Index (MUSIAL v2.4.0 API)

$ A B C D E F G H I L M N O P R S T U V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

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$Allele_proteoform - Static variable in class utility.Constants: Key used to represent the proteoform of an allele.
$Attributable_frequencyDisrupted - Static variable in class utility.Constants: Key used to represent the disrupted frequency of an attributable entity.
$Attributable_frequencyReference - Static variable in class utility.Constants: Key used to represent the reference frequency of an attributable entity.
$Contig_length - Static variable in class utility.Constants: Key used to represent the length of a contig.
$Feature_children - Static variable in class utility.Constants: Key used to represent the children of a feature.
$Feature_numberOfAlleles - Static variable in class utility.Constants: Key used to represent the number of alleles of a feature.
$Feature_numberOfProteoforms - Static variable in class utility.Constants: Key used to represent the number of proteoforms of a feature.
$Sample_meanCoverage - Static variable in class utility.Constants: Key used to represent the mean coverage of a sample wrt.
$Sample_meanQuality - Static variable in class utility.Constants: Key used to represent the mean coverage of a sample wrt.
$Sample_numberOfCalls - Static variable in class utility.Constants: Key used to represent the number of calls in a sample.
$Sample_numberOfFiltered - Static variable in class utility.Constants: Key used to represent the number of filtered calls in a sample.
$Sample_numberOfIndels - Static variable in class utility.Constants: Key used to represent the number of insertions in a sample.
$Sample_numberOfSubstitutions - Static variable in class utility.Constants: Key used to represent the number of substitutions in a sample.
$SequenceType_clusterIndex - Static variable in class utility.Constants: Key used to represent the cluster index of a sequence type.
$SequenceType_clusterLabel - Static variable in class utility.Constants: Key used to represent the cluster label of a sequence type.
$SequenceType_clusterOutlierScore - Static variable in class utility.Constants: Key used to represent the outlier score of a sequence type.
$SequenceType_effects - Static variable in class utility.Constants: Key used to represent the effects of a SequenceType.
$SequenceType_frequency - Static variable in class utility.Constants: Key used to represent the frequency of a sequence type.
$SequenceType_sequenceLengthVariation - Static variable in class utility.Constants: Key used to represent the net shift in sequence length of a sequence type.
$VariantInformation_frequency - Static variable in class utility.Constants: Key used to represent the frequency of a variant in the stored samples.

A

addAlleleOccurrence(String, String) - Method in class datastructure.VariantInformation: Adds an allele occurrence to this variant for a specific feature.
addAttributeIfAbsent(String, String) - Method in class datastructure.Attributable: Adds an attribute to this entity only if it does not already exist.
addAttributesIfAbsent(Map<String, String>) - Method in class datastructure.Attributable: Adds multiple attributes to this entity only if they do not already exist.
addContig(String, String) - Method in class datastructure.Storage: Adds a contig to the storage with the specified name and sequence.
addFeatureOccurrence(String) - Method in class datastructure.VariantInformation: Adds a feature occurrence to this variant.
addOccurrence(String) - Method in class datastructure.SequenceType: Adds an occurrence to this sequence type.
addSampleOccurrence(String) - Method in class datastructure.VariantInformation: Adds a sample occurrence to this variant.
addToDataset(String, Map<Integer, String>) - Static method in class utility.Clustering: Adds a sample to the dataset for clustering.
alleles - Variable in class datastructure.Feature: Alleles (SequenceType instances) associated with this feature.
alleles - Variable in class datastructure.Sample: A map that assigns features to their corresponding alleles.
annotateVariants() - Method in class datastructure.Storage: Annotates novel variants in the storage using SnpEff.
anyNucleotide - Static variable in class utility.Constants: Represents the nucleotide used to denote any base in a sequence.
Attributable - Class in datastructure: Base class for entities that can have attributes.
Attributable() - Constructor for class datastructure.Attributable: Constructor of Attributable.
attributesAsString() - Method in class datastructure.Attributable: Converts the attributes of this entity to a string representation in the format KEY=VALUE;....
attributesAsString(Collection<String>) - Method in class datastructure.Attributable: Converts the attributes of this entity to a string representation in the format KEY=VALUE;..., excluding attributes with keys in the specified collection.

