All Classes and Interfaces
Class
Description
Base class for entities that can have attributes.
Command Line Interface (CLI) utility class for parsing and validating command-line arguments.
A utility class that holds constant values used throughout the project.
Represents a reference sequence segment.
Representation of a genomic feature that is subject to analysis.
Utility class for input/output operations.
Logging utility class for printing messages to the console with different severity levels.
Main class of MUSIAL (MUlti Sample varIant AnaLysis), a tool to calculate SNV, gene, and whole genome alignments,
together with other relevant statistics based on .vcf files.
Enum specifying tasks of MUSIAL to choose from.Provides functionality to update (build or expand) a MUSIAL storage.
Provides functionality to generate and display various types of tables based on the data stored in the `Storage` object.
A custom exception class for handling application-specific errors.
Utility class for operating system-related functionalities.
Represents a sample containing variant calls from a single biological sample.
Utility class for performing various sequence operations.
Enum to store different modes to handle prefix gaps for global sequence alignment.
Represents a sequence type with associated variants, occurrences, and attributes.
The `Storage` class is a central component of the project, designed to manage genomic data, including contigs, features, and samples.
Factory class for creating and managing instances of
Storage.Utility class for performing various validation checks.
Stores information associated with a nucleotide variant.
Enum representing the type of variant.