Uses of Package
com.compomics.util.parameters.identification.advanced
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Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.biology.aminoacids Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.biology.aminoacids.sequence Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.biology.genes Class Description GeneParameters Contains methods for downloading gene and GO mappings. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.biology.ions Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.biology.proteins Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.amino_acid_tags Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.filtering Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.modification Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.modification.mapping Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.modification.scores Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.protein_inference Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.protein_inference.fm_index Class Description PeptideVariantsParameters Preferences for the allowed variants in peptide sequences.SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.psm_scoring Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.psm_scoring.psm_scores Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.spectrum_annotation Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.utils Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.io.identification Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.io.identification.idfilereaders Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.gui.modification Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.gui.parameters.identification.advanced Class Description FractionParameters Settings for the handling of fractions.GeneParameters Contains methods for downloading gene and GO mappings.IdMatchValidationParameters Generic class grouping the identification matches validation preferences.ModificationLocalizationParameters This class contains the modification localization preferences.PeptideVariantsParameters Preferences for the allowed variants in peptide sequences.ProteinInferenceParameters Generic class grouping the protein inference preferences.PsmScoringParameters Generic class for peptide spectrum match scoring.SequenceMatchingParameters The sequence matching options.ValidationQcParameters This class lists the criteria used for quality control of the validated matches. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.gui.spectrum Class Description SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.parameters.identification Class Description FractionParameters Settings for the handling of fractions.GeneParameters Contains methods for downloading gene and GO mappings.IdMatchValidationParameters Generic class grouping the identification matches validation preferences.ModificationLocalizationParameters This class contains the modification localization preferences.PeptideVariantsParameters Preferences for the allowed variants in peptide sequences.ProteinInferenceParameters Generic class grouping the protein inference preferences.PsmScoringParameters Generic class for peptide spectrum match scoring.SequenceMatchingParameters The sequence matching options. -
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.parameters.identification.advanced Class Description FractionParameters Settings for the handling of fractions.GeneParameters Contains methods for downloading gene and GO mappings.IdMatchValidationParameters Generic class grouping the identification matches validation preferences.ModificationLocalizationParameters This class contains the modification localization preferences.PeptideVariantsParameters Preferences for the allowed variants in peptide sequences.PeptideVariantsParameters.VariantType Enum indicating all three variant typesProteinInferenceParameters Generic class grouping the protein inference preferences.PsmScoringParameters Generic class for peptide spectrum match scoring.SequenceMatchingParameters The sequence matching options.SequenceMatchingParameters.MatchingType The different types of amino acid matching.ValidationQcParameters This class lists the criteria used for quality control of the validated matches.