Preview

boecker-lab-sirius-libs-0980134
- .gitignore
  
  327 Bytes
- .gitlab-ci.yml
  
  470 Bytes
- LICENSE
  
  35.1 kB
- README.md
  
  56.9 kB
- build.gradle
  
  4.3 kB
- chemistry_base
  - .gitignore
    
    52 Bytes
  - build.gradle
    
    745 Bytes
  - src
    - main
      - java
        
        de
        
        unijena
        
        bioinf
        
        ChemistryBase
        
        SimpleRectangularIsolationWindow.java
        
        1.6 kB
        
        algorithm
        
        Async.java
        
        5.5 kB
        
        BoundedDoubleQueue.java
        
        2.4 kB
        
        Called.java
        
        1.3 kB
        
        FastReadWriteLock.java
        
        3.0 kB
        
        Functor0.java
        
        371 Bytes
        
        HasAnnotationMap.java
        
        1.5 kB
        
        HasParameters.java
        
        1.0 kB
        
        ImmutableParameterized.java
        
        1.2 kB
        
        Parameter.java
        
        1.0 kB
        
        ParameterHelper.java
        
        10.2 kB
        
        Parameterized.java
        
        1.2 kB
        
        ParameterizedByAnnotation.java
        
        9.4 kB
        
        Ranking.java
        
        5.7 kB
        
        Scored.java
        
        1.1 kB
        
        WriteIntoDataDocument.java
        
        1.1 kB
        
        chem
        
        Charge.java
        
        2.0 kB
        
        ChemicalAlphabet.java
        
        7.5 kB
        
        CompoundWithAbstractFP.java
        
        561 Bytes
        
        ElectronIonization.java
        
        1.3 kB
        
        Element.java
        
        3.1 kB
        
        FormulaConstraints.java
        
        22.9 kB
        
        FormulaFilter.java
        
        986 Bytes
        
        ImmutableMolecularFormula.java
        
        2.7 kB
        
        InChI.java
        
        2.1 kB
        
        IonMode.java
        
        2.8 kB
        
        Ionization.java
        
        3.9 kB
        
        Isotopes.java
        
        4.0 kB
        
        MolecularFormula.java
        
        34.6 kB
        
        MutableMolecularFormula.java
        
        5.2 kB
        
        PeriodicTable.java
        
        48.7 kB
        
        PrecursorIonType.java
        
        10.6 kB
        
        RetentionTime.java
        
        1.9 kB
        
        Smiles.java
        
        1.0 kB
        
        TableSelection.java
        
        9.7 kB
        
        TableSelectionCache.java
        
        4.3 kB
        
        utils
        
        Contaminants.java
        
        4.2 kB
        
        DistributionReader.java
        
        1.4 kB
        
        ElementMap.java
        
        7.1 kB
        
        FormulaEncodingError.java
        
        1.7 kB
        
        FormulaFilterList.java
        
        2.8 kB
        
        FormulaVisitor.java
        
        1.2 kB
        
        IsotopicDistribution.java
        
        4.5 kB
        
        IsotopicDistributionBlueObeliskReader.java
        
        5.2 kB
        
        IsotopicDistributionJSONFile.java
        
        2.3 kB
        
        MolecularFormulaPacker.java
        
        20.3 kB
        
        MolecularFormulaPool.java
        
        1.0 kB
        
        MolecularFormulaScorer.java
        
        1.1 kB
        
        MolecularFormulaSet.java
        
        11.0 kB
        
        PeriodicTableBlueObeliskReader.java
        
        6.3 kB
        
        PeriodicTableJSONReader.java
        
        3.2 kB
        
        PeriodicTableReader.java
        
        1.5 kB
        
        ValenceFilter.java
        
        2.0 kB
        
        biotransformation
        
        BioTransformation.java
        
        7.6 kB
        
        BioTransformer.java
        
        2.8 kB
        
        scoring
        
        ChemicalCompoundScorer.java
        
        6.2 kB
        
        DNNFormulaScorer.java
        
        1.7 kB
        
        FormulaFeatureVector.java
        
        19.7 kB
        
        Hetero2CarbonScorer.java
        
        3.4 kB
        
        Hydrogen2CarbonScorer.java
        
        3.0 kB
        
        ImprovedHetero2CarbonScorer.java
        
        3.0 kB
        
        RDBEMassScorer.java
        
        4.5 kB
        
        RDBENormalScorer.java
        
        2.1 kB
        
        SpecialMoleculeScorer.java
        
        3.0 kB
        
        SupportVectorMolecularFormulaScorer.java
        
        21.6 kB
        
        data
        
        DataDocument.java
        
        12.0 kB
        
        DocumentFormatable.java
        
        953 Bytes
        
        DoubleDataMatrix.java
        
        16.3 kB
        
        JDKDocument.java
        
        4.7 kB
        
        TypeError.java
        
        1.3 kB
        
        exceptions
        
        InsufficientDataException.java
        
        718 Bytes
        
        InvalidInputData.java
        
        1.2 kB
        
        MultipleChargeException.java
        
        199 Bytes
        
        fp
        
        AbstractFingerprint.java
        
        3.9 kB
        
        ArrayFingerprint.java
        
        17.4 kB
        
        BooleanFingerprint.java
        
        10.1 kB
        
        CdkFingerprintVersion.java
        
        15.8 kB
        
        ClassyFireFingerprintVersion.java
        
        2.9 kB
        
        ClassyfireProperty.java
        
        1.1 kB
        
        CustomFingerprintVersion.java
        
        1.1 kB
        
        ExtendedConnectivityProperty.java
        
        17.2 kB
        
        FPIter.java
        
        2.6 kB
        
        FPIter2.java
        
        389 Bytes
        
        Fingerprint.java
        
        3.2 kB
        
        FingerprintVersion.java
        
        693 Bytes
        
        FormulaProperty.java
        
        573 Bytes
        
        MaskedFingerprintVersion.java
        
        10.6 kB
        
        MolecularProperty.java
        
        136 Bytes
        
        PredictionPerformance.java
        
        10.4 kB
        
        ProbabilityFingerprint.java
        
        12.6 kB
        