B

baseSymbols - Static variable in class utility.Constants: The base symbols of the IUPAC nucleotide and amino acid code.
BUILD - Enum constant in enum class main.Musial.Task: Task to build a MUSIAL storage file.

C

checkDirectory(File) - Static method in class utility.Validation: Checks if a File object exists, is a directory, and can be read.
checkFile(File) - Static method in class utility.Validation: Checks the validity of a File object.
clearAttributes() - Method in class datastructure.Attributable: Removes all attributes from this entity.
CLI - Class in utility: Command Line Interface (CLI) utility class for parsing and validating command-line arguments.
CLI() - Constructor for class utility.CLI
Clustering - Class in utility: Provides functionality for clustering data using the HDBSCAN algorithm (see https://tribuo.org/).
Clustering() - Constructor for class utility.Clustering
Clustering.Entry - Record Class in utility: A record to represent a clustering result entry.
COLON - Static variable in class utility.Constants: Colon string constant.
COMMA - Static variable in class utility.Constants: Comma string constant.
computeLengthVariation(List<Tuple<Integer, String>>) - Static method in class datastructure.SequenceType: Computes the net shift in sequence length caused by variants.
Constants - Class in utility: A utility class that holds constant values used throughout the project.
Constants() - Constructor for class utility.Constants
content - Static variable in class main.Musial.View: A set of supported content types for the `view` task.
contig - Variable in class datastructure.Feature: The location of the feature on the reference, i.e., the contig/chromosome/plasmid.
Contig - Class in datastructure: Represents a reference sequence segment.
Contig(String, String) - Constructor for class datastructure.Contig: Constructs a new Contig instance with the specified name and sequence.
copyResourceToFile(String, Path) - Static method in class utility.IO: Copies a resource from the application's classpath to a specified target Path.

D

datastructure - package datastructure: Contains all classes that constitute the storage data structures of the MUSIAL application.
DELETION - Enum constant in enum class datastructure.VariantInformation.Type: A deletion of one or more nucleotides
deserialize(File) - Static method in class datastructure.Storage.Factory: Initializes a Storage from a file.
detectSeparator(List<String>) - Static method in class utility.IO: Detects the separator used in a list of strings.
DOT - Static variable in class utility.Constants: Dot string constant.

E

EMPTY - Static variable in class utility.Constants: Empty string constant.
end - Variable in class datastructure.Feature: 1-based indexed end position of the feature.
Entry(String, int, int, double) - Constructor for record class utility.Clustering.Entry: Creates an instance of a Entry record class.
EQUAL - Static variable in class utility.Constants: Equals sign string constant.
equals(Object) - Method in record class utility.Clustering.Entry: Indicates whether some other object is "equal to" this one.
exceptions - package exceptions: Contains classes that define application-specific exceptions to handle various error scenarios in a structured manner.
EXPAND - Enum constant in enum class main.Musial.Task: Task to add sample data from variant call files to a MUSIAL storage file.
extendAttribute(String, String) - Method in class datastructure.Attributable: Extends an attribute by appending a value to the existing value.
extendAttributes(Map<String, String>) - Method in class datastructure.Attributable: Extends multiple attributes by appending values to the existing values.

F

Factory() - Constructor for class datastructure.Storage.Factory
Feature - Class in datastructure: Representation of a genomic feature that is subject to analysis.
Feature(String, String, Number, Number, char, String, String) - Constructor for class datastructure.Feature: Constructs a new Feature instance with the specified properties.
Feature.Allele - Class in datastructure: Represents an allele associated with a genomic feature.
Feature.Proteoform - Class in datastructure: Represents a proteoform associated with a genomic feature.
FORBID - Enum constant in enum class utility.SequenceOperations.MarginalGaps: Gaps at the end of a sequence are not allowed.
formatFrequency(double) - Static method in class utility.IO: Formats a frequency value into scientific notation.
formatNumber(double) - Static method in class utility.IO: Formats a number to three decimal places.
FREE - Enum constant in enum class utility.SequenceOperations.MarginalGaps: Gaps at the ends of a sequence are not penalized.
fromCLI() - Static method in class datastructure.Storage.Factory: Initializes a Storage from CLI parameters.

