Uses of Package
com.compomics.util.parameters.identification.advanced
Packages that use com.compomics.util.parameters.identification.advanced
Package
Description
The amino acid classes.
Classes related to the handling of protein sequences.
Classes related to genes.
Experiment classes related to ions.
Classes related to proteins.
Amino Acid Tag classes.
Classes for the filtering of identification objects.
Modification mapping and localization.
Mapping between search engine and Utilities modifications.
PTM scores.
Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation
This package contains the classes needed to generate ms2pip features.
Classes related to protein inference.
Protein sequence database indexing classes based on Burrows-Wheeler transform.
Main PSM scoring class.
Main PTM scoring classes.
Classes used for ms2 spectrum annotation.
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
This package contains utilities classes to handle identification objects.
Experiment identification classes.
Experiment classes related to reading search engine files.
PTM GUI dialogs.
Dialogs for advanced identification parameters.
Spectrum and Chromatogram visualization GUI classes.
Identification parameters.
Advanced Identification parameters.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.experiment.identification.protein_inference.fm_indexClassDescriptionPreferences for the allowed variants in peptide sequences.The sequence matching options.
-
-
-
-
-
-
-
-
-
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.gui.parameters.identification.advancedClassDescriptionSettings for the handling of fractions.Contains methods for downloading gene and GO mappings.Generic class grouping the identification matches validation preferences.This class contains the modification localization preferences.Preferences for the allowed variants in peptide sequences.Generic class grouping the protein inference preferences.Generic class for peptide spectrum match scoring.The sequence matching options.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.parameters.identificationClassDescriptionSettings for the handling of fractions.Contains methods for downloading gene and GO mappings.Generic class grouping the identification matches validation preferences.This class contains the modification localization preferences.Preferences for the allowed variants in peptide sequences.Generic class grouping the protein inference preferences.Generic class for peptide spectrum match scoring.The sequence matching options.
-
Classes in com.compomics.util.parameters.identification.advanced used by com.compomics.util.parameters.identification.advancedClassDescriptionSettings for the handling of fractions.Contains methods for downloading gene and GO mappings.Generic class grouping the identification matches validation preferences.This class contains the modification localization preferences.Preferences for the allowed variants in peptide sequences.Enum indicating all three variant typesGeneric class grouping the protein inference preferences.Generic class for peptide spectrum match scoring.The sequence matching options.The different types of amino acid matching.This class lists the criteria used for quality control of the validated matches.