        ShortestPathProperty.java
        
        654 Bytes
        
        SpecialMolecularProperty.java
        
        783 Bytes
        
        SubstructureCountProperty.java
        
        850 Bytes
        
        SubstructureProperty.java
        
        726 Bytes
        
        Tanimoto.java
        
        10.4 kB
        
        jobs
        
        SiriusJobs.java
        
        1.9 kB
        
        math
        
        ByMedianEstimatable.java
        
        952 Bytes
        
        DensityFunction.java
        
        911 Bytes
        
        ExponentialDistribution.java
        
        3.1 kB
        
        HighQualityRandom.java
        
        2.1 kB
        
        IsRealDistributed.java
        
        1.1 kB
        
        LogNormalDistribution.java
        
        2.7 kB
        
        MathUtils.java
        
        32.4 kB
        
        NormalDistribution.java
        
        2.4 kB
        
        ParetoDistribution.java
        
        4.6 kB
        
        PartialNormalDistribution.java
        
        1.7 kB
        
        PartialParetoDistribution.java
        
        2.5 kB
        
        RealDistribution.java
        
        2.3 kB
        
        Statistics.java
        
        8.2 kB
        
        ms
        
        AnnotatedPeak.java
        
        3.9 kB
        
        CollisionEnergy.java
        
        4.4 kB
        
        CompoundQuality.java
        
        5.2 kB
        
        DatasetStatistics.java
        
        432 Bytes
        
        Deviation.java
        
        4.2 kB
        
        EIIntensityDeviation.java
        
        4.2 kB
        
        EstimatedIsolationWindow.java
        
        4.6 kB
        
        FixedDatasetStatistics.java
        
        2.7 kB
        
        ImmutableIsolationWindow.java
        
        1.1 kB
        
        IsolationWindow.java
        
        40.3 kB
        
        MeasurementProfile.java
        
        1.9 kB
        
        MergedMs2Spectrum.java
        
        429 Bytes
        
        Ms2Dataset.java
        
        571 Bytes
        
        Ms2Experiment.java
        
        5.8 kB
        
        Ms2Spectrum.java
        
        1.5 kB
        
        MsInstrumentation.java
        
        3.2 kB
        
        MutableDatasetStatistics.java
        
        4.2 kB
        
        MutableMeasurementProfile.java
        
        8.4 kB
        
        MutableMs2Dataset.java
        
        4.2 kB
        
        MutableMs2Experiment.java
        
        6.2 kB
        
        MutableMs2Spectrum.java
        
        3.4 kB
        
        MutableSpectrum.java
        
        1.2 kB
        
        MzRTPeak.java
        
        1.5 kB
        
        Normalization.java
        
        3.3 kB
        
        NormalizationMode.java
        
        1.6 kB
        
        Peak.java
        
        2.1 kB
        
        PossibleAdducts.java
        
        3.5 kB
        
        PossibleIonModes.java
        
        10.9 kB
        
        Precursor.java
        
        1.6 kB
        
        Spectrum.java
        
        2.0 kB
        
        SpectrumProperty.java
        
        241 Bytes
        
        Splash.java
        
        244 Bytes
        
        ft
        
        AbstractFragmentationGraph.java
        
        22.6 kB
        
        Beautified.java
        
        863 Bytes
        
        FGraph.java
        
        20.2 kB
        
        FTree.java
        
        11.1 kB
        
        Fragment.java
        
        6.2 kB
        
        FragmentAnnotation.java
        
        2.7 kB
        
        InsourceFragmentation.java
        
        384 Bytes
        
        IonTreeUtils.java
        
        9.9 kB
        
        IsotopicMarker.java
        
        468 Bytes
        
        Loss.java
        
        3.2 kB
        
        LossAnnotation.java
        
        2.6 kB
        
        Ms1IsotopePattern.java
        
        815 Bytes
        
        Ms2IsotopePattern.java
        
        428 Bytes
        
        RecalibrationFunction.java
        
        3.2 kB
        
        Score.java
        
        4.2 kB
        
        TreeScoring.java
        
        5.3 kB
        
        UnconsideredCandidatesUpperBound.java
        
        988 Bytes
        
        ZodiacScore.java
        
        273 Bytes
        
        model
        
        FormulaSettings.java
        
        3.4 kB
        
        inputValidators
        
        ChimericAnnotator.java
        
        7.4 kB
        
        EmptySpectraValidator.java
        
        1.5 kB
        
        FewPeaksAnnotator.java
        
        4.7 kB
        
        InvalidException.java
        
        989 Bytes
        
        LowIntensityAnnotator.java
        
        2.6 kB
        
        MissingMergedSpectrumValidator.java
        
        5.3 kB
        
        Ms2DatasetValidator.java
        
        370 Bytes
        
        Ms2ExperimentValidator.java
        
        1.1 kB
        
        MultipleChargedAnnotator.java
        
        743 Bytes
        
        NoMs1PeakAnnotator.java
        
        2.4 kB
        
        NotMonoisotopicAnnotator.java
        
        3.3 kB
        
        QualityAnnotator.java
        
        511 Bytes
        
        Warning.java
        
        1.2 kB
        
        utils
        
        AbstractSpectrum.java
        
        2.9 kB
        
        ArrayWrapperSpectrum.java
        
        3.6 kB
        
        BasicMutableSpectrum.java
        
        3.6 kB
        
        BasicSpectrum.java
        
        1.7 kB
        
        ChargedPeak.java
        
        1.6 kB
        
        ChargedSpectrum.java
        
        2.0 kB
        
        MsExperiments.java
        
        5.7 kB
        
        OrderedSpectrum.java
        
        1.1 kB
        
        PeaklistSpectrum.java
        
        1.9 kB
        
        SimpleMutableSpectrum.java
        
        1.4 kB
        
        SimpleSpectrum.java
        
        2.3 kB
        
        Spectrums.java
        
        62.6 kB
        
        properties
        
        PersistentProperties.java
        
        3.1 kB
        
        PropertyFileListener.java
        
        182 Bytes
        
        PropertyFileWatcher.java
        
        4.1 kB
        