G

gapChar - Static variable in class utility.Constants: Character representation of a gap in a sequence.
gapString - Static variable in class utility.Constants: String representation of a gap in a sequence.
generateGffContent(Storage) - Static method in class utility.IO: Generates the content of a GFF (General Feature Format) file from the given Storage object.
generateReferenceFastaContent(Storage) - Static method in class utility.IO: Generates the content of a reference FASTA file from the given Storage object.
generateVcfContent(ArrayList<Tuple<Triple<String, Integer, String>, VariantInformation>>) - Static method in class utility.IO: Generates the content of a plain VCF (Variant Call Format) file.
getAllele(String) - Method in class datastructure.Feature: Retrieves an allele associated with this feature by its unique identifier (uid) or name.
getAlleleCount() - Method in class datastructure.Feature: Retrieves the number of alleles associated with this feature.
getAlleleCount() - Method in class datastructure.Sample: Retrieves the number of alleles in this sample.
getAlleles() - Method in class datastructure.Feature: Retrieves all alleles associated with this feature.
getAlleles() - Method in class datastructure.Sample: Retrieves the entries of the alleles map for this sample.
getAttribute(String) - Method in class datastructure.Attributable: Retrieves the value of an attribute associated with this entity.
getAttributeAsCollection(String) - Method in class datastructure.Attributable: Retrieves the value of an attribute as a collection of strings.
getAttributeOrDefault(String, String) - Method in class datastructure.Attributable: Retrieves the value of an attribute associated with this entity.
getAttributes() - Method in class datastructure.Attributable: Retrieves all attributes associated with this entity.
getCanonicalVariants(String, String) - Static method in class utility.SequenceOperations: Transforms two sequences into canonical VCF variants.
getChildren() - Method in class datastructure.Feature: Retrieves a sorted map of child features associated with this feature.
getClusteringResult() - Static method in class utility.Clustering: Retrieves the clustering results as a list of Clustering.Entry instances.
getContig(String) - Method in class datastructure.Storage: Retrieves a contig by its name.
getContigs() - Method in class datastructure.Storage: Returns a collection view of the contigs stored in the storage.
getCount() - Method in class datastructure.SequenceType: Retrieves the count of occurrences of this sequence type.
getDate() - Static method in class utility.Logging: Returns the current date formatted as a string.
getFastaHeader(String) - Method in class datastructure.SequenceType: Generates a FASTA header for the sequence type.
getFeature(String) - Method in class datastructure.Storage: Retrieve a Feature by its name.
getFeatures() - Method in class datastructure.Storage: Returns a collection view of the features stored in the storage.
getName() - Method in class datastructure.SequenceType: Retrieves the name of this sequence type.
getNameOrUid() - Method in class datastructure.SequenceType: Retrieves the name of this sequence type or its unique identifier (uid), if no name is set.
getOccurrence() - Method in class datastructure.SequenceType: Retrieves the entities (by their unique identifiers) associated with this sequence type.
getProcessedGenotypes() - Method in class datastructure.Storage: Retrieves the number of processed genotype records.
getProteoform(String) - Method in class datastructure.Feature: Retrieves a proteoform associated with this feature by its unique identifier.
getProteoformCount() - Method in class datastructure.Feature: Retrieves the number of proteoforms associated with this feature.
getProteoforms() - Method in class datastructure.Feature: Retrieves all proteoforms associated with this feature.
getReferenceBaseString(boolean) - Method in class datastructure.VariantInformation: Retrieves the reference base content of this variant.
getReferenceOfCall(String) - Static method in class datastructure.Sample: Extracts the reference base character from the starting position of a variant call string.
getSample(String) - Method in class datastructure.Storage: Retrieve a Sample by its name.
getSampleOccurrence() - Method in class datastructure.VariantInformation: Retrieves the occurrences of this variant in samples.
getSamples() - Method in class datastructure.Storage: Returns a collection view of the samples stored in the storage.
getSamplesToUpdate() - Method in class datastructure.Storage: Retrieves a collection of samples that need to be updated based on the presence of variant records.
getSequence() - Method in class datastructure.Contig: Retrieves the nucleotide sequence of this contig or an empty string if no sequence is stored.
getSOTerms(int) - Static method in class datastructure.Storage: Retrieve a collection of sequence ontology terms for a given level.
getSubsequence(int, int) - Method in class datastructure.Contig: Retrieves a subsequence of this contig, caching the result to optimize performance.
getTimestamp() - Static method in class utility.Logging: Returns the current timestamp formatted as a string.
getVariant(int) - Method in class datastructure.SequenceType: Retrieves the variant at the specified position associated with this sequence type.
getVariantCalls(String) - Method in class datastructure.Sample: Retrieves the variant calls for the specified contig in this sample.
getVariantInformation(int, String) - Method in class datastructure.Contig: Retrieves the VariantInformation associated with a specific variant on this contig.
getVariants() - Method in class datastructure.Contig: Retrieves all variants located on this contig.
getVariants() - Method in class datastructure.SequenceType: Retrieves the variants associated with this sequence type.
getVariantsByAlleles(Feature, Set<String>) - Method in class datastructure.Contig: Retrieves variants associated with specific alleles of a feature.
getVariantsByLocation(int, int) - Method in class datastructure.Contig: Retrieves variants located within a specified range on this contig.
getVariantsBySample(String) - Method in class datastructure.Contig: Retrieves variants associated with a specific sample.
getVariantsBySampleAndLocation(String, int, int) - Method in class datastructure.Contig: Retrieves variants associated with a specific sample within a specified location range.
getVariantsCount() - Method in class datastructure.Contig: Calculates the total number of variants located on this contig.
getVariantsCount() - Method in class datastructure.Storage: Returns the total number of variants stored.
getVariantsEffects(List<Tuple<Integer, String>>) - Method in class datastructure.Contig: Extracts and aggregates the SnpEff effects from a list of variants.
globalNucleotideSequenceAlignment(String, String, int, int, SequenceOperations.MarginalGaps, SequenceOperations.MarginalGaps, Integer) - Static method in class utility.SequenceOperations: Performs global nucleotide sequence alignment using a simple scoring matrix.
globalProteinSequenceAlignment(String, String, int, int, SequenceOperations.MarginalGaps, SequenceOperations.MarginalGaps, Integer) - Static method in class utility.SequenceOperations: Performs global protein sequence alignment using the BLOSUM80 scoring matrix.
gzipCompress(String) - Static method in class utility.IO: Compresses a string using GZIP compression and encodes the result in Base64.
gzipDecompress(String) - Static method in class utility.IO: Decompresses a Base64-encoded GZIP-compressed string.

