundParser.java │ │ └── test │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── babelms │ │ │ └── cef │ │ │ └── AgilentCefCompoundParserTest.java │ │ └── resources │ │ ├── 221021 After Gap Filling.cef │ │ ├── 221021 Before Gap Filling.cef │ │ ├── ForTox_TestMix_AMSMS(1 Cmpd).cef │ │ ├── ForTox_TestMix_AMSMS(15 cmpds).cef │ │ ├── ForTox_TestMix_AMSMS_MFE+MS2Extr(1 Cmpds).cef │ │ ├── ForTox_TestMix_AMSMS_MFE+MS2Extr(15 Cmpds).cef │ │ ├── ForTox_TestMix_TMSMS(1 Cmpd).cef │ │ └── ForTox_TestMix_TMSMS(13 cmpds).cef └── ms_persistence_model_oss │ ├── build.gradle │ └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ └── persistence │ │ │ ├── Configs.java │ │ │ └── model │ │ │ ├── core │ │ │ ├── Compound.java │ │ │ ├── DataSource.java │ │ │ ├── QualityReport.java │ │ │ ├── feature │ │ │ │ ├── AbstractAlignedFeatures.java │ │ │ │ ├── AbstractFeature.java │ │ │ │ ├── AlignedFeatures.java │ │ │ │ ├── AlignedIsotopicFeatures.java │ │ │ │ ├── CorrelatedIonPair.java │ │ │ │ ├── DetectedAdduct.java │ │ │ │ ├── DetectedAdducts.java │ │ │ │ └── Feature.java │ │ │ ├── networks │ │ │ │ ├── AdductEdge.java │ │ │ │ ├── AdductNetwork.java │ │ │ │ └── AdductNode.java │ │ │ ├── run │ │ │ │ ├── AbstractLCMSRun.java │ │ │ │ ├── Chromatography.java │ │ │ │ ├── Fragmentation.java │ │ │ │ ├── InstrumentConfig.java │ │ │ │ ├── InstrumentConfigs.java │ │ │ │ ├── Ionization.java │ │ │ │ ├── LCMSRun.java │ │ │ │ ├── MassAnalyzer.java │ │ │ │ ├── MergedLCMSRun.java │ │ │ │ ├── RetentionTimeAxis.java │ │ │ │ └── SampleStatistics.java │ │ │ ├── scan │ │ │ │ ├── AbstractScan.java │ │ │ │ ├── MSMSScan.java │ │ │ │ └── Scan.java │ │ │ ├── spectrum │ │ │ │ ├── IsotopePattern.java │ │ │ │ ├── MSData.java │ │ │ │ └── MergedMSnSpectrum.java │ │ │ ├── statistics │ │ │ │ ├── AggregationType.java │ │ │ │ ├── FoldChange.java │ │ │ │ ├── ForeignKey.java │ │ │ │ ├── QuantMeasure.java │ │ │ │ └── Statistics.java │ │ │ ├── tags │ │ │ │ ├── Tag.java │ │ │ │ ├── TagDefinition.java │ │ │ │ ├── TagGroup.java │ │ │ │ ├── ValueDefinition.java │ │ │ │ ├── ValueFormatter.java │ │ │ │ └── ValueType.java │ │ │ └── trace │ │ │ │ ├── AbstractTrace.java │ │ │ │ ├── MergedTrace.java │ │ │ │ ├── RawTraceRef.java │ │ │ │ ├── SourceTrace.java │ │ │ │ └── TraceRef.java │ │ │ ├── properties │ │ │ ├── ProjectSourceFormats.java │ │ │ └── ProjectType.java │ │ │ └── sirius │ │ │ ├── AlignedFeatureAnnotation.java │ │ │ ├── CanopusPrediction.java │ │ │ ├── ComputedSubtools.java │ │ │ ├── CsiPrediction.java │ │ │ ├── CsiStructureMatch.java │ │ │ ├── CsiStructureSearchResult.java │ │ │ ├── DenovoStructureMatch.java │ │ │ ├── FTreeResult.java │ │ │ ├── FormulaAnnotation.java │ │ │ ├── FormulaAnnotationWithId.java │ │ │ ├── FormulaCandidate.java │ │ │ ├── Parameters.java │ │ │ ├── SpectraMatch.java │ │ │ ├── StructureMatch.java │ │ │ ├── StructureSearchResult.java │ │ │ └── serializers │ │ │ ├── CanopusPredictionDeserializer.java │ │ │ └── CsiPredictionDeserializer.java │ └── resources │ │ ├── dissociation.csv │ │ ├── ionization.csv │ │ └── mass_analyzers.csv │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── ms │ └── persistence │ └── model │ └── core │ └── run │ └── InstrumentConfigTest.java ├── networks ├── build.gradle └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── networks │ ├── Correlation.java │ ├── EdgeType.java │ ├── MolecularNetwork.java │ ├── NetworkBuilder.java │ ├── NetworkEdge.java │ ├── NetworkNode.java │ ├── de │ └── unijena │ │ └── bioinf │ │ └── pvalues │ │ └── SimpleIndepDP.java │ └── serialization │ ├── AbstractConnection.java │ ├── ConnectionTable.java │ ├── ConnectionTableSerializer.java │ └── CorrelationConnection.java ├── passatutto ├── build.gradle ├── passatutto_project_space │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── babelms │ │ │ └── projectspace │ │ │ └── PassatuttoSerializer.java │ │ └── resources │ │ └── LICENSE.txt └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── passatutto │ │ ├── Decoy.java │ │ ├── Passatutto.java │ │ ├── ReferenceCompound.java │ │ ├── RerootedTree.java │ │ └── RerootingTreeMethod.java │ └── resources │ └── LICENSE.txt ├── preprocessing ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── sirius │ │ │ ├── MS2Peak.java │ │ │ ├── Ms1Preprocessor.java │ │ │ ├── Ms2Preprocessor.java │ │ │ ├── PeakAnnotation.java │ │ │ ├── ProcessedInput.java │ │ │ ├── ProcessedPeak.java │ │ │ ├── SiriusPreprocessor.java │ │ │ ├── annotations │ │ │ ├── DecompositionList.java │ │ │ ├── NoiseThresholdSettings.java │ │ │ └── SpectralRecalibration.java │ │ │ ├── deisotope │ │ │ ├── IsotopePatternDetection.java │ │ │ └── TargetedIsotopePatternDetection.java │ │ │ ├── elementdetection │ │ │ ├── DeepNeuralNetworkElementDetector.java │ │ │ ├── DetectedFormulaConstraints.java │ │ │ ├── ElementDetection.java │ │ │ ├── TransformerElementDetector.java │ │ │ ├── prediction │ │ │ │ ├── DNNElementPredictor.java │ │ │ │ ├── DNNRegressionPredictor.java │ │ │ │ ├── ElementPredictor.java │ │ │ │ ├── FeatureVector.java │ │ │ │ └── TrainedElementDetectionNetwork.java │ │ │ └── transformer │ │ │ │ ├── Activation.java │ │ │ │ ├── EmbeddingLayer.java │ │ │ │ ├── FourierEncoder.java │ │ │ │ ├── FullyConnectedLayer.java │ │ │ │ ├── IOUtils.java │ │ │ │ ├── LayerNorm.java │ │ │ │ ├── Transformer.java │ │ │ │ ├── TransformerBasedPredictor.java │ │ │ │ └── TransformerPrediction.java │ │ │ ├── iondetection │ │ │ ├── AdductDetection.java │ │ │ ├── DetectIonsFromMs1.java │ │ │ └── NH3DetectorSVM.java │ │ │ ├── merging │ │ │ ├── HighIntensityMsMsMerger.java │ │ │ ├── Ms1Merging.java │ │ │ └── Ms2Merger.java │ │ │ ├── peakprocessor │ │ │ ├── DecomposedSpectrumProcessor.java │ │ │ ├── MergedSpectrumProcessor.java │ │ │ ├── NoiseIntensityThresholdFilter.java │ │ │ ├── NormalizeToSumPreprocessor.java │ │ │ └── UnmergedSpectrumProcessor.java │ │ │ └── validation │ │ │ ├── Ms1Validator.java │ │ │ └── Ms2Validator.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── de.unijena.bioinf.ms.defaults │ │ ├── preprocessing.auto.config │ │ └── preprocessing.class.map │ │ ├── dnn_element_detection_3.param │ │ ├── dnn_element_detection_4.param │ │ ├── dnn_element_detection_5.param │ │ ├── regression3.param │ │ ├── regression4.param │ │ ├── regression5.param │ │ └── transformer.bin │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── sirius │ └── elementdetection │ └── TransformerElementDetectorTest.java ├── quality_assessment ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── quality_assessment │ │ └── TreeQualityEvaluator.java │ └── resources │ └── LICENSE.txt ├── rabbitmq-support ├── build.gradle └── src │ └── main │ └── java │ └── de │ └── unijena │ └── bioinf │ └── rabbitmq │ ├── RabbitMqChannelPool.java │ ├── RabbitMqConnector.java │ └── RabbitUtils.java ├── retention_order_prediction_oss ├── build.gradle ├── retention_cli │ ├── build.gradle │ └── src │ │ └── main │ │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── retention │ │ │ ├── ALIGNF.java │ │ │ ├── Main.java │ │ │ └── Test.java │ │ └── resources │ │ └── LICENSE.txt └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ ├── retention │ │ ├── PredictableCompound.java │ │ ├── RetentionOrderDataset.java │ │ ├── RetentionOrderPredictionTrain.java │ │ ├── SimpleCompound.java │ │ └── kernels │ │ │ ├── CircularFingerprinter.java │ │ │ ├── EStateKernel.java │ │ │ ├── ElectroPathKernel.java │ │ │ ├── LongestPathKernel.java │ │ │ ├── MACCSFingerprinter.java │ │ │ ├── MoleculeKernel.java │ │ │ ├── OutGroupKernel.java │ │ │ ├── QSARKernel.java │ │ │ ├── ShapeKernel.java │ │ │ ├── ShortestPathKernel.java │ │ │ ├── SubstructureKernel.java │ │ │ ├── SubstructureLinearKernel.java │ │ │ ├── SubstructurePathKernel.java │ │ │ └── SubstructurePathKernel2.java │ │ └── svm │ │ └── RankSVM.java │ └── resources │ └── LICENSE.txt ├── scripts ├── sirius.bat.templ └── sirius.sh.templ ├── settings.gradle ├── sirius-sdk ├── README.md ├── build.gradle ├── openapi-gen-config.json ├── sirius-sdk.jjobs │ ├── build.gradle │ └── src │ │ └── main │ │ └── java │ │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── ms │ │ └── nightsky │ │ └── sdk │ │ └── jjobs │ │ └── SseProgressJJob.java ├── sirius-sdk.openapi │ ├── .openapi-generator-ignore │ ├── .openapi-generator │ │ ├── FILES │ │ └── VERSION │ ├── README.md │ ├── build.gradle │ ├── docs │ │ ├── AccountCredentials.md │ │ ├── AccountInfo.md │ │ ├── ActuatorApi.md │ │ ├── AdductEdgeExperimental.md │ │ ├── AdductNetworkExperimental.md │ │ ├── AdductNodeExperimental.md │ │ ├── AggregationType.md │ │ ├── AlignedFeature.md │ │ ├── AlignedFeatureOptField.md │ │ ├── AlignedFeatureQualityExperimental.md │ │ ├── AllowedFeatures.md │ │ ├── AnnotatedMsMsData.md │ │ ├── AnnotatedPeak.md │ │ ├── AnnotatedSpectrum.md │ │ ├── Axes.md │ │ ├── BackgroundComputationsStateEvent.md │ │ ├── BasicSpectrum.md │ │ ├── BinaryFingerprint.md │ │ ├── BioTransformerParameters.md │ │ ├── BioTransformerSequenceStep.md │ │ ├── Canopus.md │ │ ├── CanopusPrediction.md │ │ ├── Category.md │ │ ├── CommandSubmission.md │ │ ├── Compound.md │ │ ├── CompoundClass.md │ │ ├── CompoundClassType.md │ │ ├── CompoundClasses.md │ │ ├── CompoundImport.md │ │ ├── CompoundOptField.md │ │ ├── CompoundStatisticsApi.md │ │ ├── CompoundsApi.md │ │ ├── ComputeFoldChangeForBlankSubtractionRequest.md │ │ ├── ComputedSubtools.md │ │ ├── ConfidenceMode.md │ │ ├── ConnectionCheck.md │ │ ├── ConnectionError.md │ │ ├── ConnectionErrorClass.md │ │ ├── ConnectionErrorType.md │ │ ├── ConsensusAnnotationsCSI.md │ │ ├── ConsensusAnnotationsDeNovo.md │ │ ├── ConsensusCriterionCSI.md │ │ ├── ConsensusCriterionDeNovo.md │ │ ├── Cyp450Mode.md │ │ ├── DBLink.md │ │ ├── DataImportEvent.md │ │ ├── DataQuality.md │ │ ├── Deviation.md │ │ ├── FeatureAnnotations.md │ │ ├── FeatureImport.md │ │ ├── FeatureStatisticsApi.md │ │ ├── FeaturesApi.md │ │ ├── FingerprintPrediction.md │ │ ├── FoldChange.md │ │ ├── FormulaCandidate.md │ │ ├── FormulaCandidateOptField.md │ │ ├── FragmentNode.md │ │ ├── FragmentationTree.md │ │ ├── GuiApi.md │ │ ├── GuiInfo.md │ │ ├── ImportResult.md │ │ ├── Info.md │ │ ├── InfoApi.md │ │ ├── InstrumentProfile.md │ │ ├── IsotopeMs2Strategy.md │ │ ├── IsotopePatternAnnotation.md │ │ ├── Job.md │ │ ├── JobEffect.md │ │ ├── JobOptField.md │ │ ├── JobProgress.md │ │ ├── JobState.md │ │ ├── JobSubmission.md │ │ ├── JobsApi.md │ │ ├── LcmsSubmissionParameters.md │ │ ├── LicenseInfo.md │ │ ├── LipidAnnotation.md │ │ ├── LoginAndAccountApi.md │ │ ├── LossEdge.md │ │ ├── MetabolicTransformation.md │ │ ├── MsData.md │ │ ├── MsNovelist.md │ │ ├── P2Mode.md │ │ ├── PageMetadata.md │ │ ├── PagedModelAlignedFeature.md │ │ ├── PagedModelCompound.md │ │ ├── PagedModelFormulaCandidate.md │ │ ├── PagedModelJob.md │ │ ├── PagedModelRun.md │ │ ├── PagedModelSpectralLibraryMatch.md │ │ ├── PagedModelStructureCandidateFormula.md │ │ ├── PagedModelStructureCandidateScored.md │ │ ├── ParentPeak.md │ │ ├── PeakAnnotation.md │ │ ├── PeakPair.md │ │ ├── ProjectChangeEvent.md │ │ ├── ProjectEventType.md │ │ ├── ProjectInfo.md │ │ ├── ProjectInfoOptField.md │ │ ├── ProjectType.md │ │ ├── ProjectsApi.md │ │ ├── QualityItem.md │ │ ├── QualityWeight.md │ │ ├── QuantMeasure.md │ │ ├── QuantRowType.md │ │ ├── QuantTableExperimental.md │ │ ├── Run.md │ │ ├── RunOptField.md │ │ ├── RunsApi.md │ │ ├── SampleTypeFoldChangeRequest.md │ │ ├── SearchableDatabase.md │ │ ├── SearchableDatabaseParameters.md │ │ ├── SearchableDatabasesApi.md │ │ ├── SimplePeak.md │ │ ├── Sirius.md │ │ ├── Solver.md │ │ ├── SpectralLibraryMatch.md │ │ ├── SpectralLibraryMatchOptField.md │ │ ├── SpectralLibraryMatchSummary.md │ │ ├── SpectralLibrarySearch.md │ │ ├── SpectralMatchType.md │ │ ├── SpectralMatchingType.md │ │ ├── SpectrumAnnotation.md │ │ ├── SpectrumType.md │ │ ├── StatisticsTable.md │ │ ├── StatisticsType.md │ │ ├── StoredJobSubmission.md │ │ ├── StructureCandidate.md │ │ ├── StructureCandidateFormula.md │ │ ├── StructureCandidateOptField.md │ │ ├── StructureCandidateScored.md │ │ ├── StructureDbSearch.md │ │ ├── Subscription.md │ │ ├── SubscriptionConsumables.md │ │ ├── Tag.md │ │ ├── TagDefinition.md │ │ ├── TagDefinitionImport.md │ │ ├── TagGroup.md │ │ ├── TagsApi.md │ │ ├── Term.md │ │ ├── Timeout.md │ │ ├── TraceAnnotationExperimental.md │ │ ├── TraceAnnotationTypeExperimental.md │ │ ├── TraceExperimental.md │ │ ├── TraceSetExperimental.md │ │ ├── UseHeuristic.md │ │ ├── ValueType.md │ │ ├── Zodiac.md │ │ ├── ZodiacAnalogueNodes.md │ │ ├── ZodiacEdgeFilterThresholds.md │ │ ├── ZodiacEpochs.md │ │ └── ZodiacLibraryScoring.md │ └── src │ │ ├── main │ │ └── java │ │ │ └── io │ │ │ └── sirius │ │ │ └── ms │ │ │ └── sdk │ │ │ ├── api │ │ │ ├── ActuatorApi.java │ │ │ ├── CompoundStatisticsApi.java │ │ │ ├── CompoundsApi.java │ │ │ ├── FeatureStatisticsApi.java │ │ │ ├── FeaturesApi.java │ │ │ ├── GuiApi.java │ │ │ ├── InfoApi.java │ │ │ ├── JobsApi.java │ │ │ ├── LoginAndAccountApi.java │ │ │ ├── ProjectsApi.java │ │ │ ├── RunsApi.java │ │ │ ├── SearchableDatabasesApi.java │ │ │ └── TagsApi.java │ │ │ ├── client │ │ │ ├── ApiClient.java │ │ │ ├── RFC3339DateFormat.java │ │ │ ├── ServerConfiguration.java │ │ │ ├── ServerVariable.java │ │ │ ├── StringUtil.java │ │ │ └── auth │ │ │ │ ├── ApiKeyAuth.java │ │ │ │ ├── Authentication.java │ │ │ │ ├── HttpBasicAuth.java │ │ │ │ └── HttpBearerAuth.java │ │ │ └── model │ │ │ ├── AccountCredentials.java │ │ │ ├── AccountInfo.java │ │ │ ├── AdductEdgeExperimental.java │ │ │ ├── AdductNetworkExperimental.java │ │ │ ├── AdductNodeExperimental.java │ │ │ ├── AggregationType.java │ │ │ ├── AlignedFeature.java │ │ │ ├── AlignedFeatureOptField.java │ │ │ ├── AlignedFeatureQualityExperimental.java │ │ │ ├── AllowedFeatures.java │ │ │ ├── AnnotatedMsMsData.java │ │ │ ├── AnnotatedPeak.java │ │ │ ├── AnnotatedSpectrum.java │ │ │ ├── Axes.java │ │ │ ├── BackgroundComputationsStateEvent.java │ │ │ ├── BasicSpectrum.java │ │ │ ├── BinaryFingerprint.java │ │ │ ├── BioTransformerParameters.java │ │ │ ├── BioTransformerSequenceStep.java │ │ │ ├── Canopus.java │ │ │ ├── CanopusPrediction.java │ │ │ ├── Category.java │ │ │ ├── CommandSubmission.java │ │ │ ├── Compound.java │ │ │ ├── CompoundClass.java │ │ │ ├── CompoundClassType.java │ │ │ ├── CompoundClasses.java │ │ │ ├── CompoundImport.java │ │ │ ├── CompoundOptField.java │ │ │ ├── ComputeFoldChangeForBlankSubtractionRequest.java │ │ │ ├── ComputedSubtools.java │ │ │ ├── ConfidenceMode.java │ │ │ ├── ConnectionCheck.java │ │ │ ├── ConnectionError.java │ │ │ ├── ConnectionErrorClass.java │ │ │ ├── ConnectionErrorType.java │ │ │ ├── ConsensusAnnotationsCSI.java │ │ │ ├── ConsensusAnnotationsDeNovo.java │ │ │ ├── ConsensusCriterionCSI.java │ │ │ ├── ConsensusCriterionDeNovo.java │ │ │ ├── Cyp450Mode.java │ │ │ ├── DBLink.java │ │ │ ├── DataImportEvent.java │ │ │ ├── DataQuality.java │ │ │ ├── Deviation.java │ │ │ ├── FeatureAnnotations.java │ │ │ ├── FeatureImport.java │ │ │ ├── FingerprintPrediction.java │ │ │ ├── FoldChange.java │ │ │ ├── FormulaCandidate.java │ │ │ ├── FormulaCandidateOptField.java │ │ │ ├── FragmentNode.java │ │ │ ├── FragmentationTree.java │ │ │ ├── GuiInfo.java │ │ │ ├── ImportResult.java │ │ │ ├── Info.java │ │ │ ├── InstrumentProfile.java │ │ │ ├── IsotopeMs2Strategy.java │ │ │ ├── IsotopePatternAnnotation.java │ │ │ ├── Job.java │ │ │ ├── JobEffect.java │ │ │ ├── JobOptField.java │ │ │ ├── JobProgress.java │ │ │ ├── JobState.java │ │ │ ├── JobSubmission.java │ │ │ ├── LcmsSubmissionParameters.java │ │ │ ├── LicenseInfo.java │ │ │ ├── LipidAnnotation.java │ │ │ ├── LossEdge.java │ │ │ ├── MetabolicTransformation.java │ │ │ ├── MsData.java │ │ │ ├── MsNovelist.java │ │ │ ├── P2Mode.java │ │ │ ├── PageMetadata.java │ │ │ ├── PagedModelAlignedFeature.java │ │ │ ├── PagedModelCompound.java │ │ │ ├── PagedModelFormulaCandidate.java │ │ │ ├── PagedModelJob.java │ │ │ ├── PagedModelRun.java │ │ │ ├── PagedModelSpectralLibraryMatch.java │ │ │ ├── PagedModelStructureCandidateFormula.java │ │ │ ├── PagedModelStructureCandidateScored.java │ │ │ ├── ParentPeak.java │ │ │ ├── PeakAnnotation.java │ │ │ ├── PeakPair.java │ │ │ ├── ProjectChangeEvent.java │ │ │ ├── ProjectEventType.java │ │ │ ├── ProjectInfo.java │ │ │ ├── ProjectInfoOptField.java │ │ │ ├── ProjectType.java │ │ │ ├── QualityItem.java │ │ │ ├── QualityWeight.java │ │ │ ├── QuantMeasure.java │ │ │ ├── QuantRowType.java │ │ │ ├── QuantTableExperimental.java │ │ │ ├── Run.java │ │ │ ├── RunOptField.java │ │ │ ├── SampleTypeFoldChangeRequest.java │ │ │ ├── SearchableDatabase.java │ │ │ ├── SearchableDatabaseParameters.java │ │ │ ├── SimplePeak.java │ │ │ ├── Sirius.java │ │ │ ├── Solver.java │ │ │ ├── SpectralLibraryMatch.java │ │ │ ├── SpectralLibraryMatchOptField.java │ │ │ ├── SpectralLibraryMatchSummary.java │ │ │ ├── SpectralLibrarySearch.java │ │ │ ├── SpectralMatchType.java │ │ │ ├── SpectralMatchingType.java │ │ │ ├── SpectrumAnnotation.java │ │ │ ├── SpectrumType.java │ │ │ ├── StatisticsTable.java │ │ │ ├── StatisticsType.java │ │ │ ├── StoredJobSubmission.java │ │ │ ├── StructureCandidate.java │ │ │ ├── StructureCandidateFormula.java │ │ │ ├── StructureCandidateOptField.java │ │ │ ├── StructureCandidateScored.java │ │ │ ├── StructureDbSearch.java │ │ │ ├── Subscription.java │ │ │ ├── SubscriptionConsumables.java │ │ │ ├── Tag.java │ │ │ ├── TagDefinition.java │ │ │ ├── TagDefinitionImport.java │ │ │ ├── TagGroup.java │ │ │ ├── Term.java │ │ │ ├── Timeout.java │ │ │ ├── TraceAnnotationExperimental.java │ │ │ ├── TraceAnnotationTypeExperimental.java │ │ │ ├── TraceExperimental.java │ │ │ ├── TraceSetExperimental.java │ │ │ ├── UseHeuristic.java │ │ │ ├── ValueType.java │ │ │ ├── Zodiac.java │ │ │ ├── ZodiacAnalogueNodes.java │ │ │ ├── ZodiacEdgeFilterThresholds.java │ │ │ ├── ZodiacEpochs.java │ │ │ └── ZodiacLibraryScoring.java │ │ └── test │ │ ├── java │ │ └── io │ │ │ └── sirius │ │ │ └── ms │ │ │ └── sdk │ │ │ └── api │ │ │ ├── ActuatorApiTest.java │ │ │ ├── CompoundStatisticsApiTest.java │ │ │ ├── CompoundsApiTest.java │ │ │ ├── FeatureStatisticsApiTest.java │ │ │ ├── FeaturesApiTest.java │ │ │ ├── InfoApiTest.java │ │ │ ├── JobsApiTest.java │ │ │ ├── LoginAndAccountApiTest.java │ │ │ ├── ProjectsApiTest.java │ │ │ ├── RunsApiTest.java │ │ │ ├── SearchableDatabasesApiTest.java │ │ │ ├── SiriusSpringHandler.java │ │ │ ├── TagsApiTest.java │ │ │ └── TestSetup.java │ │ └── resources │ │ ├── META-INF │ │ └── services │ │ │ └── org.junit.platform.launcher.TestExecutionListener │ │ └── data │ │ ├── 221021_After_Gap_Filling.cef │ │ ├── 221021_Before_Gap_Filling.cef │ │ ├── ForTox_TestMix_AMSMS.cef │ │ ├── Kaempferol.ms │ │ ├── SM801101.txt │ │ ├── custom-db-sirius-demo-structures.tsv │ │ ├── laudanosine.mgf │ │ ├── test-project-results │ │ └── test-project-results.sirius │ │ ├── test-project-to-open │ │ └── test-project-open.sirius │ │ ├── test-project_compounds │ │ └── test-project-compounds.sirius │ │ └── test-searchable-database │ │ └── customDbID.siriusdb ├── src │ └── main │ │ └── java │ │ └── io │ │ └── sirius │ │ └── ms │ │ ├── sdk │ │ ├── SiriusClient.java │ │ ├── SiriusSDK.java │ │ ├── SiriusSDKErrorResponse.java │ │ ├── SiriusSDKUtils.java │ │ └── api │ │ │ └── ServerSentEventApi.java │ │ └── sse │ │ ├── DataEventType.java │ │ ├── DataObjectEvent.java │ │ ├── DataObjectEvents.java │ │ ├── FluxToFlowBroadcast.java │ │ └── PropertyChangeSubscriber.java └── templates │ └── licenseInfo.mustache ├── sirius_api ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── sirius │ │ │ ├── FTreeMetricsHelper.java │ │ │ ├── Feedback.java │ │ │ ├── FeedbackFlag.java │ │ │ ├── IdentificationResult.java │ │ │ ├── Profile.java │ │ │ ├── Progress.java │ │ │ ├── Sirius.java │ │ │ ├── SiriusCachedFactory.java │ │ │ ├── SiriusFactory.java │ │ │ └── scores │ │ │ ├── IsotopeScore.java │ │ │ ├── SiriusScore.java │ │ │ └── TreeScore.java │ └── resources │ │ ├── LICENSE.txt │ │ └── de.unijena.bioinf.ms.defaults │ │ ├── sirius_api.auto.config │ │ └── sirius_api.class.map │ └── test │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── sirius │ │ └── SiriusTest.java │ └── resources │ ├── Bicuculline.ms │ └── Kaempferol.ms ├── sirius_cli ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ ├── isas │ │ │ └── mztab2 │ │ │ │ └── io │ │ │ │ ├── MZTabParameter.java │ │ │ │ ├── SiriusMZTabParameter.java │ │ │ │ ├── SiriusWorkspaceMzTabNonValidatingWriter.java │ │ │ │ └── SiriusWorkspaceMzTabValidatingWriter.java │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── ms │ │ │ ├── annotations │ │ │ │ ├── PrintCitations.java │ │ │ │ └── RecomputeResults.java │ │ │ └── frontend │ │ │ │ ├── DefaultParameter.java │ │ │ │ ├── Run.java │ │ │ │ ├── SiriusCLIApplication.java │ │ │ │ ├── bibtex │ │ │ │ └── BibtexManager.java │ │ │ │ ├── completion │ │ │ │ └── DataSourceCandidates.java │ │ │ │ ├── core │ │ │ │ ├── ApplicationCore.java │ │ │ │ ├── PasswordCrypter.java │ │ │ │ ├── SiriusPCS.java │ │ │ │ ├── SiriusProperties.java │ │ │ │ └── Workspace.java │ │ │ │ ├── logging │ │ │ │ ├── ConsoleSimpleFormatter.java │ │ │ │ └── ResultOutputHandler.java │ │ │ │ ├── subtools │ │ │ │ ├── AlignedFeaturesFilterOptions.java │ │ │ │ ├── CLIRootOptions.java │ │ │ │ ├── DataSetJob.java │ │ │ │ ├── InputFilesOptions.java │ │ │ │ ├── InstanceJob.java │ │ │ │ ├── OutputOptions.java │ │ │ │ ├── PostprocessingJob.java │ │ │ │ ├── PostprocessingTool.java │ │ │ │ ├── PreprocessingJob.java │ │ │ │ ├── PreprocessingTool.java │ │ │ │ ├── Provide.java │ │ │ │ ├── RootOptions.java │ │ │ │ ├── StandaloneTool.java │ │ │ │ ├── ToolChainJob.java │ │ │ │ ├── ToolChainJobImpl.java │ │ │ │ ├── ToolChainOptions.java │ │ │ │ ├── canopus │ │ │ │ │ ├── CanopusOptions.java │ │ │ │ │ └── CanopusSubToolJob.java │ │ │ │ ├── config │ │ │ │ │ ├── AddConfigsJob.java │ │ │ │ │ └── DefaultParameterConfigLoader.java │ │ │ │ ├── custom_db │ │ │ │ │ ├── AddDBOptions.java │ │ │ │ │ ├── BioTransformerOptions.java │ │ │ │ │ ├── CreateDBOptions.java │ │ │ │ │ ├── CustomDBOptions.java │ │ │ │ │ ├── CustomDBPropertyUtils.java │ │ │ │ │ ├── ImportDBOptions.java │ │ │ │ │ ├── ImportDBWorkflow.java │ │ │ │ │ ├── RemoveDBOptions.java │ │ │ │ │ ├── ShowDBOptions.java │ │ │ │ │ └── ShowWorkflowUtil.java │ │ │ │ ├── decomp │ │ │ │ │ ├── AlphabetParser.java │ │ │ │ │ ├── DecompOptions.java │ │ │ │ │ ├── DecompWorkflow.java │ │ │ │ │ ├── FilterLevel.java │ │ │ │ │ └── Test.java │ │ │ │ ├── export │ │ │ │ │ └── mgf │ │ │ │ │ │ ├── MgfExporterOptions.java │ │ │ │ │ │ └── MgfExporterWorkflow.java │ │ │ │ ├── fingerblast │ │ │ │ │ ├── FingerblastOptions.java │ │ │ │ │ └── FingerblastSubToolJob.java │ │ │ │ ├── fingerprint │ │ │ │ │ ├── FingerprintOptions.java │ │ │ │ │ └── FingerprintSubToolJob.java │ │ │ │ ├── fingerprinter │ │ │ │ │ ├── FingerprinterOptions.java │ │ │ │ │ └── FingerprinterWorkflow.java │ │ │ │ ├── lcms_align │ │ │ │ │ ├── DataSmoothing.java │ │ │ │ │ ├── LcmsAlignOptions.java │ │ │ │ │ ├── LcmsAlignSubToolJobNoSql.java │ │ │ │ │ └── LcmsAlignSubToolJobSiriusPs.java │ │ │ │ ├── login │ │ │ │ │ └── LoginOptions.java │ │ │ │ ├── msnovelist │ │ │ │ │ ├── MsNovelistOptions.java │ │ │ │ │ ├── MsNovelistSubToolJob.java │ │ │ │ │ └── NumberOfMsNovelistCandidates.java │ │ │ │ ├── passatutto │ │ │ │ │ ├── PassatuttoOptions.java │ │ │ │ │ └── PassatuttoSubToolJob.java │ │ │ │ ├── project │ │ │ │ │ └── ProjectOptions.java │ │ │ │ ├── selftest │ │ │ │ │ ├── SelfTestOptions.java │ │ │ │ │ └── SelfTestWorkflow.java │ │ │ │ ├── settings │ │ │ │ │ └── SettingsOptions.java │ │ │ │ ├── similarity │ │ │ │ │ ├── SimilarityMatrixOptions.java │ │ │ │ │ └── SimilarityMatrixWorkflow.java │ │ │ │ ├── sirius │ │ │ │ │ ├── SiriusOptions.java │ │ │ │ │ └── SiriusSubToolJob.java │ │ │ │ ├── spectra_search │ │ │ │ │ ├── AnalogueSearchSettings.java │ │ │ │ │ ├── IdentitySearchSettings.java │ │ │ │ │ ├── SpectraCache.java │ │ │ │ │ ├── SpectraSearchOptions.java │ │ │ │ │ ├── SpectraSearchSubtoolJob.java │ │ │ │ │ └── SpectralSearchLog.java │ │ │ │ ├── summaries │ │ │ │ │ ├── ChemVistaSummaryWriter.java │ │ │ │ │ ├── CsvTableWriter.java │ │ │ │ │ ├── DataQualitySummaryWriter.java │ │ │ │ │ ├── DelimitedTableWriter.java │ │ │ │ │ ├── NoSqlCanopusSummaryWriter.java │ │ │ │ │ ├── NoSqlDeNovoSummaryWriter.java │ │ │ │ │ ├── NoSqlFormulaSummaryWriter.java │ │ │ │ │ ├── NoSqlSpectrumSummaryWriter.java │ │ │ │ │ ├── NoSqlStructureSummaryWriter.java │ │ │ │ │ ├── NoSqlSummarySubToolJob.java │ │ │ │ │ ├── SiriusProjectSpaceSummarySubToolJob.java │ │ │ │ │ ├── SummaryOptions.java │ │ │ │ │ ├── SummaryTable.java │ │ │ │ │ ├── SummaryTableWriter.java │ │ │ │ │ ├── TsvTableWriter.java │ │ │ │ │ ├── XlsxTableWriter.java │ │ │ │ │ ├── ZipTableWriter.java │ │ │ │ │ └── mztab │ │ │ │ │ │ └── NoSqlMztabMSummaryWriter.java │ │ │ │ ├── updatefps │ │ │ │ │ ├── UpdateFingerprintOptions.java │ │ │ │ │ └── UpdateFingerprintsWorkflow.java │ │ │ │ └── zodiac │ │ │ │ │ ├── ZodiacOptions.java │ │ │ │ │ └── ZodiacSubToolJob.java │ │ │ │ ├── utils │ │ │ │ ├── AutoCompletionScript.java │ │ │ │ ├── FormatedTableBuilder.java │ │ │ │ ├── PicoUtils.java │ │ │ │ └── Progressbar │ │ │ │ │ ├── ProgressVisualizer.java │ │ │ │ │ ├── ProgressbarCalculator.java │ │ │ │ │ ├── ProgressbarDefaultCalculator.java │ │ │ │ │ └── ProgressbarDefaultVisualizer.java │ │ │ │ └── workflow │ │ │ │ ├── DymmyExpResultJob.java │ │ │ │ ├── ExtendableInstanceBuffer.java │ │ │ │ ├── InstanceBuffer.java │ │ │ │ ├── InstanceBufferFactory.java │ │ │ │ ├── SimpleInstanceBuffer.java │ │ │ │ ├── ToolChainWorkflow.java │ │ │ │ ├── WorkFlowSupplier.java │ │ │ │ ├── Workflow.java │ │ │ │ └── WorkflowBuilder.java │ │ │ └── projectspace │ │ │ ├── AbstractProjectSpaceManager.java │ │ │ ├── CsvMS2ExpIterator.java │ │ │ ├── FCandidate.java │ │ │ ├── IncompatibleFingerprintDataException.java │ │ │ ├── InstIterProvider.java │ │ │ ├── Instance.java │ │ │ ├── InstanceImportIteratorMS2Exp.java │ │ │ ├── InstanceImporter.java │ │ │ ├── MS2ExpInputIterator.java │ │ │ ├── MsExperiments2.java │ │ │ ├── NitriteProjectSpaceManagerFactory.java │ │ │ ├── NoSQLInstance.java │ │ │ ├── NoSQLProjectSpaceManager.java │ │ │ ├── NoSqlFCandidate.java │ │ │ ├── ProjectSpaceManager.java │ │ │ ├── ProjectSpaceManagerFactory.java │ │ │ ├── SiriusProjectSpaceFCandidate.java │ │ │ ├── SiriusProjectSpaceInstance.java │ │ │ ├── SiriusProjectSpaceManager.java │ │ │ ├── SiriusProjectSpaceManagerFactory.java │ │ │ ├── invalidation │ │ │ └── Invalidator.java │ │ │ └── summaries │ │ │ ├── CanopusSummaryWriter.java │ │ │ ├── FormulaSummaryWriter.java │ │ │ ├── StructureCSVExporter.java │ │ │ ├── StructureSummaryWriter.java │ │ │ ├── SummaryLocations.java │ │ │ └── mztab │ │ │ ├── JenaMSAdditionalKeys.java │ │ │ └── MztabMExporter.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── cite.bibtex │ │ ├── de.unijena.bioinf.ms.defaults │ │ ├── sirius_cli.auto.config │ │ └── sirius_cli.class.map │ │ ├── de.unijena.bioinf.ms.frontend.subtools.selftest │ │ ├── Kaempferol.ms │ │ ├── Laudanosine.mgf │ │ └── Valium.cef │ │ ├── logging.properties │ │ ├── sirius.properties │ │ └── sirius_frontend.build.properties │ └── test │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── ms │ │ ├── CLITest.java │ │ ├── FeatureFilterTest.java │ │ ├── LcmsAlignAcceptanceTest.java │ │ └── OutputOptionsTest.java │ └── test_results │ ├── mgf_candidates │ ├── formula_candidates.tsv │ └── structure_candidates.tsv │ ├── ms_candidates │ ├── compound_class_annotation │ │ ├── formula_candidates.tsv │ │ └── structure_candidates.tsv │ ├── formula_annotation │ │ └── formula_candidates.tsv │ └── ignore_formula │ │ └── formula_candidates.tsv │ └── txt_candidates │ └── formula_candidates.tsv ├── sirius_dist ├── README.md ├── build.gradle ├── sirius_docker │ └── Dockerfile ├── sirius_gui_dist │ └── build.gradle └── src │ └── test │ └── java │ ├── MgfTestLocal.java │ ├── MsTestLocal.java │ ├── TestMethods.java │ └── TxtTestLocal.java ├── sirius_gui ├── build.gradle └── src │ ├── main │ ├── java │ │ ├── de │ │ │ └── unijena │ │ │ │ └── bioinf │ │ │ │ ├── ms │ │ │ │ ├── frontend │ │ │ │ │ ├── io │ │ │ │ │ │ ├── ByteRingBufferOutputStream.java │ │ │ │ │ │ └── FileChooserPanel.java │ │ │ │ │ └── splash │ │ │ │ │ │ └── Splash.java │ │ │ │ └── gui │ │ │ │ │ ├── SiriusGui.java │ │ │ │ │ ├── SiriusGuiFactory.java │ │ │ │ │ ├── actions │ │ │ │ │ ├── AbstractGuiAction.java │ │ │ │ │ ├── AbstractUserPortalAction.java │ │ │ │ │ ├── AcceptTermsAction.java │ │ │ │ │ ├── ActionUtils.java │ │ │ │ │ ├── CheckConnectionAction.java │ │ │ │ │ ├── ComputeAction.java │ │ │ │ │ ├── ComputeAllAction.java │ │ │ │ │ ├── CopyIDAction.java │ │ │ │ │ ├── DeleteExperimentAction.java │ │ │ │ │ ├── ExplorerLicRegisterAction.java │ │ │ │ │ ├── FBMNExportAction.java │ │ │ │ │ ├── ImportAction.java │ │ │ │ │ ├── InvertFilterAction.java │ │ │ │ │ ├── OpenInDocsAction.java │ │ │ │ │ ├── OpenLogAction.java │ │ │ │ │ ├── OpenOnlineDocumentationAction.java │ │ │ │ │ ├── OpenPortalAction.java │ │ │ │ │ ├── OpenQuickstartDocumentationAction.java │ │ │ │ │ ├── OrderCompoundByConfidence.java │ │ │ │ │ ├── OrderCompoundById.java │ │ │ │ │ ├── OrderCompoundByMass.java │ │ │ │ │ ├── OrderCompoundByName.java │ │ │ │ │ ├── OrderCompoundByQuality.java │ │ │ │ │ ├── OrderCompoundByRT.java │ │ │ │ │ ├── PasswdResetAction.java │ │ │ │ │ ├── ProjectCreateAction.java │ │ │ │ │ ├── ProjectOpenAction.java │ │ │ │ │ ├── ProjectSaveAction.java │ │ │ │ │ ├── ResetFilterAction.java │ │ │ │ │ ├── SelectActiveSubscriptionAction.java │ │ │ │ │ ├── ShowAboutDialogAction.java │ │ │ │ │ ├── ShowAccountDialog.java │ │ │ │ │ ├── ShowDBDialogAction.java │ │ │ │ │ ├── ShowJobsDialogAction.java │ │ │ │ │ ├── ShowLCMSRunsDialogAction.java │ │ │ │ │ ├── ShowSettingsDialogAction.java │ │ │ │ │ ├── SignInAction.java │ │ │ │ │ ├── SignOutAction.java │ │ │ │ │ ├── SignUpAction.java │ │ │ │ │ ├── SiriusActions.java │ │ │ │ │ ├── SummarizeAllAction.java │ │ │ │ │ ├── SummarizeSelectedAction.java │ │ │ │ │ └── SwitchConfidenceModeAction.java │ │ │ │ │ ├── blank_subtraction │ │ │ │ │ └── BlankSubtraction.java │ │ │ │ │ ├── canopus │ │ │ │ │ └── compound_classes │ │ │ │ │ │ ├── CompoundClassBean.java │ │ │ │ │ │ ├── CompoundClassDetailView.java │ │ │ │ │ │ ├── CompoundClassList.java │ │ │ │ │ │ ├── CompoundClassTableFormat.java │ │ │ │ │ │ └── CompoundClassTableView.java │ │ │ │ │ ├── compute │ │ │ │ │ ├── ActFingerblastConfigPanel.java │ │ │ │ │ ├── ActFingerprintAndCanopusConfigPanel.java │ │ │ │ │ ├── ActFormulaIDConfigPanel.java │ │ │ │ │ ├── ActMSNovelistConfigPanel.java │ │ │ │ │ ├── ActSpectraSearchConfigPanel.java │ │ │ │ │ ├── ActZodiacConfigPanel.java │ │ │ │ │ ├── ActivatableConfigPanel.java │ │ │ │ │ ├── AdditionalElementDialog.java │ │ │ │ │ ├── AdductSelectionList.java │ │ │ │ │ ├── BatchComputeController.java │ │ │ │ │ ├── BatchComputeDialog.java │ │ │ │ │ ├── ComputeActionsPanel.java │ │ │ │ │ ├── ComputePresetAndBannerPanel.java │ │ │ │ │ ├── ComputeToolPanel.java │ │ │ │ │ ├── ConfigPanel.java │ │ │ │ │ ├── DBSelectionList.java │ │ │ │ │ ├── DBSelectionListPanel.java │ │ │ │ │ ├── DummyProgress.java │ │ │ │ │ ├── ElementsPanel.java │ │ │ │ │ ├── FingerblastConfigPanel.java │ │ │ │ │ ├── FingerprintAndCanopusConfigPanel.java │ │ │ │ │ ├── FormulaIDConfigPanel.java │ │ │ │ │ ├── FormulaSearchStrategy.java │ │ │ │ │ ├── FormulaSource.java │ │ │ │ │ ├── GlobalConfigPanel.java │ │ │ │ │ ├── JobDialog.java │ │ │ │ │ ├── ParameterBinding.java │ │ │ │ │ ├── ParameterProvider.java │ │ │ │ │ ├── SpectraSearchConfigPanel.java │ │ │ │ │ ├── SubToolConfigPanel.java │ │ │ │ │ ├── SubToolConfigPanelAdvancedParams.java │ │ │ │ │ ├── ZodiacConfigPanel.java │ │ │ │ │ └── jjobs │ │ │ │ │ │ ├── Jobs.java │ │ │ │ │ │ └── LoadingBackroundTask.java │ │ │ │ │ ├── configs │ │ │ │ │ ├── Buttons.java │ │ │ │ │ ├── ColorGenerator.java │ │ │ │ │ ├── Colors.java │ │ │ │ │ ├── Fonts.java │ │ │ │ │ └── Icons.java │ │ │ │ │ ├── dialogs │ │ │ │ │ ├── AboutDialog.java │ │ │ │ │ ├── CitationDialog.java │ │ │ │ │ ├── CloseDialogNoSaveReturnValue.java │ │ │ │ │ ├── CloseDialogReturnValue.java │ │ │ │ │ ├── CompoundFilterOptionsDialog.java │ │ │ │ │ ├── DialogHeader.java │ │ │ │ │ ├── DoNotShowAgainDialog.java │ │ │ │ │ ├── ElementSelectionDialog.java │ │ │ │ │ ├── ErrorWithDetailsDialog.java │ │ │ │ │ ├── ExceptionDialog.java │ │ │ │ │ ├── ExecutionDialog.java │ │ │ │ │ ├── FilePresentDialog.java │ │ │ │ │ ├── InfoDialog.java │ │ │ │ │ ├── LCMSRunDialog.java │ │ │ │ │ ├── LoadablePanelDialog.java │ │ │ │ │ ├── QuestionDialog.java │ │ │ │ │ ├── SoftwareTourInitialDialog.java │ │ │ │ │ ├── SoftwareTourMessage.java │ │ │ │ │ ├── WarningDialog.java │ │ │ │ │ └── input │ │ │ │ │ │ ├── DragAndDrop.java │ │ │ │ │ │ └── ImportMSDataDialog.java │ │ │ │ │ ├── fingerid │ │ │ │ │ ├── CandidateCellRenderer.java │ │ │ │ │ ├── CandidateListDetailView.java │ │ │ │ │ ├── CandidateListTableHeaderRenderer.java │ │ │ │ │ ├── CandidateListTableView.java │ │ │ │ │ ├── CandidateListView.java │ │ │ │ │ ├── CandidateTableFormat.java │ │ │ │ │ ├── CompoundMatchHighlighter.java │ │ │ │ │ ├── CompoundStructureImage.java │ │ │ │ │ ├── DBFilterPanel.java │ │ │ │ │ ├── DatabaseLabel.java │ │ │ │ │ ├── EmptyLabel.java │ │ │ │ │ ├── ExpansiveSearchLabel.java │ │ │ │ │ ├── FasterSmartsQueryTool.java │ │ │ │ │ ├── FingerprintAgreement.java │ │ │ │ │ ├── FingerprintCandidateBean.java │ │ │ │ │ ├── LipidLabel.java │ │ │ │ │ ├── LoadMoleculeJob.java │ │ │ │ │ ├── SketcherDialog.java │ │ │ │ │ ├── StructureList.java │ │ │ │ │ ├── StructureSearcher.java │ │ │ │ │ ├── candidate_filters │ │ │ │ │ │ ├── CandidateStringMatcherEditor.java │ │ │ │ │ │ ├── DatabaseFilterMatcherEditor.java │ │ │ │ │ │ ├── FMetFilter.java │ │ │ │ │ │ ├── MolecularPropertyMatcherEditor.java │ │ │ │ │ │ └── SmartFilterMatcherEditor.java │ │ │ │ │ ├── custom_db │ │ │ │ │ │ ├── BiotransformerConfigPanel.java │ │ │ │ │ │ ├── DatabaseDialog.java │ │ │ │ │ │ ├── DatabaseImportConfigPanel.java │ │ │ │ │ │ └── ImportDatabaseDialog.java │ │ │ │ │ └── fingerprints │ │ │ │ │ │ ├── FingerIdPropertyBean.java │ │ │ │ │ │ ├── FingerprintList.java │ │ │ │ │ │ ├── FingerprintTableFormat.java │ │ │ │ │ │ ├── FingerprintTableView.java │ │ │ │ │ │ ├── FingerprintVisualization.java │ │ │ │ │ │ ├── MolecularPropertyBean.java │ │ │ │ │ │ └── StructurePreview.java │ │ │ │ │ ├── io │ │ │ │ │ └── filefilter │ │ │ │ │ │ ├── MsBatchDataFormatFilter.java │ │ │ │ │ │ ├── NoSQLProjectFileFilter.java │ │ │ │ │ │ ├── ProjectArchivedFilter.java │ │ │ │ │ │ └── ProjectDirectoryFilter.java │ │ │ │ │ ├── lcms_viewer │ │ │ │ │ ├── LCMSCompoundSummaryPanel.java │ │ │ │ │ ├── LCMSViewerPanel.java │ │ │ │ │ └── TitledIconBorder.java │ │ │ │ │ ├── logging │ │ │ │ │ ├── JobLogDialog.java │ │ │ │ │ ├── LogDialog.java │ │ │ │ │ ├── LoggingPanel.java │ │ │ │ │ ├── TextAreaHandler.java │ │ │ │ │ ├── TextAreaJJobContainer.java │ │ │ │ │ └── TextAreaOutputStream.java │ │ │ │ │ ├── login │ │ │ │ │ ├── AccountDialog.java │ │ │ │ │ ├── AccountPanel.java │ │ │ │ │ ├── SubscriptionDialog.java │ │ │ │ │ ├── SubscriptionHTMLRenderer.java │ │ │ │ │ └── UserLoginDialog.java │ │ │ │ │ ├── mainframe │ │ │ │ │ ├── MainFrame.java │ │ │ │ │ ├── SiriusToolbar.java │ │ │ │ │ ├── WebServiceInfoPanel.java │ │ │ │ │ ├── instance_panel │ │ │ │ │ │ ├── CompoundCellRenderer.java │ │ │ │ │ │ ├── CompoundContextMenu.java │ │ │ │ │ │ ├── CompoundList.java │ │ │ │ │ │ ├── CompoundListView.java │ │ │ │ │ │ ├── ExperimentListChangeListener.java │ │ │ │ │ │ └── FilterableCompoundListPanel.java │ │ │ │ │ └── result_panel │ │ │ │ │ │ ├── LandingPage.java │ │ │ │ │ │ ├── PanelDescription.java │ │ │ │ │ │ ├── ResultPanel.java │ │ │ │ │ │ └── tabs │ │ │ │ │ │ ├── CandidateListDetailViewPanel.java │ │ │ │ │ │ ├── CompoundClassPanel.java │ │ │ │ │ │ ├── DeNovoStructureListDetailViewPanel.java │ │ │ │ │ │ ├── EpimetheusPanel.java │ │ │ │ │ │ ├── FingerprintPanel.java │ │ │ │ │ │ ├── FormulaOverviewPanel.java │ │ │ │ │ │ ├── KendrickMassDefectPanel.java │ │ │ │ │ │ ├── SketcherPanel.java │ │ │ │ │ │ ├── SpectraTreePanel.java │ │ │ │ │ │ ├── SpectralMatchingPanel.java │ │ │ │ │ │ ├── SpectrumAnnotationJJob.java │ │ │ │ │ │ └── SubstructurePanel.java │ │ │ │ │ ├── molecular_formular │ │ │ │ │ ├── FormulaList.java │ │ │ │ │ ├── FormulaListCompactView.java │ │ │ │ │ ├── FormulaListDetailView.java │ │ │ │ │ ├── FormulaListHeaderPanel.java │ │ │ │ │ ├── FormulaListTextCellRenderer.java │ │ │ │ │ └── FormulaResultTableFormat.java │ │ │ │ │ ├── net │ │ │ │ │ ├── ConnectionCheckPanel.java │ │ │ │ │ ├── ConnectionChecks.java │ │ │ │ │ ├── ConnectionDialog.java │ │ │ │ │ └── ConnectionMonitor.java │ │ │ │ │ ├── properties │ │ │ │ │ ├── ConfidenceDisplayMode.java │ │ │ │ │ ├── GuiProperties.java │ │ │ │ │ └── MolecularStructuresDisplayColors.java │ │ │ │ │ ├── settings │ │ │ │ │ ├── AdductSettingsPanel.java │ │ │ │ │ ├── GeneralSettingsPanel.java │ │ │ │ │ ├── ILPSettings.java │ │ │ │ │ ├── NetworkSettingsPanel.java │ │ │ │ │ ├── ProjectSettingsPanel.java │ │ │ │ │ ├── SettingsDialog.java │ │ │ │ │ └── SettingsPanel.java │ │ │ │ │ ├── spectral_matching │ │ │ │ │ ├── SpectralMatchBean.java │ │ │ │ │ ├── SpectralMatchList.java │ │ │ │ │ ├── SpectralMatchTableFormat.java │ │ │ │ │ ├── SpectralMatchingCache.java │ │ │ │ │ └── SpectralMatchingTableView.java │ │ │ │ │ ├── subtools │ │ │ │ │ ├── export │ │ │ │ │ │ └── mgf │ │ │ │ │ │ │ └── MgfExporterConfigPanel.java │ │ │ │ │ └── summaries │ │ │ │ │ │ └── SummaryConfigPanel.java │ │ │ │ │ ├── table │ │ │ │ │ ├── AbstractBarTableCellRenderer.java │ │ │ │ │ ├── ActionList.java │ │ │ │ │ ├── ActionListDetailView.java │ │ │ │ │ ├── ActionListView.java │ │ │ │ │ ├── ActionTable.java │ │ │ │ │ ├── ActiveElementChangedListener.java │ │ │ │ │ ├── ActiveElements.java │ │ │ │ │ ├── BarTableCellRenderer.java │ │ │ │ │ ├── FilterRangeSlider.java │ │ │ │ │ ├── LinkedSiriusTableCellRenderer.java │ │ │ │ │ ├── ListStatBarTableCellRenderer.java │ │ │ │ │ ├── MinMaxMatcherEditor.java │ │ │ │ │ ├── SiriusGlazedLists.java │ │ │ │ │ ├── SiriusListCellRenderer.java │ │ │ │ │ ├── SiriusResultTableCellRenderer.java │ │ │ │ │ ├── SiriusTableCellRenderer.java │ │ │ │ │ ├── SiriusTableFormat.java │ │ │ │ │ ├── StringMatcherEditor.java │ │ │ │ │ └── list_stats │ │ │ │ │ │ ├── DoubleListStats.java │ │ │ │ │ │ └── ListStats.java │ │ │ │ │ ├── update │ │ │ │ │ └── UpdatePanel.java │ │ │ │ │ └── utils │ │ │ │ │ ├── ActionJLabel.java │ │ │ │ │ ├── BooleanJlabel.java │ │ │ │ │ ├── CompactComboBox.java │ │ │ │ │ ├── CompoundFilterMatcher.java │ │ │ │ │ ├── CompoundFilterMatcherEditor.java │ │ │ │ │ ├── CompoundFilterModel.java │ │ │ │ │ ├── DebouncedRunnable.java │ │ │ │ │ ├── DropImage.java │ │ │ │ │ ├── ErrorReportingDocumentListener.java │ │ │ │ │ ├── ErrorReportingInputVerifier.java │ │ │ │ │ ├── GuiUtils.java │ │ │ │ │ ├── HyperlinkJTextPane.java │ │ │ │ │ ├── JListDropImage.java │ │ │ │ │ ├── JTextAreaDropImage.java │ │ │ │ │ ├── MatcherEditorWithOptionalInvert.java │ │ │ │ │ ├── MaxDoubleAsInfinityTextFormatterFactory.java │ │ │ │ │ ├── MessageBanner.java │ │ │ │ │ ├── NameFilterRangeSlider.java │ │ │ │ │ ├── PlaceholderTextField.java │ │ │ │ │ ├── PrecursorIonTypeSelector.java │ │ │ │ │ ├── RelativeLayout.java │ │ │ │ │ ├── ReturnValue.java │ │ │ │ │ ├── SliderWithTextField.java │ │ │ │ │ ├── TextHeaderBoxPanel.java │ │ │ │ │ ├── TextHeaderPanel.java │ │ │ │ │ ├── ThemedAtomColors.java │ │ │ │ │ ├── ToggableSidePanel.java │ │ │ │ │ ├── ToolbarButton.java │ │ │ │ │ ├── ToolbarToggleButton.java │ │ │ │ │ ├── TwoColumnPanel.java │ │ │ │ │ ├── VerticalJLabel.java │ │ │ │ │ ├── WrapLayout.java │ │ │ │ │ ├── jCheckboxList │ │ │ │ │ ├── CheckBoxListItem.java │ │ │ │ │ ├── CheckboxCellRenderer.java │ │ │ │ │ ├── JCheckBoxList.java │ │ │ │ │ └── JCheckboxListPanel.java │ │ │ │ │ ├── loading │ │ │ │ │ ├── JProgressBarPanel.java │ │ │ │ │ ├── LazyLoadingPanel.java │ │ │ │ │ ├── Loadable.java │ │ │ │ │ ├── LoadablePanel.java │ │ │ │ │ ├── ProgressPanel.java │ │ │ │ │ ├── SiriusCardLayout.java │ │ │ │ │ └── SpinnerProgressPanel.java │ │ │ │ │ ├── matchers │ │ │ │ │ └── BackgroundJJobMatcheEditor.java │ │ │ │ │ ├── softwaretour │ │ │ │ │ ├── SoftwareTourInfo.java │ │ │ │ │ ├── SoftwareTourInfoStore.java │ │ │ │ │ └── SoftwareTourUtils.java │ │ │ │ │ └── toggleswitch │ │ │ │ │ ├── swing │ │ │ │ │ └── shadow │ │ │ │ │ │ └── GraphicsUtilities.java │ │ │ │ │ └── toggle │ │ │ │ │ ├── JToggleSwitch.java │ │ │ │ │ ├── ToggleAdapter.java │ │ │ │ │ └── ToggleListener.java │ │ │ │ └── projectspace │ │ │ │ ├── FormulaResultBean.java │ │ │ │ ├── GuiProjectManager.java │ │ │ │ └── InstanceBean.java │ │ ├── eu │ │ │ └── hansolo │ │ │ │ └── rangeslider │ │ │ │ ├── ConicalGradientPaint.java │ │ │ │ ├── RangeSlider.java │ │ │ │ └── RangeSliderUI.java │ │ └── io │ │ │ └── sirius │ │ │ └── ms │ │ │ └── gui │ │ │ └── webView │ │ │ ├── BrowserDialog.java │ │ │ ├── BrowserPanel.java │ │ │ ├── BrowserPanelProvider.java │ │ │ ├── LinkInterception.java │ │ │ ├── WebViewIO.java │ │ │ ├── WebViewUtils.java │ │ │ └── jxbrowser │ │ │ ├── JxBrowserPanel.java │ │ │ └── JxBrowserPanelProvider.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── icons │ │ ├── circular-icons-svg │ │ │ ├── c-add-doc.svg │ │ │ ├── c-bug.svg │ │ │ ├── c-clipboard.svg │ │ │ ├── c-controls-play.svg │ │ │ ├── c-db.svg │ │ │ ├── c-document.svg │ │ │ ├── c-documents.svg │ │ │ ├── c-dragndrop.svg │ │ │ ├── c-export.svg │ │ │ ├── c-fbmn.svg │ │ │ ├── c-filter-down.svg │ │ │ ├── c-filter-up.svg │ │ │ ├── c-fingerprint.svg │ │ │ ├── c-fmet.svg │ │ │ ├── c-folder-close.svg │ │ │ ├── c-folder-file.svg │ │ │ ├── c-folder-open.svg │ │ │ ├── c-folder.svg │ │ │ ├── c-gear.svg │ │ │ ├── c-information.svg │ │ │ ├── c-key.svg │ │ │ ├── c-list-add.svg │ │ │ ├── c-list-edit.svg │ │ │ ├── c-list-remove.svg │ │ │ ├── c-loadAll.svg │ │ │ ├── c-log.svg │ │ │ ├── c-magnify-minus.svg │ │ │ ├── c-magnify-plus.svg │ │ │ ├── c-molecularProperty.svg │ │ │ ├── c-msnovelist.svg │ │ │ ├── c-network-no.svg │ │ │ ├── c-network-warn.svg │ │ │ ├── c-network-yes.svg │ │ │ ├── c-network.svg │ │ │ ├── c-no.svg │ │ │ ├── c-question_blue.svg │ │ │ ├── c-refresh.svg │ │ │ ├── c-remove-doc.svg │ │ │ ├── c-sample.svg │ │ │ ├── c-sirius.svg │ │ │ ├── c-spec-match.svg │ │ │ ├── c-user-no-login.svg │ │ │ ├── c-user.svg │ │ │ ├── c-user_green.svg │ │ │ ├── c-yes.svg │ │ │ ├── c-zodiac.svg │ │ │ ├── db-lens.svg │ │ │ ├── green.svg │ │ │ ├── green_thick_border.svg │ │ │ ├── red.svg │ │ │ ├── red_exclamation-mark.svg │ │ │ ├── red_exclamation-mark_thick_border.svg │ │ │ ├── red_thick_border.svg │ │ │ ├── yellow.svg │ │ │ └── yellow_thick_border.svg │ │ ├── fb_loader.svg │ │ ├── fb_loader@0.5x.gif │ │ ├── landing-page │ │ │ ├── bug2-dark.svg │ │ │ ├── bug2-white.svg │ │ │ ├── docu-dark.svg │ │ │ ├── docu-white.svg │ │ │ ├── download-dark.svg │ │ │ ├── download-white.svg │ │ │ ├── github-dark.svg │ │ │ ├── github-white.svg │ │ │ ├── matrix-dark.svg │ │ │ ├── matrix-white.svg │ │ │ ├── rocket-dark.svg │ │ │ ├── rocket-white.svg │ │ │ ├── sirius-welcome-bg.svg │ │ │ ├── sirius-welcome-white.svg │ │ │ ├── yt-dark.svg │ │ │ └── yt-white.svg │ │ ├── no-results-icon-160.png │ │ ├── nothing-found.png │ │ ├── sirius-wordmark-bg.svg │ │ ├── sirius-wordmark-white.svg │ │ ├── sirius.ico │ │ ├── sirius.png │ │ ├── sirius_icon.png │ │ └── sirius_splash_scribble.gif │ │ ├── js │ │ ├── snow.js │ │ ├── styles-dark.css │ │ └── styles.css │ │ ├── logback.xml │ │ ├── sirius │ │ ├── about.html │ │ ├── feature_examples.tsv │ │ ├── style-dark.css │ │ ├── style-light.css │ │ ├── test.html │ │ └── text.html │ │ └── ttf │ │ ├── DejaVuSans.ttf │ │ ├── Roboto-Bold.ttf │ │ ├── Roboto-BoldItalic.ttf │ │ ├── Roboto-Italic.ttf │ │ ├── Roboto-Medium.ttf │ │ ├── Roboto-MediumItalic.ttf │ │ ├── Roboto-Regular.ttf │ │ └── RobotoMono-Regular.ttf │ └── test │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ ├── io │ │ └── ByteRingBufferOutputStreamTest.java │ │ └── jjobs │ │ └── SiriusJobsTest.java │ └── resources │ ├── example_tree.json │ └── treeviewer.html ├── sirius_project_space ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── projectspace │ │ ├── CandidateSummarizer.java │ │ ├── ComponentSerializer.java │ │ ├── CompoundContainer.java │ │ ├── CompoundContainerId.java │ │ ├── CompoundContainerIterator.java │ │ ├── CompoundContainerSerializer.java │ │ ├── CompressionFormat.java │ │ ├── ContainerEvent.java │ │ ├── ContainerListener.java │ │ ├── ContainerSerializer.java │ │ ├── FileSystemManager.java │ │ ├── FilenameFormatter.java │ │ ├── FormulaResult.java │ │ ├── FormulaResultId.java │ │ ├── FormulaResultSerializer.java │ │ ├── FormulaScoring.java │ │ ├── FormulaScoringSerializer.java │ │ ├── LCMSPeakSerializer.java │ │ ├── Location.java │ │ ├── MsExperimentSerializer.java │ │ ├── PSLocations.java │ │ ├── PathProjectSpaceIO.java │ │ ├── PathProjectSpaceIOProvider.java │ │ ├── PathProjectSpaceReader.java │ │ ├── PathProjectSpaceWriter.java │ │ ├── PosNegFpProperty.java │ │ ├── PosNegProperty.java │ │ ├── ProgressListener.java │ │ ├── ProjectIO.java │ │ ├── ProjectIOProvider.java │ │ ├── ProjectReader.java │ │ ├── ProjectSpaceConfig.java │ │ ├── ProjectSpaceConfigSerializer.java │ │ ├── ProjectSpaceConfiguration.java │ │ ├── ProjectSpaceContainer.java │ │ ├── ProjectSpaceContainerId.java │ │ ├── ProjectSpaceEvent.java │ │ ├── ProjectSpaceIO.java │ │ ├── ProjectSpaceListener.java │ │ ├── ProjectWriter.java │ │ ├── SerializerParameter.java │ │ ├── SiriusLocations.java │ │ ├── SiriusProjectSpace.java │ │ ├── SpectralSearchLocations.java │ │ ├── StackedProgressListener.java │ │ ├── StandardMSFilenameFormatter.java │ │ ├── Summarizer.java │ │ ├── TemporaryProjectSpaceCleanUp.java │ │ ├── TreeSerializer.java │ │ ├── VersionInfo.java │ │ ├── Zip4JProjectSpaceIO.java │ │ ├── Zip4JProjectSpaceIOProvider.java │ │ ├── Zip4JProjectSpaceReader.java │ │ ├── Zip4JProjectSpaceWriter.java │ │ ├── Zip4jvmProjectSpaceIO.java │ │ ├── Zip4jvmProjectSpaceIOProvider.java │ │ ├── Zip4jvmProjectSpaceReader.java │ │ ├── Zip4jvmProjectSpaceWriter.java │ │ ├── ZipFSProjectSpaceIOProvider.java │ │ └── ZipProvider.java │ └── resources │ └── LICENSE.txt ├── sirius_rest_service ├── .gitignore ├── README.md ├── build.gradle ├── openapi-spec-enums-as-ref.json ├── openapi-spec-enums-as-string.json └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── ms │ │ │ ├── backgroundruns │ │ │ ├── BackgroundRuns.java │ │ │ ├── BlankSubtractionWorkflow.java │ │ │ ├── ComputeRootOption.java │ │ │ ├── FoldChangeWorkflow.java │ │ │ ├── ImportMsFromResourceWorkflow.java │ │ │ └── ImportPeaksFomResourceWorkflow.java │ │ │ ├── frontend │ │ │ └── subtools │ │ │ │ └── middleware │ │ │ │ └── MiddlewareAppOptions.java │ │ │ └── middleware │ │ │ ├── ProxyDisconnector.java │ │ │ ├── SiriusContext.java │ │ │ ├── SiriusMiddlewareApplication.java │ │ │ ├── configuration │ │ │ ├── GlobalConfig.java │ │ │ ├── SwaggerConfig.java │ │ │ └── project │ │ │ │ └── NitriteNoSqlProjectConfig.java │ │ │ ├── controller │ │ │ ├── AlignedFeatureController.java │ │ │ ├── AlignedFeatureStatisticsController.java │ │ │ ├── CompoundController.java │ │ │ ├── CompoundStatisticsController.java │ │ │ ├── GuiController.java │ │ │ ├── GuiControllerAdvanced.java │ │ │ ├── InfoController.java │ │ │ ├── JobController.java │ │ │ ├── LoginController.java │ │ │ ├── ProjectController.java │ │ │ ├── RedirectController.java │ │ │ ├── RunController.java │ │ │ ├── SearchableDatabaseController.java │ │ │ ├── SseController.java │ │ │ ├── TagController.java │ │ │ ├── WebAppController.java │ │ │ └── mixins │ │ │ │ ├── ComputeServiceController.java │ │ │ │ ├── ProjectProvidingController.java │ │ │ │ ├── StatisticsController.java │ │ │ │ └── TaggableController.java │ │ │ ├── model │ │ │ ├── MultipartInputResource.java │ │ │ ├── annotations │ │ │ │ ├── BinaryFingerprint.java │ │ │ │ ├── CanopusLevels.java │ │ │ │ ├── CanopusPrediction.java │ │ │ │ ├── CompoundClass.java │ │ │ │ ├── CompoundClasses.java │ │ │ │ ├── ConsensusAnnotations.java │ │ │ │ ├── ConsensusAnnotationsCSI.java │ │ │ │ ├── ConsensusAnnotationsDeNovo.java │ │ │ │ ├── FeatureAnnotations.java │ │ │ │ ├── FormulaCandidate.java │ │ │ │ ├── FragmentNode.java │ │ │ │ ├── FragmentationTree.java │ │ │ │ ├── IsotopePatternAnnotation.java │ │ │ │ ├── LipidAnnotation.java │ │ │ │ ├── LossEdge.java │ │ │ │ ├── SpectralLibraryMatch.java │ │ │ │ ├── SpectralLibraryMatchSummary.java │ │ │ │ ├── StructureCandidate.java │ │ │ │ ├── StructureCandidateFormula.java │ │ │ │ └── StructureCandidateScored.java │ │ │ ├── compounds │ │ │ │ ├── Compound.java │ │ │ │ └── CompoundImport.java │ │ │ ├── compute │ │ │ │ ├── AbstractImportSubmission.java │ │ │ │ ├── AbstractSubmission.java │ │ │ │ ├── CommandSubmission.java │ │ │ │ ├── ImportLocalFilesSubmission.java │ │ │ │ ├── ImportMultipartFilesSubmission.java │ │ │ │ ├── InstrumentProfile.java │ │ │ │ ├── Job.java │ │ │ │ ├── JobEffect.java │ │ │ │ ├── JobProgress.java │ │ │ │ ├── JobSubmission.java │ │ │ │ ├── LcmsSubmissionParameters.java │ │ │ │ ├── NullCheckMapBuilder.java │ │ │ │ ├── StoredJobSubmission.java │ │ │ │ └── tools │ │ │ │ │ ├── Canopus.java │ │ │ │ │ ├── FingerprintPrediction.java │ │ │ │ │ ├── MsNovelist.java │ │ │ │ │ ├── Sirius.java │ │ │ │ │ ├── SpectralLibrarySearch.java │ │ │ │ │ ├── StructureDbSearch.java │ │ │ │ │ ├── Tool.java │ │ │ │ │ └── Zodiac.java │ │ │ ├── databases │ │ │ │ ├── BioTransformerParameters.java │ │ │ │ ├── SearchableDatabase.java │ │ │ │ ├── SearchableDatabaseParameters.java │ │ │ │ └── SearchableDatabases.java │ │ │ ├── events │ │ │ │ ├── BackgroundComputationsStateEvent.java │ │ │ │ ├── DataImportEvent.java │ │ │ │ ├── ProjectChangeEvent.java │ │ │ │ ├── ProjectEventType.java │ │ │ │ ├── ServerEvent.java │ │ │ │ ├── ServerEventImpl.java │ │ │ │ └── ServerEvents.java │ │ │ ├── features │ │ │ │ ├── AlignedFeature.java │ │ │ │ ├── AlignedFeatureQuality.java │ │ │ │ ├── AnnotatedMsMsData.java │ │ │ │ ├── Feature.java │ │ │ │ ├── FeatureImport.java │ │ │ │ ├── FeatureImports.java │ │ │ │ ├── LCMSFeatureQuality.java │ │ │ │ ├── MsData.java │ │ │ │ ├── QuantRowType.java │ │ │ │ ├── QuantTable.java │ │ │ │ ├── Run.java │ │ │ │ └── TraceSet.java │ │ │ ├── gui │ │ │ │ ├── GuiInfo.java │ │ │ │ ├── GuiParameters.java │ │ │ │ └── GuiResultTab.java │ │ │ ├── info │ │ │ │ ├── Info.java │ │ │ │ └── LicenseInfo.java │ │ │ ├── login │ │ │ │ ├── AccountCredentials.java │ │ │ │ ├── AccountInfo.java │ │ │ │ └── Subscription.java │ │ │ ├── networks │ │ │ │ └── AdductNetwork.java │ │ │ ├── projects │ │ │ │ ├── ImportResult.java │ │ │ │ └── ProjectInfo.java │ │ │ ├── spectra │ │ │ │ ├── AbstractSpectrum.java │ │ │ │ ├── AnnotatedPeak.java │ │ │ │ ├── AnnotatedSpectrum.java │ │ │ │ ├── BasicSpectrum.java │ │ │ │ ├── ParentPeak.java │ │ │ │ ├── PeakAnnotation.java │ │ │ │ ├── SpectrumAnnotation.java │ │ │ │ └── Spectrums.java │ │ │ ├── statistics │ │ │ │ ├── FoldChange.java │ │ │ │ ├── SampleTypeFoldChangeRequest.java │ │ │ │ ├── Statistics.java │ │ │ │ ├── StatisticsTable.java │ │ │ │ └── StatisticsType.java │ │ │ └── tags │ │ │ │ ├── Tag.java │ │ │ │ ├── TagDefinition.java │ │ │ │ ├── TagDefinitionImport.java │ │ │ │ └── TagGroup.java │ │ │ ├── security │ │ │ ├── Authorities.java │ │ │ ├── SecurityConfig.java │ │ │ ├── exceptions │ │ │ │ ├── ExceptionErrorResponseHandler.java │ │ │ │ └── FieldValidationError.java │ │ │ ├── filters │ │ │ │ ├── AddBypassAuthoritiesFilter.java │ │ │ │ ├── AddFeatureAuthoritiesFilter.java │ │ │ │ ├── BypassRule.java │ │ │ │ ├── ExceptionHandlerFilter.java │ │ │ │ └── WebApiAuthenticationProviderFilter.java │ │ │ └── validation │ │ │ │ └── ImportFormatValidationService.java │ │ │ └── service │ │ │ ├── annotations │ │ │ └── AnnotationUtils.java │ │ │ ├── compute │ │ │ ├── ComputeService.java │ │ │ └── ComputeServiceImpl.java │ │ │ ├── databases │ │ │ ├── ChemDbService.java │ │ │ └── ChemDbServiceImpl.java │ │ │ ├── events │ │ │ ├── EventService.java │ │ │ └── SseEventService.java │ │ │ ├── gui │ │ │ ├── GuiService.java │ │ │ └── GuiServiceImpl.java │ │ │ ├── info │ │ │ └── ConnectionChecker.java │ │ │ ├── job │ │ │ └── JobConfigService.java │ │ │ ├── lucene │ │ │ └── LuceneUtils.java │ │ │ ├── projects │ │ │ ├── NoSQLProjectImpl.java │ │ │ ├── NoSQLProjectProviderImpl.java │ │ │ ├── Project.java │ │ │ ├── ProjectSpaceManagerProvider.java │ │ │ └── ProjectsProvider.java │ │ │ └── search │ │ │ ├── FakeLuceneSearchService.java │ │ │ └── SearchService.java │ └── resources │ │ ├── LICENSE.txt │ │ ├── application.properties │ │ ├── favicon.ico │ │ └── templates │ │ ├── hello-world │ │ └── index.html │ │ └── sirius_java_integrated │ │ ├── Roboto-Regular.woff2 │ │ ├── assets │ │ ├── emotion-react-jsx-runtime.browser.esm-CQXaw_9w.js │ │ ├── index-Bc9u8EZp.js │ │ ├── index-C9AU78VZ.css │ │ ├── index.modern-1f95b312-C8WPG42H.js │ │ └── index.modern-C19uPkWI.js │ │ └── index.html │ └── test │ ├── java │ ├── FragmentationTreeTest.java │ ├── NoSQLProjectTest.java │ ├── SpectrumsTest.java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── ms │ │ └── middleware │ │ └── model │ │ └── compute │ │ └── JobSubmissionTest.java │ └── resources │ └── data │ └── C14H12N2O4 │ ├── C14H12N2O4_M+H+.json │ ├── C14H12N2O4_M+NH4+.json │ ├── C14H12N2O4_M-H2O+H+.json │ ├── merged_ms2.json │ └── ms-data.json ├── spectral_alignment ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bionf │ │ │ ├── fastcosine │ │ │ ├── FastCosine.java │ │ │ ├── SearchPreparedMergedSpectrum.java │ │ │ └── SearchPreparedSpectrum.java │ │ │ └── spectral_alignment │ │ │ ├── AbstractSpectralMatching.java │ │ │ ├── AllowedMassDifference.java │ │ │ ├── CosineQuerySpectrum.java │ │ │ ├── CosineQueryUtils.java │ │ │ ├── CosineSpectraMatcher.java │ │ │ ├── GaussianSpectralMatching.java │ │ │ ├── IntensityWeightedSpectralAlignment.java │ │ │ ├── ModifiedCosine.java │ │ │ ├── OrderedSpectraMatcher.java │ │ │ ├── RecallSpectralAlignment.java │ │ │ ├── SpectralMatchJJob.java │ │ │ ├── SpectralMatchMasterJJob.java │ │ │ ├── SpectralMatchingType.java │ │ │ ├── SpectralSimilarity.java │ │ │ └── WeightedRecallSpectralAlignment.java │ └── resources │ │ └── LICENSE.txt │ └── test │ └── java │ └── de │ └── unijena │ └── bionf │ ├── fastcosine │ ├── FastCosineBoundTest.java │ └── FastCosineTest.java │ └── spectral_alignment │ ├── RecallSpectralAlignmentTest.java │ ├── SpectralAlignmentTest.java │ ├── SpectralMatchingTest.java │ └── SpectralMatchingTypeTest.java ├── structure_matching ├── build.gradle ├── res │ └── SideChainLists │ │ ├── sideChains.txt │ │ └── sideChains2.txt └── src │ ├── main │ └── java │ │ ├── evaluate │ │ ├── Evaluation.java │ │ ├── FileMoleculesMatcher.java │ │ └── Main.java │ │ └── matching │ │ ├── algorithm │ │ ├── EDIC.java │ │ ├── ElectronPairWiseEDIC.java │ │ ├── MCESDist2.java │ │ ├── Matcher.java │ │ ├── MatcherFactory.java │ │ └── MinimalWeightedPlacements.java │ │ ├── datastructures │ │ ├── AtomContainerE.java │ │ ├── AtomE.java │ │ ├── Pair.java │ │ ├── SideChain.java │ │ └── SideChainList.java │ │ ├── io │ │ └── SideChainListReader.java │ │ └── utils │ │ ├── HungarianAlgorithm.java │ │ └── MoleculeManipulator.java │ └── test │ ├── java │ ├── ElectronPairWiseEDICTest.java │ ├── HungarianAlgorithmTest.java │ ├── MCESDist2Test.java │ ├── MinimalWeightedPlacementsTest.java │ ├── MoleculeManipulatorTest.java │ └── SideChainListReaderTest.java │ └── resources │ ├── sideChains.txt │ └── sideChainsTest.txt ├── tree_motif_search ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── treemotifs │ │ └── model │ │ ├── MotifDbFile.java │ │ ├── MotifMatch.java │ │ ├── TreeMotif.java │ │ ├── TreeMotifDB.java │ │ └── TreeMotifPlugin.java │ └── resources │ ├── LICENSE.txt │ └── de.unijena.bioinf.ms.defaults │ ├── tree_motif_search.auto.config │ └── tree_motif_search.class.map ├── utils ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ └── utils │ │ │ ├── PrimsSpanningTree.java │ │ │ ├── SiriusTestDataManager.java │ │ │ └── clustering │ │ │ ├── ClusteringTree.java │ │ │ ├── CompleteLinkage.java │ │ │ ├── Distance.java │ │ │ ├── DistanceMeasureStrategy.java │ │ │ └── HierarchicalClustering.java │ └── resources │ │ └── LICENSE.txt │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── utils │ ├── PrimSpanningTreeTest.java │ └── clustering │ └── HierarchicalClusteringTest.java └── web_service_oss ├── build.gradle ├── client_auth_oss ├── build.gradle └── src │ └── main │ └── java │ ├── com │ └── github │ │ └── scribejava │ │ └── apis │ │ ├── Auth0Api.java │ │ └── auth0 │ │ └── Auth0Service.java │ └── de │ └── unijena │ └── bioinf │ └── auth │ ├── AuthService.java │ ├── AuthServices.java │ ├── LoginException.java │ └── UserPortal.java ├── jwt_utils ├── build.gradle └── src │ ├── main │ └── java │ │ └── io │ │ └── sirius │ │ └── ms │ │ └── utils │ │ └── jwt │ │ ├── AccessTokens.java │ │ ├── IdTokens.java │ │ ├── JwtTokenFactory.java │ │ ├── JwtTokenFactoryImpl.java │ │ ├── TokenType.java │ │ ├── TokenWrapper.java │ │ ├── Tokens.java │ │ ├── auth │ │ └── AuthServiceJwtToken.java │ │ ├── auth0 │ │ └── Auth0JwtToken.java │ │ ├── claims │ │ ├── ClaimKey.java │ │ └── StandardClaimKeys.java │ │ └── spring │ │ └── SpringJwtToken.java │ └── test │ └── java │ └── io │ └── sirius │ └── ms │ └── utils │ └── jwt │ ├── AccessTokensTest.java │ ├── Auth0JwtTokenTest.java │ ├── IdTokensTest.java │ └── JwtTokenFactoryImplTest.java ├── rest_client_oss ├── build.gradle └── src │ └── main │ ├── java │ └── de │ │ └── unijena │ │ └── bioinf │ │ └── ms │ │ └── rest │ │ └── client │ │ ├── AbstractClient.java │ │ ├── AbstractCsiClient.java │ │ ├── account │ │ └── AccountClient.java │ │ ├── canopus │ │ └── CanopusClient.java │ │ ├── chemdb │ │ ├── ChemDBClient.java │ │ └── StructureSearchClient.java │ │ ├── fingerid │ │ └── FingerIdClient.java │ │ ├── info │ │ └── InfoClient.java │ │ ├── jobs │ │ └── JobsClient.java │ │ └── utils │ │ ├── HTTPFunction.java │ │ └── HTTPSupplier.java │ └── resources │ └── LICENSE.txt ├── scribejava-httpclient-apache5 ├── build.gradle └── src │ └── main │ └── java │ └── com │ └── github │ └── scribejava │ └── httpclient │ └── apache │ ├── ApacheHttpClient.java │ ├── ApacheHttpClientConfig.java │ ├── ApacheHttpFuture.java │ ├── ApacheProvider.java │ └── OAuthAsyncCompletionHandler.java ├── sirius_web_client ├── build.gradle └── src │ ├── main │ ├── java │ │ └── de │ │ │ └── unijena │ │ │ └── bioinf │ │ │ ├── chemdb │ │ │ ├── FingerblastSearchEngine.java │ │ │ ├── WebWithCustomDatabase.java │ │ │ ├── annotations │ │ │ │ ├── FormulaSearchDB.java │ │ │ │ ├── SearchableDBAnnotation.java │ │ │ │ ├── SpectralSearchDB.java │ │ │ │ └── StructureSearchDB.java │ │ │ └── custom │ │ │ │ ├── CustomDatabaseImporter.java │ │ │ │ ├── CustomDatabases.java │ │ │ │ ├── DatabaseNameAlreadyExistsException.java │ │ │ │ └── UnsupportedDatabaseNameException.java │ │ │ ├── fingerid │ │ │ ├── AbstractStructurePredictor.java │ │ │ ├── AddExternalStructureJJob.java │ │ │ ├── CSIPredictor.java │ │ │ ├── CanopusWebResultConverter.java │ │ │ ├── ConfidenceJJob.java │ │ │ ├── ConfidenceResult.java │ │ │ ├── ConfidenceScore.java │ │ │ ├── ConfidenceScoreApproximate.java │ │ │ ├── CovtreeWebResultConverter.java │ │ │ ├── DeNovoStructureUtils.java │ │ │ ├── FingerIdResult.java │ │ │ ├── FingerblastJJob.java │ │ │ ├── FingerblastSearchJJob.java │ │ │ ├── FingerprintDependentJJob.java │ │ │ ├── FingerprintJJob.java │ │ │ ├── FingerprintPreprocessingJJob.java │ │ │ ├── FingerprintResult.java │ │ │ ├── FingerprintWebResultConverter.java │ │ │ ├── FormulaJob.java │ │ │ ├── FormulaWhiteListJob.java │ │ │ ├── IOKRPredictor.java │ │ │ ├── MCESJJob.java │ │ │ ├── MsNovelistFingerblastJJob.java │ │ │ ├── MsNovelistFingerblastResult.java │ │ │ ├── StructurePredictor.java │ │ │ ├── StructureSearchResult.java │ │ │ ├── SubstructureAnnotationJJob.java │ │ │ ├── SubstructureAnnotationResult.java │ │ │ ├── TrainingStructuresPerPredictor.java │ │ │ ├── TrainingStructuresSet.java │ │ │ └── annotations │ │ │ │ ├── FormulaResultThreshold.java │ │ │ │ └── NumberOfStructureCandidates.java │ │ │ ├── spectraldb │ │ │ ├── IndexedQuerySpectrumWrapper.java │ │ │ ├── InjectSpectralLibraryMatchFormulas.java │ │ │ ├── Ms2ReferenceSpectrumWrapper.java │ │ │ ├── SpectraMatchingJJob.java │ │ │ ├── SpectralSearchResult.java │ │ │ ├── SpectralSearchResultSerializer.java │ │ │ └── SpectralSearchResults.java │ │ │ └── webapi │ │ │ ├── AbstractWebAPI.java │ │ │ ├── WebAPI.java │ │ │ └── rest │ │ │ ├── RestAPI.java │ │ │ ├── RestWebJJob.java │ │ │ └── WebJobWatcher.java │ └── resources │ │ ├── LICENSE.txt │ │ └── de.unijena.bioinf.ms.defaults │ │ ├── sirius_web_client.auto.config │ │ └── sirius_web_client.class.map │ └── test │ └── java │ └── de │ └── unijena │ └── bioinf │ └── spectraldb │ └── SpectraMatchingJJobTest.java └── web_core_oss ├── build.gradle └── src └── main ├── java └── de │ └── unijena │ └── bioinf │ ├── ms │ ├── rest │ │ └── model │ │ │ ├── Job.java │ │ │ ├── JobBase.java │ │ │ ├── JobId.java │ │ │ ├── JobInputs.java │ │ │ ├── JobState.java │ │ │ ├── JobTable.java │ │ │ ├── JobUpdate.java │ │ │ ├── JobUpdateDeserializer.java │ │ │ ├── JobWithPredictor.java │ │ │ ├── LicensingException.java │ │ │ ├── ProblemResponse.java │ │ │ ├── ProblemResponses.java │ │ │ ├── SecurityService.java │ │ │ ├── WorkerType.java │ │ │ ├── canopus │ │ │ ├── CanopusCfData.java │ │ │ ├── CanopusJob.java │ │ │ ├── CanopusJobInput.java │ │ │ ├── CanopusJobOutput.java │ │ │ └── CanopusNpcData.java │ │ │ ├── covtree │ │ │ ├── CovtreeJob.java │ │ │ ├── CovtreeJobInput.java │ │ │ └── CovtreeJobOutput.java │ │ │ ├── fingerid │ │ │ ├── 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