        PropertyManager.java
        
        4.9 kB
        
        sirius
        
        projectspace
        
        Index.java
        
        276 Bytes
        
        utils
        
        FileUtils.java
        
        19.1 kB
      - resources
        
        LICENSE.txt
        
        26.5 kB
        
        additional_elements.json
        
        224 Bytes
        
        blueobelisk_elements.xml
        
        208.6 kB
        
        blueobelisk_isotopes.xml
        
        792.5 kB
        
        chemcalc_distribution.json
        
        3.7 kB
        
        elements.json
        
        5.0 kB
        
        fingerprints
        
        biosmarts.txt
        
        9.7 kB
        
        classyfire_smarts.txt
        
        10.5 kB
        
        ringsystems.txt
        
        27.1 kB
        
        shortest_paths.txt
        
        59.6 kB
        
        index_fingerprints.txt
        
        230.6 kB
        
        isotopic_distributions.json
        
        358 Bytes
        
        merged.json
        
        3.6 kB
        
        merged_distribution.json
        
        3.7 kB
        
        molecules.txt
        
        154 Bytes
        
        obsidian.xml
        
        792.5 kB
    - test
      - java
        
        de
        
        unijena
        
        bioinf
        
        ChemistryBase
        
        chem
        
        FormulaConstraintsTest.java
        
        3.5 kB
        
        FormulaPackerTest.java
        
        9.0 kB
        
        FormulaTest.java
        
        3.9 kB
        
        IonTest.java
        
        1.8 kB
        
        ParserTest.java
        
        6.2 kB
        
        QuicksortTest.java
        
        1.6 kB
        
        TanimotoTest.java
        
        2.7 kB
        
        data
        
        TableTest.java
        
        2.7 kB
        
        jobs
        
        SiriusJobsTest.java
        
        1.8 kB
        
        ms
        
        FPTest.java
        
        13.8 kB
        
        TreeTest.java
        
        1.7 kB
        
        utils
        
        SpectrumsTest.java
        
        6.0 kB
        
        properties
        
        PropertyManagerTest.java
        
        334 Bytes
        
        transfomation
        
        TransformerTest.java
        
        1.8 kB
        
        utils
        
        ConnectionPoolTest.java
        
        4.7 kB
      - resources
        
        test.build.properties
        
        40 Bytes
- fragmentation_tree
  - .gitignore
    
    43 Bytes
  - FastFragmentationTreeAlign
    - .gitignore
      
      35 Bytes
    - AlignmentViewer
      - pom.xml
        
        3.7 kB
      - pom.xml.backup
        
        3.7 kB
      - src
        
        main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        ftalign
        
        view
        
        AlignmentWindow.java
        
        21.2 kB
        
        ApplicationState.java
        
        13.6 kB
        
        ApplicationWindow.java
        
        1.6 kB
        
        DataElement.java
        
        2.2 kB
        
        LoadWindow.java
        
        7.6 kB
        
        Main.java
        
        1.3 kB
        
        MakeStatistics.java
        
        10.4 kB
        
        Pair.java
        
        1.7 kB
        
        PlotWindow.java
        
        5.0 kB
        
        Progress.java
        
        943 Bytes
        
        StandardScoringWithWhiteList.java
        
        2.5 kB
        
        net
        
        iharder
        
        FileDrop.java
        
        36.9 kB
    - ClassicTreeAlign
      - pom.xml
        
        1.8 kB
      - pom.xml.backup
        
        1.8 kB
      - src
        
        main
        
        java
        
        fragtreealigner
        
        CmlUtil.java
        
        2.1 kB
        
        FragmentationTreeAligner.java
        
        38.5 kB
        
        algorithm
        
        ScoringFunction.java
        
        2.2 kB
        
        ScoringFunctionNeutralLosses.java
        
        14.0 kB
        
        ScoringFunctionSimple.java
        
        2.8 kB
        
        TreeAligner.java
        
        47.9 kB
        
        domainobjects
        
        Alignment.java
        
        13.3 kB
        
        AlignmentComparator.java
        
        1.6 kB
        
        chem
        
        basics
        
        ChemInfo.java
        
        21.2 kB
        
        Element.java
        
        1.6 kB
        
        ElementTable.java
        
        2.5 kB
        
        MolecularFormula.java
        
        6.6 kB
        
        components
        
        ChemicalComponent.java
        
        3.7 kB
        
        Compound.java
        
        1.8 kB
        
        FunctionalGroup.java
        
        1.3 kB
        
        FunctionalGroupSubstitution.java
        
        2.1 kB
        
        NeutralLoss.java
        
        3.0 kB
        
        structure
        
        BondType.java
        
        967 Bytes
        
        MolecularStructure.java
        
        4.7 kB
        
        MolecularStructureAtom.java
        
        2.9 kB
        
        MolecularStructureBond.java
        
        1.8 kB
        
        db
        
        DatabaseStatistics.java
        
        3.9 kB
        
        FragmentationTreeDatabase.java
        
        27.5 kB
        
        FragmentationTreeDatabaseEntry.java
        
        2.5 kB
        
        graphs
        
        AlignmentResTree.java
        
        2.5 kB
        
        AlignmentResTreeEdge.java
        
        1.5 kB
        
        AlignmentResTreeNode.java
        
        3.5 kB
        
        AlignmentTree.java
        
        3.5 kB
        
        AlignmentTreeEdge.java
        
        1.5 kB
        
        AlignmentTreeNode.java
        
        2.6 kB
        
        Edge.java
        
        2.2 kB
        
        FragmentationTree.java
        
        29.6 kB
        
        FragmentationTreeEdge.java
        
        2.9 kB
        
        FragmentationTreeNode.java
        
        3.8 kB
        
        Graph.java
        
        11.3 kB
        
        Node.java
        
        3.6 kB
        
        Tree.java
        
        3.1 kB
        