H

hasAttribute(String) - Method in class datastructure.Attributable: Checks if an attribute with the specified key exists in this entity.
hasAttributes() - Method in class datastructure.Attributable: Checks if this entity has any attributes.
hasContig(String) - Method in class datastructure.Storage: Query whether a contig is stored in this instance by its name.
hasData() - Static method in class utility.Clustering: Checks if the dataset contains any samples.
hasFeature(String) - Method in class datastructure.Storage: Query whether a feature is stored in this instance by its name.
hashCode() - Method in record class utility.Clustering.Entry: Returns a hash code value for this object.
hasMissingContigSequences() - Method in class datastructure.Storage: Checks if all contigs in the storage have a non-empty sequence.
hasNovelVariants() - Method in class datastructure.Storage: Checks if there are any novel variants stored in the storage.
hasOccurrence(String) - Method in class datastructure.SequenceType: Checks if this sequence type is associated with an entity by its identifier.
hasOccurrence(String) - Method in class datastructure.VariantInformation: Checks whether this variant has an occurrence in a specific feature.
hasOccurrence(String, String) - Method in class datastructure.VariantInformation: Checks whether this variant has an occurrence in a sample or allele.
hasReference() - Method in class datastructure.Storage: Return whether Storage.reference is set.
hasSample(String) - Method in class datastructure.Storage: Query whether a sample is stored in this instance by its name.
hasSequence() - Method in class datastructure.Contig: Checks if this contig has an associated nucleotide sequence.
hasVariant(int) - Method in class datastructure.SequenceType: Checks if this sequence type has a variant at the specified position.

