All Classes and Interfaces

Class	Description
Allele	Represents an allele, which is a specific sequence type associated with a set of samples and a proteoform.
AminoacidSequenceGenerator	The AminoacidSequenceGenerator class is responsible for generating aminoacid sequences based on genomic data contained in a Storage instance.
Attributes	Base class for entities to store arbitrary attributes as Strings.
Bio	Utility class for performing various sequence related operations.
Bio.ReferenceContext	Represents information about a single position in a reference sequence.
CLI	Interface representing a Command Line Interface (CLI) component.
CLIBuild	Handles the build task CLI parameters.
CLIExpand	Handles the expand task CLI parameters.
CLIProfile	Handles the profile task CLI parameters.
CLIProfile.Content	The content type to profile.
CLISequence	Handles the sequence task CLI parameters.
CLISequence.Content	The content type to generate sequences of.
CLISequence.Split	The mode to split output files by.
CLIView	Handles the view task CLI parameters.
CLIView.Content	The content type to view.
Constants	Utility class that holds constant values used throughout the application.
Constants.AttributesKeys	A nested utility class that defines keys for various attributes used in the application.
Contig	Represents a reference genomic location.
ExecutorBuild	The ExecutorBuild class is responsible for executing the build task to compile genomic data.
ExecutorExpand	The ExecutorExpand class is responsible for executing the expand task to extend existing genomic data.
ExecutorProfile	The ExecutorProfile class is responsible for executing the profile task to profile samples.
ExecutorSequence	The ExecutorSequence class is responsible for executing the sequence task to profile samples.
ExecutorView	The ExecutorView class is responsible for executing the view task for inspecting data.
Feature	Representation of a genomic feature.
Feature.SubFeature	Represents a sub-feature of a genomic feature.
FeatureLoader	The FeatureLoader class is responsible for loading and validating genomic features.
IO	Utility class for I/O related operations.
Logging	Logging utility class for printing messages to the console with different severity levels.
Musial	Main class of MUSIAL (MUlti Sample varIant AnaLysis).
MusialException	A custom exception class for handling application-specific errors.
MusialTask	Enum specifying MUSIAL tasks.
NucleotideSequenceGenerator	The NucleotideSequenceGenerator class is responsible for generating nucleotide sequences based on genomic data contained in a Storage instance.
OS	Utility class for operating system-related functionalities.
Proteoform	Represents a proteoform, which is a specific sequence type associated with a set of alleles.
Sample	Represents a single biological sample.
SequenceGenerator	Interface for generating sequences based on a sample identifier.
SequenceType	Represents a sequence type with associated variants and attributes.
Storage	Central component of the MUSIAL model, designed to manage genomic data, including contigs, features, and samples.
Storage.Parameters	The parameters used for configuring the storage of variant data.
StorageFactory	Factory class for creating and loading Storage objects.
StorageIO	The StorageIO class provides utility methods for serializing and deserializing genomic data.
StorageTable	The StorageTable class provides functionality to create and manage tabular representations of genomic data stored in a Storage instance using the tablesaw library.
StorageUpdater	Encapsulates complex update logic for genomic data storage from the Storage class itself.
Variant	Represents a nucleotide variant.
Variant.Stub	Represents a simplified variant stub with position and alternative allele information.
Variant.Type	Enum representing the type of variant.
VariantAnnotator	The VariantAnnotator class provides functionality to annotate variants.
VariantCall	Represents a variant call in a biological sample.
VariantCall.CallAlternative	Represents one alternative in the context of a variant call.
VariantCall.Flag	Enumeration of flags representing the status of a variant call.
VariantCall.VariantCallSerializer	Serializer for the VariantCall class.
VCFProcessor	The VCFProcessor class is responsible for processing Variant Call Format (VCF) files.
VCFProcessor.UpstreamDeletion	Represents an upstream deletion affecting a sample.