        TreeEdge.java
        
        1.5 kB
        
        TreeNode.java
        
        1.9 kB
        
        util
        
        Coordinate.java
        
        1.3 kB
        
        ui
        
        GraphPanelListener.java
        
        5.8 kB
        
        MainFrame.java
        
        24.5 kB
        
        util
        
        Classifier.java
        
        4.4 kB
        
        Macros.java
        
        3.7 kB
        
        MathUtils.java
        
        26.2 kB
        
        Normalizer.java
        
        8.8 kB
        
        PValue.java
        
        9.1 kB
        
        Parameters.java
        
        7.9 kB
        
        ParseToAlignmentInstance.java
        
        11.0 kB
        
        ParseToAlignmentTree.java
        
        3.0 kB
        
        Session.java
        
        1.9 kB
        
        Sim2Dist.java
        
        7.5 kB
        
        StructureScore2Distance.java
        
        7.9 kB
        
        VertexMatcher.java
        
        7.4 kB
        
        ml
        
        options
        
        OptionData.java
        
        10.2 kB
        
        OptionSet.java
        
        13.2 kB
        
        Options.java
        
        32.1 kB
    - FTAlignmentTool
      - build.gradle
        
        283 Bytes
      - pom.xml
        
        4.1 kB
      - pom.xml.backup
        
        4.1 kB
      - src
        
        main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        ftalign
        
        Benchmarker.java
        
        6.0 kB
        
        CIDBase.java
        
        2.3 kB
        
        CSVHandler.java
        
        992 Bytes
        
        CSVMatrix.java
        
        8.1 kB
        
        CSVReader.java
        
        3.7 kB
        
        CommonLossScoring.java
        
        2.7 kB
        
        DecoyDatabase.java
        
        3.8 kB
        
        Main.java
        
        27.9 kB
        
        ScoreFormula.java
        
        2.3 kB
        
        StandardScoring.java
        
        10.3 kB
        
        StandardScoring2.java
        
        10.8 kB
        
        TestScoring.java
        
        9.7 kB
        
        TraceLog2.java
        
        2.6 kB
        
        WeightingReader.java
        
        3.7 kB
        
        analyse
        
        FTDataElement.java
        
        4.6 kB
        
        FTDataset.java
        
        11.3 kB
        
        Normalizer.java
        
        1.2 kB
        
        Pearson.java
        
        2.3 kB
        
        TreeSizeNormalizer.java
        
        1.6 kB
        
        graphics
        
        GraphicalBacktrace.java
        
        26.3 kB
        
        GraphicalBacktrace2.java
        
        6.9 kB
        
        parallelograms
        
        ParaCount.java
        
        2.8 kB
        
        ParaNodes.java
        
        1.4 kB
        
        ParallelogramIterator.java
        
        6.1 kB
        
        resources
        
        lossweights.csv
        
        2.0 kB
    - FTBlast
      - build.gradle
        
        126 Bytes
      - pom.xml
        
        1.8 kB
      - pom.xml.backup
        
        1.8 kB
      - src
        
        main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        ftblast
        
        CLI.java
        
        3.0 kB
        
        Dataset.java
        
        8.0 kB
        
        Query.java
        
        1.2 kB
        
        ScoreTable.java
        
        7.2 kB
    - FastTreeAlign
      - build.gradle
        
        71 Bytes
      - pom.xml
        
        1.7 kB
      - pom.xml.backup
        
        1.7 kB
      - src
        
        main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        counting
        
        AlignmentWrapper.java
        
        1.9 kB
        
        CompleteTreeDecorator.java
        
        1.8 kB
        
        DPPathCounting.java
        
        3.6 kB
        
        DPSubtreeCounter.java
        
        1.3 kB
        
        WeightedPathCounting.java
        
        4.3 kB
        
        Weighting.java
        
        901 Bytes
        
        treealign
        
        AbstractBacktrace.java
        
        1.5 kB
        
        AlignmentTree.java
        
        11.4 kB
        
        AlignmentTreeBacktrace.java
        
        3.0 kB
        
        Backtrace.java
        
        1.3 kB
        
        Set.java
        
        5.4 kB
        
        StackedBacktrace.java
        
        3.4 kB
        
        TraceItem.java
        
        1.4 kB
        
        TraceLog.java
        
        2.6 kB
        
        Tree.java
        
        3.4 kB
        
        TreeAlignmentAlgorithm.java
        
        3.2 kB
        
        TreeDecorator.java
        
        2.0 kB
        
        dp
        
        DPTreeAlign.java
        
        23.8 kB
        
        Table.java
        
        3.5 kB
        
        TreeMap.java
        
        1.9 kB
        
        map
        
        IntFloatArrayMap.java
        
        4.4 kB
        
        IntFloatHashMap.java
        
        8.3 kB
        
        IntFloatIterator.java
        
        1.4 kB
        
        IntFloatMap.java
        
        1.2 kB
        
        IntPairFloatArrayMap.java
        
        5.7 kB
        
        IntPairFloatHashMap.java
        
        12.3 kB
        
        IntPairFloatIterator.java
        
        1.6 kB
        
        IntPairFloatMap.java
        
        1.6 kB
        
        MapInspectable.java
        
        1.0 kB
        
        MapInspector.java
        
        923 Bytes
        
        multijoin
        
        DPMultiJoin.java
        
        33.9 kB
        
        HashTable.java
        
        10.2 kB
        
        MultiJoinTraceItem.java
        
        1.5 kB
        
        TreeHashMap.java
        
        1.5 kB
        
        scoring
        
        AbstractMultijoinScoring.java
        
        1.3 kB
        
        AbstractScoring.java
        
        2.0 kB
        
        Scoring.java
        
        3.4 kB
        
        SimpleEqualityScoring.java
        
        1.1 kB
        
        sparse
        
        DPSparseTreeAlign.java
        
        30.9 kB
        
        HashTable.java
        