I

idx() - Method in record class utility.Clustering.Entry: Returns the value of the idx record component.
init(Level) - Static method in class utility.Logging: Initializes the logging system with a specified logging level.
initializeVCFFileReader(File) - Static method in class utility.IO: Initializes a VCFFileReader instance for the passed VCF file.
INSERTION - Enum constant in enum class datastructure.VariantInformation.Type: An insertion of one or more nucleotides
integrateVariants(Contig, Feature, NavigableMap<Integer, String>, boolean) - Static method in class utility.SequenceOperations: Integrates variants into a reference sequence for a given feature.
IO - Class in utility: Utility class for input/output operations.
IO() - Constructor for class utility.IO
isCanonicalVariant(String, String) - Static method in class datastructure.VariantInformation: Determines whether a variant is canonical.
isCoding() - Method in class datastructure.Feature: Determines if this feature is a coding feature.
isDeletion(String) - Static method in class datastructure.VariantInformation: Determines whether a variant is a deletion based on its alternative content.
isDeletion(String, String, boolean) - Static method in class datastructure.VariantInformation: Determines whether a variant is a deletion, i.e., either the reference base content is a string of any length of Constants.baseSymbols and the alternative base content is a single base of Constants.baseSymbols followed by Constants.gapStrings matching the reference content's length (padded canonical), or the reference base content is a string of any length of Constants.baseSymbols and the alternative content is a single base of Constants.baseSymbols (un-padded canonical).
isInsertion(String) - Static method in class datastructure.VariantInformation: Determines whether a variant is an insertion based on its alternative content.
isInsertion(String, String, boolean) - Static method in class datastructure.VariantInformation: Determines whether a variant is an insertion, i.e., either the alternative base content is a string of any length of Constants.baseSymbols and the reference base content is a single base of Constants.baseSymbols followed by Constants.gapStrings matching the alternative content's length (padded canonical), or the reference base content is a single base of Constants.baseSymbols and the alternative content is a string of any length of Constants.baseSymbols (un-padded canonical).
isPaddedCanonicalVariant(String, String) - Static method in class datastructure.VariantInformation: Determines whether a variant is padded canonical.
isPercentage(String) - Static method in class utility.Validation: Checks if a String represents a percentage value.
isPositionExcluded(String, int) - Method in class datastructure.Storage: Whether position is excluded on contig.
isPositiveDouble(String) - Static method in class utility.Validation: Checks if a String represents a positive double value.
isReverse() - Method in class datastructure.Feature: Checks if this feature is on the reverse strand.
isSubstitution(String) - Static method in class datastructure.VariantInformation: Determines whether a given alternative base content represents a substitution.
isSubstitution(String, String) - Static method in class datastructure.VariantInformation: Determines whether a variant is a substitution; i.e., both the reference and alternative base content match a single base of Constants.baseSymbols.
isVariantExcluded(String, int, String, String) - Method in class datastructure.Storage: Whether variant is excluded on contig at position.

L

label() - Method in record class utility.Clustering.Entry: Returns the value of the label record component.
lineSeparator - Static variable in class utility.Constants: The system-dependent line separator string.
logConfig(String) - Static method in class utility.Logging: Logs a configuration message to the console with a timestamp.
logDone(String) - Static method in class utility.Logging: Logs a message indicating completion with a timestamp.
logDump - Static variable in class utility.Logging: Set to keep track of logged warnings to avoid duplicate messages.
logExit(String) - Static method in class utility.Logging: Logs a critical exit message to the console with a timestamp.
logger - Static variable in class utility.Logging: Logger instance for the application.
Logging - Class in utility: Logging utility class for printing messages to the console with different severity levels.
Logging() - Constructor for class utility.Logging
logInfo(String) - Static method in class utility.Logging: Logs an informational message to the console with a timestamp.
logSevere(String) - Static method in class utility.Logging: Logs an error message to the console with a timestamp.
logWarning(String) - Static method in class utility.Logging: Logs a warning message to the console with a timestamp.
logWarningOnce(String, String) - Static method in class utility.Logging: Logs a warning message to the console with a timestamp, but only once for each unique key.
lowCoverageCallPrefix - Static variable in class utility.Constants: Prefix used to indicate low coverage variant calls.
lowFrequencyCallPrefix - Static variable in class utility.Constants: Prefix used to indicate low frequency variant calls.

M

main - package main: Contains the core classes and entry points for the application.
main(String[]) - Static method in class main.Musial: The main entry point of the MUSIAL application.
md5Hash(String) - Static method in class utility.IO: Generates the MD5 hash of the given string.
minimumCoverage() - Method in class datastructure.Storage: Retrieves the minimum coverage parameter.
minimumFrequency() - Method in class datastructure.Storage: Retrieves the minimum frequency parameter.
Musial - Class in main: 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.
Musial() - Constructor for class main.Musial
Musial.Task - Enum Class in main: Enum specifying tasks of MUSIAL to choose from.
Musial.Update - Class in main: Provides functionality to update (build or expand) a MUSIAL storage.
Musial.View - Class in main: Provides functionality to generate and display various types of tables based on the data stored in the `Storage` object.
MusialException - Exception Class in exceptions: A custom exception class for handling application-specific errors.
MusialException(String) - Constructor for exception class exceptions.MusialException: Constructs a new MusialException with the specified detail message.

N

name - Variable in class datastructure.Contig: The name or internal identifier of this contig.
name - Variable in class datastructure.Feature: The name or internal identifier of this genomic feature.
name - Variable in class datastructure.Sample: The name or internal identifier of this sample.
name - Variable in class datastructure.SequenceType: Optional name to describe this sequence type.
name() - Method in record class utility.Clustering.Entry: Returns the value of the name record component.

O

occurrence - Variable in class datastructure.SequenceType: A set representing the occurrences of this sequence type.
occurrence - Variable in class datastructure.VariantInformation: A mapping of occurrences of this variant in samples and alleles.
occurrenceAsString() - Method in class datastructure.SequenceType: Converts the occurrences of this sequence type to a comma-separated string.
OS - Class in utility: Utility class for operating system-related functionalities.
OS() - Constructor for class utility.OS
outlierScore() - Method in record class utility.Clustering.Entry: Returns the value of the outlierScore record component.
outputDirectory - Static variable in class main.Musial: Specifies the output directory for the program.

P

padGaps(String, int) - Static method in class utility.SequenceOperations: Pads a string with gap characters to reach a specified length.
parameters - Static variable in class utility.CLI: A map to store parsed command-line parameters.
parse(String[]) - Static method in class utility.CLI: Parses the command-line arguments and executes the corresponding task.
PENALIZE - Enum constant in enum class utility.SequenceOperations.MarginalGaps: Gaps at the end of a sequence are penalized normally.
PIPE - Static variable in class utility.Constants: Pipe string constant.
printSoftwareInfo() - Static method in class utility.Logging: Prints the software information to the console.
proteoforms - Variable in class datastructure.Feature: Proteoforms (SequenceType instances) associated with this feature.

R

readFile(File) - Static method in class utility.IO: Reads the content of a file line by line and returns a list of non-empty, trimmed lines.
readTabularFileAsNestedMap(File) - Static method in class utility.IO: Reads a tabular file and converts its content into a nested map structure.
reference - Variable in class datastructure.VariantInformation: The reference base content of this variant.
removeAttribute(String) - Method in class datastructure.Attributable: Removes an attribute with the specified key from this entity.
reset() - Static method in class utility.Clustering: Resets the clustering state by clearing the dataset, labels, and model.
runCommand(String[], String, String, String) - Static method in class utility.OS: Executes a command-line command using a ProcessBuilder.
runId - Static variable in class main.Musial: Unique run ID of this program instance; generated from the current date and time.
runProteoformInference() - Method in class datastructure.Storage: Checks if proteoform inference should be run.