        9.2 kB
        
        Mode.java
        
        1.9 kB
        
        QueueItem.java
        
        1.0 kB
        
        TreeHashMap.java
        
        1.8 kB
        
        util
        
        Iterators.java
        
        5.5 kB
        
        test
        
        java
        
        de
        
        unijena
        
        bioinf
        
        counting
        
        PathCounterTest.java
        
        1.9 kB
        
        SubtreeCounterTest.java
        
        2.0 kB
        
        TestTree.java
        
        2.1 kB
        
        WeightCounterTest.java
        
        1.9 kB
        
        treealign
        
        map
        
        IntFloatHashMapTest.java
        
        5.9 kB
        
        IntPairFloatMapTest.java
        
        3.8 kB
    - SpectralAlignment
      - build.gradle
        
        120 Bytes
      - pom.xml
        
        3.3 kB
      - pom.xml.backup
        
        3.1 kB
      - src
        
        main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        spectralign
        
        Main.java
        
        10.2 kB
        
        SpectralAligner.java
        
        12.6 kB
    - build.gradle
      
      55 Bytes
    - pom.xml
      
      2.7 kB
    - pom.xml.backup
      
      2.7 kB
  - build.gradle
    
    776 Bytes
  - fragmentation_tree_construction
    - build.gradle
      
      0 Bytes
    - src
      - main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        FragmentationTreeConstruction
        
        computation
        
        AbstractTreeComputationInstance.java
        
        3.7 kB
        
        DoubleEndWeightedQueue.java
        
        3.9 kB
        
        DoubleEndWeightedQueue2.java
        
        3.7 kB
        
        FasterTreeComputationInstance.java
        
        21.2 kB
        
        FragmentationPatternAnalysis.java
        
        88.9 kB
        
        Ms2ExperimentShallowCopy.java
        
        3.1 kB
        
        NormalizationType.java
        
        916 Bytes
        
        TreeComputationInstance.java
        
        30.0 kB
        
        TreeIterator.java
        
        1.3 kB
        
        filtering
        
        AtLeastInTwoSpectraFilter.java
        
        4.1 kB
        
        DynamicBaselineFilter.java
        
        5.1 kB
        
        Initializable.java
        
        443 Bytes
        
        IsotopePeakFilter.java
        
        5.7 kB
        
        IsotopePeakWithKnownParentFilter.java
        
        10.0 kB
        
        LimitNumberOfPeaksFilter.java
        
        3.2 kB
        
        LimitNumberOfPeaksMassDistributedFilter.java
        
        8.2 kB
        
        MostRelevantPeaksFilter.java
        
        6.2 kB
        
        NoiseEstimateFilter.java
        
        8.6 kB
        
        NoiseThresholdFilter.java
        
        3.8 kB
        
        NormalizeToSumPreprocessor.java
        
        3.2 kB
        
        PostProcessor.java
        
        1.3 kB
        
        Preprocessor.java
        
        1.2 kB
        
        graph
        
        GraphBuilder.java
        
        1.4 kB
        
        GraphReduction.java
        
        1.8 kB
        
        SimpleReduction.java
        
        6.5 kB
        
        SubFormulaGraphBuilder.java
        
        7.9 kB
        
        reduction
        
        ACommandable.java
        
        4.9 kB
        
        CEdgeColorEndpointComperator.java
        
        1.2 kB
        
        CEdgeUBComperator.java
        
        1.0 kB
        
        SInEdgesToColor.java
        
        2.9 kB
        
        TComperator.java
        
        9.4 kB
        
        TGraphicalOutput.java
        
        12.7 kB
        
        TMinimalController.java
        
        2.3 kB
        
        TReduce.java
        
        43.8 kB
        
        TReductionController.java
        
        51.8 kB
        
        TTypeDependentFunctions.java
        
        4.3 kB
        
        inputValidator
        
        GCMSMissingValueValidator.java
        
        3.2 kB
        
        MissingValueValidator.java
        
        19.9 kB
        
        merging
        
        HighIntensityMerger.java
        
        7.1 kB
        
        MergeStrategy.java
        
        1.8 kB
        
        Merger.java
        
        1.5 kB
        
        PeakMerger.java
        
        1.8 kB
        
        normalizing
        
        LeaveOutParentPeakMaxNormalizer.java
        
        3.6 kB
        
        NormalizationType.java
        
        928 Bytes
        
        Normalizer.java
        
        2.0 kB
        
        parentpeak
        
        ParentPeakDetector.java
        
        1.6 kB
        
        SearchMatchingInputParentPeak.java
        
        5.3 kB
        
        recalibration
        
        AbstractRecalibrationStrategy.java
        
        7.3 kB
        
        ExpRek.java
        
        3.5 kB
        
        HypothesenDrivenRecalibration2.java
        
        3.6 kB
        
        LeastSquare.java
        
        2.9 kB
        
        MedianSlope.java
        
        5.5 kB
        
        RecalibrationMethod.java
        
        3.6 kB
        
        RecalibrationStrategy.java
        
        1.4 kB
        
        SpectralRecalibration.java
        
        2.9 kB
        
        scoring
        
        AdductFragmentScorer.java
        
        2.7 kB
        
        AdductTypeScorer.java
        
        1.3 kB
        
        ChemicalPriorEdgeScorer.java
        
        4.3 kB
        
        ChemicalPriorScorer.java
        
        4.5 kB
        
        ClippedPeakIsNoiseScorer.java
        
        2.9 kB
        
        CollisionEnergyEdgeScorer.java
        
        16.9 kB
        
        CommonFragmentsScore.java
        
        13.3 kB
        
        CommonLossEdgeScorer.java
        
        17.9 kB
        
        DBELossScorer.java
        
        2.4 kB
        
        DecompositionScorer.java
        
        1.5 kB
        
        DynamicTreeSizeScorer.java
        
        6.8 kB
        
        EICommonLossEdgeScorer.java
        
        7.4 kB
        
        FractionOfParentLossScorer.java
        
        3.1 kB
        
        FragmentSizeScorer.java
        
        2.9 kB
        