S

Sample - Class in datastructure: Represents a sample containing variant calls from a single biological sample.
Sample(String, int) - Constructor for class datastructure.Sample: Constructs a new Sample instance with the specified name and initial capacity for the alleles map.
sampleOccurrence - Static variable in class datastructure.Attributable: Key used to represent the occurrence of samples in classes that extend Attributable.
SEMICOLON - Static variable in class utility.Constants: Semicolon string constant.
sequence - Variable in class datastructure.Contig: The sequence of this contig.
SEQUENCE - Enum constant in enum class main.Musial.Task: Task to export sequence data from a MUSIAL storage file.
sequenceCache - Variable in class datastructure.Contig: Cache to store the sequence of a contig for a specific start and end position.
SequenceOperations - Class in utility: Utility class for performing various sequence operations.
SequenceOperations() - Constructor for class utility.SequenceOperations
SequenceOperations.MarginalGaps - Enum Class in utility: Enum to store different modes to handle prefix gaps for global sequence alignment.
SequenceType - Class in datastructure: Represents a sequence type with associated variants, occurrences, and attributes.
SequenceType(String, List<Tuple<Integer, String>>) - Constructor for class datastructure.SequenceType: Constructs a new SequenceType instance with the specified unique identifier and variants.
serialize(Storage, File) - Static method in class datastructure.Storage.Factory: Writes the given `Storage` object to a file in JSON format.
setAllele(String, String) - Method in class datastructure.Sample: Associates a specific allele with a feature in this sample.
setAttribute(String, String) - Method in class datastructure.Attributable: Adds an attribute to this entity.
setAttributes(Map<String, String>) - Method in class datastructure.Attributable: Adds multiple attributes to this entity.
setChildren(SortedMap<String, List<Tuple<Integer, Integer>>>) - Method in class datastructure.Feature: Stores the child features of this feature as a serialized string in the "children" attribute.
setName(String) - Method in class datastructure.SequenceType: Sets the name of this sequence type.
setSampleInformation(Storage, File) - Static method in class datastructure.Storage.Factory: Sets sample information in the storage from a specified file.
setVcfFiles(Storage, List<String>) - Static method in class datastructure.Storage.Factory: Sets the VCF files in the storage from a list of file paths.
SIGN - Static variable in class utility.Constants: Number sign string constant.
skipSnpEff() - Method in class datastructure.Storage: Checks if the SnpEff annotation process should be skipped.
snpEffAttributeKeyPrefix - Static variable in class utility.Constants: Prefix for SnpEff attribute keys.
snpEffKeys - Static variable in class utility.Constants: SnpEff annotation field names.
SNV - Enum constant in enum class datastructure.VariantInformation.Type: Single Nucleotide Variant.
SO - Static variable in class datastructure.Storage: Map of sequence ontology (SO) terms and their respective hierarchy levels as used by MUSIAL.
softwareContact - Static variable in class main.Musial: Author contact of the software; parsed from `/src/main/resources/info.properties`.
softwareLicense - Static variable in class main.Musial: License information of the software; parsed from `/src/main/resources/info.properties`.
softwareName - Static variable in class main.Musial: Name of the software; parsed from `/src/main/resources/info.properties`.
softwareVersion - Static variable in class main.Musial: Version of the software; parsed from `/src/main/resources/info.properties`.
start - Variable in class datastructure.Feature: 1-based indexed starting position of the feature.
startTime - Static variable in class main.Musial: Start time of the program.
stopCodon - Static variable in class utility.Constants: Represents the stop codon in a sequence.
Storage - Class in datastructure: The `Storage` class is a central component of the project, designed to manage genomic data, including contigs, features, and samples.
Storage.Factory - Class in datastructure: Factory class for creating and managing instances of Storage.
storageExtension - Static variable in class main.Musial: File extension used for MUSIAL storage files.
storeFiltered() - Method in class datastructure.Storage: Retrieves whether filtered calls should be retained as ambiguous bases (N).
strand - Variable in class datastructure.Feature: Strand of the feature.
stripGaps(String) - Static method in class utility.SequenceOperations: Removes all gap characters from the input string.
synonymous - Static variable in class utility.Constants: Represents the term used for synonymous Feature.Alleles that are not actually stored.

T

TAB - Static variable in class utility.Constants: Tabulator string constant.
task - Static variable in class main.Musial: Specifies the task to execute.
toGffString() - Method in class datastructure.Feature: Converts this feature and its child features into a GFF3 format string.
toString() - Method in class datastructure.Feature: Converts this feature into a tab-delimited string representation.
toString() - Method in class datastructure.Sample: Converts this sample to its string representation.
toString() - Method in class datastructure.SequenceType: Returns a string representation of this sequence type in the format identifier attributes variants.
toString() - Method in record class utility.Clustering.Entry: Returns a string representation of this record class.
train() - Static method in class utility.Clustering: Trains the HDBSCAN model using the current dataset.
transferSampleInformation() - Method in class datastructure.Storage: Transfers sample information from variant records to the storage.
transferVariantsInformation() - Method in class datastructure.Storage: Transfers variant information from sample variant calls to the storage.
translateSequence(String, boolean) - Static method in class utility.SequenceOperations: Translates a DNA sequence into an amino-acid sequence.
type - Variable in class datastructure.Feature: The type of this genomic feature.
type - Variable in class datastructure.VariantInformation: The type of this variant (e.g., SNV, insertion, deletion).

U

uid - Variable in class datastructure.Feature: Unique identifier of this feature.
uid - Variable in class datastructure.SequenceType: The unique identifier of this entity.
UNDEFINED - Enum constant in enum class main.Musial.Task: Task is undefined.
Update() - Constructor for class main.Musial.Update
updateAllele(Contig, ArrayList<Tuple<Integer, String>>, Sample) - Method in class datastructure.Feature: Updates or creates an allele associated with a given contig and sample.
updateProteoform(Contig, String) - Method in class datastructure.Feature: Updates or creates a proteoform associated with a given allele and contig.
updateSequenceTypes() - Method in class datastructure.Storage: Updates sequence types for all samples and features in the storage.
updateStatistics() - Method in class datastructure.Storage: Updates various statistics for samples, contigs, and features in the storage.
updateVariants() - Method in class datastructure.Storage: Updates the variants in the storage by processing VCF files and transferring the relevant information.
utility - package utility: Contains helper classes and functions that perform common operations such as file handling, data processing, and other reusable utilities to support the application's functionality.

V

Validation - Class in utility: Utility class for performing various validation checks.
Validation() - Constructor for class utility.Validation
valueOf(String) - Static method in enum class datastructure.VariantInformation.Type: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class main.Musial.Task: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class utility.SequenceOperations.MarginalGaps: Returns the enum constant of this class with the specified name.
values() - Static method in enum class datastructure.VariantInformation.Type: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class main.Musial.Task: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class utility.SequenceOperations.MarginalGaps: Returns an array containing the constants of this enum class, in the order they are declared.
variantCallPattern - Static variable in class datastructure.Sample: Regular expression pattern to match variant call strings.
variantCalls - Variable in class datastructure.Sample: Hierarchical map structure to store variant calls.
VariantInformation - Class in datastructure: Stores information associated with a nucleotide variant.
VariantInformation(String, String) - Constructor for class datastructure.VariantInformation: Constructor for VariantInformation.
VariantInformation.Type - Enum Class in datastructure: Enum representing the type of variant.
variants - Variable in class datastructure.Contig: Hierarchical map structure to store variants located on this contig.
variants - Variable in class datastructure.SequenceType: Variants defining this entity.
variantsAsString() - Method in class datastructure.SequenceType: Converts the variants of this sequence type to a string representation.
variantsAsString(List<Tuple<Integer, String>>) - Static method in class datastructure.SequenceType: Converts a list of variants to a string representation.
variantsAsString(Map<Integer, String>) - Static method in class datastructure.SequenceType: Converts a map of variants to a string representation.
View() - Constructor for class main.Musial.View
VIEW - Enum constant in enum class main.Musial.Task: Task to view content of a MUSIAL storage file.

W

writeFile(Path, String) - Static method in class utility.IO: Writes the specified content to a file at the given path.

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