        FreeRadicalEdgeScorer.java
        
        6.2 kB
        
        IntrinsicallyChargedScorer.java
        
        2.7 kB
        
        IsotopeMs1Scorer.java
        
        1.9 kB
        
        IsotopePatternInMs2Scorer.java
        
        25.6 kB
        
        LossScorer.java
        
        1.3 kB
        
        LossSizeScorer.java
        
        5.7 kB
        
        MassDeviationVertexScorer.java
        
        4.1 kB
        
        NoIsotopePatternPenalty.java
        
        1.9 kB
        
        PeakIsNoiseScorer.java
        
        3.0 kB
        
        PeakIsNoiseScorer2.java
        
        2.5 kB
        
        PeakPairScorer.java
        
        1.3 kB
        
        PeakScorer.java
        
        1.2 kB
        
        PenalizeLowIntensiveParentsScore.java
        
        2.2 kB
        
        PhosphorScorer.java
        
        3.3 kB
        
        PureCarbonNitrogenLossScorer.java
        
        2.9 kB
        
        RelativeLossSizeScorer.java
        
        2.1 kB
        
        SmallestLossScorer.java
        
        2.5 kB
        
        SmallestLossScorer2.java
        
        2.6 kB
        
        StrangeElementFragmentScorer.java
        
        3.1 kB
        
        StrangeElementLossScorer.java
        
        5.6 kB
        
        StrangeElementRootScorer.java
        
        3.6 kB
        
        StrangeElementScorer.java
        
        4.9 kB
        
        StrangeElementSmallFragmentScorer.java
        
        2.9 kB
        
        TmsToDmsLossScorer.java
        
        3.8 kB
        
        TreeSizeScorer.java
        
        3.4 kB
        
        tree
        
        TreeBuilder.java
        
        3.1 kB
        
        TreeBuilderFactory.java
        
        6.5 kB
        
        ilp
        
        AbstractSolver.java
        
        17.1 kB
        
        AbstractTreeBuilder.java
        
        998 Bytes
        
        CPLEXSolver.java
        
        8.3 kB
        
        GLPKSolver.java
        
        14.1 kB
        
        GrbSolver.java
        
        7.5 kB
        
        IlpFactory.java
        
        512 Bytes
        
        maximumColorfulSubtree
        
        DP.java
        
        19.8 kB
        
        DPTable.java
        
        1.8 kB
        
        MaximumColorfulSubtreeAlgorithm.java
        
        4.2 kB
        
        TraceItem.java
        
        1.3 kB
        
        ftheuristics
        
        AbstractHeuristic.java
        
        2.9 kB
        
        CriticalPathInsertionHeuristic.java
        
        8.2 kB
        
        CriticalPathInsertionHeuristic2.java
        
        8.6 kB
        
        CriticalPathInsertionWithIsotopePeaksHeuristic.java
        
        3.7 kB
        
        DeepSearchHeuristic.java
        
        1.7 kB
        
        ExtendedCriticalPathHeuristic.java
        
        9.9 kB
        
        FastInsertionHeuristic.java
        
        5.1 kB
        
        GreedyHeuristic.java
        
        2.3 kB
        
        LegacyInsertionHeuristic.java
        
        3.5 kB
        
        PrimStarHeuristic.java
        
        2.0 kB
        
        TopDownHeuristic.java
        
        1.6 kB
        
        solver
        
        CriticalPathSolver.java
        
        5.2 kB
        
        GreedyRDESolver.java
        
        672 Bytes
        
        GreedyRDSSolver.java
        
        671 Bytes
        
        GreedySolver.java
        
        6.1 kB
        
        HeuristicSolver.java
        
        7.5 kB
        
        InsertionSolver.java
        
        5.3 kB
        
        PrimStyleRDESolver.java
        
        662 Bytes
        
        PrimStyleRDSSolver.java
        
        666 Bytes
        
        PrimStyleSolver.java
        
        2.7 kB
        
        PrimStyleStarSolver.java
        
        1.7 kB
        
        TopDownSolver.java
        
        2.0 kB
        
        treebuilder
        
        ExtendedCriticalPathHeuristicTreeBuilder.java
        
        1.4 kB
        
        GreedyBuilder.java
        
        1.6 kB
        
        inspection
        
        GraphOutput.java
        
        4.4 kB
        
        Inspectable.java
        
        1.6 kB
        
        TreeAnnotation.java
        
        13.7 kB
        
        model
        
        Decomposition.java
        
        1.2 kB
        
        DecompositionList.java
        
        5.5 kB
        
        EnforceHeuristic.java
        
        641 Bytes
        
        ExtractedIsotopePattern.java
        
        1.1 kB
        
        ForbidRecalibration.java
        
        685 Bytes
        
        FormulaSettings.java
        
        3.5 kB
        
        IsotopeScoring.java
        
        499 Bytes
        
        MS2Peak.java
        
        2.6 kB
        
        Ms2IsotopePatternMatch.java
        
        868 Bytes
        
        PeakAnnotation.java
        
        1.7 kB
        
        ProcessedInput.java
        
        10.9 kB
        
        ProcessedPeak.java
        
        7.9 kB
        
        ScoredFormulaMap.java
        
        1.1 kB
        
        Scoring.java
        
        1.5 kB
        
        Timeout.java
        
        2.0 kB
        
        Whiteset.java
        
        1.7 kB
        
        resources
        
        LICENSE.txt
        
        26.5 kB
        
        profiles
        
        default.json
        
        22.5 kB
        
        orbitrap.json
        
        22.5 kB
        
        qtof.json
        
        22.5 kB
      - test
        
        java
        
        de
        
        unijena
        
        bioinf
        
        FragmentationTreeConstruction
        
        computation
        
        PreprocessingTest.java
        
        6.6 kB
- gibbs_sampling
  - build.gradle
    
    796 Bytes
  - src
    - main
      - java
        
        de
        
        unijena
        
        bioinf
        
        GibbsSampling
        
        GibbsSamplerMain.java
        
        141.1 kB
        
        GibbsSamplerOptions.java
        
        5.0 kB
        
        LibraryHitQuality.java
        
        164 Bytes
        
        Zodiac.java
        
        20.0 kB
        
        ZodiacUtils.java
        
        43.5 kB
        
        model
        
        AbstractEdgeFilter.java
        
        1.7 kB
        
        AllOrNothingLibraryHitsScorer.java
        
        1.0 kB
        
        Candidate.java
        
        2.9 kB
        
        CombinedReaction.java
        
        5.9 kB
        
        CompoundResult.java
        
        2.1 kB
        
        Connectivity.java
        
        362 Bytes
        
        DummyFragmentCandidate.java
        
        2.4 kB
        
        EdgeFilter.java
        
        480 Bytes
        
        EdgeScorer.java
        
        500 Bytes
        
        EdgeThresholdFilter.java
        
        1.4 kB
        
        EdgeThresholdMinConnectionsFilter.java
        
        11.8 kB
        
        FormulaFactory.java
        
        844 Bytes
        
        FragmentWithIndex.java
        
        901 Bytes
        
        FragmentsAndLosses.java
        
        1.2 kB
        
        FragmentsCandidate.java
        
        17.3 kB
        
        GibbsMFCorrectionNetwork.java
        
        22.7 kB
        
        GibbsParallel.java
        
        6.3 kB
        
        Graph.java
        
        37.2 kB
        
        GraphBuilder.java
        
        14.0 kB
        
        GraphValidationMessage.java
        
        700 Bytes
        
        HasFormula.java
        
        229 Bytes
        
        HasLibraryHit.java
        
        525 Bytes
        
        LibraryHit.java
        
        1.8 kB
        
        LibraryHitScorer.java
        
        5.2 kB
        
        LocalEdgeFilter.java
        
        3.3 kB
        
        NoEdgeFilter.java
        
        1.1 kB
        
        NodeScorer.java
        
        130 Bytes
        
        RankNodeScorer.java
        
        1.6 kB
        
        Reaction.java
        
        462 Bytes
        
        ReactionStepSizeScorer.java
        
        980 Bytes
        
        SimpleReaction.java
        
        1.8 kB
        
        StandardCandidate.java
        
        3.3 kB
        
        StandardNodeScorer.java
        
        2.3 kB
        
        ThreePhaseGibbsSampling.java
        
        21.7 kB
        
        Transformation.java
        
        2.3 kB
        
        TwoPhaseGibbsSampling.java
        
        12.0 kB
        
        ZodiacResult.java
        
        628 Bytes
        
        ZodiacResultsWithClusters.java
        
        662 Bytes
        
        distributions
        
        DummyScoreProbabilityDistribution.java
        
        751 Bytes
        
        EmpiricalScoreProbabilityDistribution.java
        
        1.6 kB
        
        ExponentialDistribution.java
        
        3.0 kB
        
        LogNormalDistribution.java
        
        5.3 kB
        
        ParetoDistribution.java
        
        2.9 kB
        
        ScoreProbabilityDistribution.java
        
        572 Bytes
        
        ScoreProbabilityDistributionEstimator.java
        
        9.2 kB
        
        ScoreProbabilityDistributionFix.java
        
        1.0 kB
        
        scorer
        
        CommonFragmentAndLossScorer.java
        
        15.6 kB
        
        CommonFragmentAndLossScorerNoiseIntensityWeighted.java
        
        8.3 kB
        
        CommonFragmentAndLossWithTreeScoresScorer.java
        
        5.9 kB
        
        CommonFragmentScorer.java
        
        15.8 kB
        
        CommonRootLossScorer.java
        
        8.2 kB
        
        EdgeScorings.java
        
        155 Bytes
        
        FTAlignScorer.java
        
        5.2 kB
        
        ReactionScorer.java
        
        3.4 kB
        
        SameIonizationScorer.java
        
        1.7 kB
- io
  - .gitignore
    
    43 Bytes
  - build.gradle
    
    550 Bytes
  - src
    - main
      - java
        
        de
        
        unijena
        
        bioinf
        
        babelms
        
        CloseableIterator.java
        
        1.3 kB
        
        ConsistencyValidator.java
        
        928 Bytes
        
        DataWriter.java
        
        1.0 kB
        
        GenericParser.java
        
        5.0 kB
        
        GenericParserJJob.java
        
        859 Bytes
        
        GenericWriter.java
        
        1.6 kB
        
        MSExperimentParsingJJob.java
        
        2.0 kB
        
        Main.java
        
        938 Bytes
        
        MsExperimentParser.java
        
        2.3 kB
        
        Parser.java
        
        1.7 kB
        
        SpectralParser.java
        
        2.1 kB
        
        ZippedSpectraParser.java
        
        7.8 kB
        
        binary
        
        FTreeBinaryReader.java
        
        4.8 kB
        
        FTreeBinaryWriter.java
        
        3.5 kB
        
        SpectrumBinaryReader.java
        
        1.1 kB
        
        SpectrumBinaryWriter.java
        
        1.0 kB
        
        chemdb
        
        CacheEntry.java
        
        1.0 kB
        
        CompoundQuery.java
        
        1.3 kB
        
        DBMolecularFormulaCache.java
        
        7.0 kB
        
        Databases.java
        
        1.2 kB
        
        chemspider
        
        ChemSpider.java
        
        5.4 kB
        
        descriptor
        
        DefaultDescriptors.java
        
        27.5 kB
        
        Descriptor.java
        
        1.1 kB
        
        DescriptorRegistry.java
        
        3.0 kB
        
        dot
        
        DotHandler.java
        
        1.1 kB
        
        DotParser.java
        
        9.7 kB
        
        Edge.java
        
        2.3 kB
        
        FTDotReader.java
        
        5.8 kB
        
        FTDotWriter.java
        
        19.4 kB
        
        Graph.java
        
        5.5 kB
        
        Vertex.java
        
        3.1 kB
        
        json
        
        FTJsonReader.java
        
        6.5 kB
        
        FTJsonWriter.java
        
        5.7 kB
        
        JSONDocumentType.java
        
        7.9 kB
        
        massbank
        
        MassbankParser.java
        
        872 Bytes
        
        mgf
        
        MgfParser.java
        
        16.9 kB
        
        MgfWriter.java
        
        6.1 kB
        
        ms
        
        AnnotatedSpectrumWriter.java
        
        2.7 kB
        
        CsvParser.java
        
        2.0 kB
        
        JenaMsParser.java
        
        17.4 kB
        
        JenaMsWriter.java
        
        5.8 kB
        
        pubchem
        
        Pubchem.java
        
        7.8 kB
        
        utils
        
        Base64.java
        
        87.7 kB
        
        FTGraphWriter.java
        
        2.4 kB
        
        Fingerprint2Base64.java
        
        2.4 kB
      - resources
        
        LICENSE.txt
        
        26.5 kB
    - test
      - java
        
        de
        
        unijena
        
        bioinf
        
        babelms
        
        ms
        
        FTioTest.java
        
        2.5 kB
        
        MsParserTest.java
        
        1.7 kB
      - resources
        
        Adenosine.ms
        
        4.4 kB
        
        de
        
        unijena
        
        bioinf
        
        babelms
        
        ms
        
        casmi2016_084.json
        
        9.6 kB
- isotope_pattern
  - .gitignore
    
    24 Bytes
  - build.gradle
    
    0 Bytes
  - isogen_cli
    - .settings
      - org.eclipse.jdt.core.prefs
        
        329 Bytes
    - build.gradle
      
      282 Bytes
    - src
      - main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        IsotopePatternAnalysis
        
        isogencli
        
        Main.java
        
        8.9 kB
        
        Options.java
        
        2.3 kB
        
        resources
        
        LICENSE.txt
        
        26.5 kB
      - test
        
        java
        
        de
        
        unijena
        
        bioinf
        
        IsotopePatternAnalysis
        
        isogencli
        
        TestMain.java
        
        1.3 kB
  - isotope_pattern_analysis
    - .settings
      - org.eclipse.jdt.core.prefs
        
        329 Bytes
    - build.gradle
      
      179 Bytes
    - src
      - main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        IsotopePatternAnalysis
        
        IsotopePattern.java
        
        1.7 kB
        
        IsotopePatternAnalysis.java
        
        20.1 kB
        
        Main.java
        
        6.2 kB
        
        PatternGenerator.java
        
        13.0 kB
        
        extraction
        
        SimpleTargetedPatternExtractor.java
        
        3.6 kB
        
        TargetedPatternExtraction.java
        
        392 Bytes
        
        generation
        
        CachedIsoTable.java
        
        1.9 kB
        
        FastIsotopePatternGenerator.java
        
        6.7 kB
        
        FastTwoPeakSimulator.java
        
        3.1 kB
        
        FineStructureMerger.java
        
        4.7 kB
        
        FinestructureGenerator.java
        
        10.6 kB
        
        FinestructurePatternGenerator.java
        
        3.4 kB
        
        FragmentIsotopeGenerator.java
        
        8.9 kB
        
        IsotopePatternGenerator.java
        
        4.6 kB
        
        Isotopologue.java
        
        1.3 kB
        
        IsotopologueTable.java
        
        6.2 kB
        
        Isotopologues.java
        
        958 Bytes
        
        SimpleIsotopologues.java
        
        3.4 kB
        
        prediction
        
        DNNElementPredictor.java
        
        5.9 kB
        
        DNNRegressionPredictor.java
        
        6.7 kB
        
        ElementPredictor.java
        
        581 Bytes
        
        FeatureVector.java
        
        10.4 kB
        
        TrainedElementDetectionNetwork.java
        
        9.2 kB
        
        scoring
        
        IsotopePatternScorer.java
        
        1.7 kB
        
        LogNormDistributedIntensityScorer.java
        
        2.6 kB
        
        MassDeviationScorer.java
        
        3.1 kB
        
        MassDifferenceDeviationScorer.java
        
        3.3 kB
        
        MissingPeakScorer.java
        
        2.0 kB
        
        MzMineScorer.java
        
        1.7 kB
        
        NormalDistributedIntensityScorer.java
        
        6.8 kB
        
        ScorePerPeak.java
        
        1.2 kB
        
        util
        
        FixedBagIntensityDependency.java
        
        3.4 kB
        
        FixedIntensity.java
        
        1.8 kB
        
        IntensityDependency.java
        
        1.1 kB
        
        LinearIntensityDependency.java
        
        3.0 kB
        
        MathUtils.java
        
        26.8 kB
        
        PiecewiseLinearFunctionIntensityDependency.java
        
        2.6 kB
        
        resources
        
        LICENSE.txt
        
        26.5 kB
        
        dnn_element_detection_3.param
        
        36.7 kB
        
        dnn_element_detection_4.param
        
        45.5 kB
        
        dnn_element_detection_5.param
        
        50.7 kB
        
        regression3.param
        
        36.6 kB
        
        regression4.param
        
        45.4 kB
        
        regression5.param
        
        50.6 kB
      - test
        
        java
        
        de
        
        unijena
        
        bioinf
        
        IsotopePatternAnalysis
        
        PatternExtractionTest.java
        
        5.5 kB
        
        PatternGeneratorTest.java
        
        6.1 kB
- mass_decomposition
  - .gitignore
    
    32 Bytes
  - .settings
    - org.eclipse.jdt.core.prefs
      
      330 Bytes
  - build.gradle
    
    0 Bytes
  - decomp_cli
    - build.gradle
      
      259 Bytes
    - src
      - main
        
        java
        
        de
        
        unijena
        
        bioinf
        
        MassDecomposer
        
        AlphabetParser.java
        
        3.6 kB
        
        FilterLevel.java
        
        908 Bytes
        
        Main.java
        
        8.3 kB
        
        Options.java
        
        2.6 kB
        
        Test.java
        
        1.5 kB
      - resources
        
        LICENSE.txt
        
        26.5 kB
  - mass_decomposer
    - build.gradle
      
      56 Bytes
    - src
      - main
        
        java
        
        de
        
        unijena
        
        bioinf

boecker-lab/sirius-libs-v4.0.1_with_ZODIAC.zip