A C D E F G H I J L M N O P R S T U V W

G

gapchar - Static variable in class compbio.data.sequence.ClustalAlignmentUtil

Dash char to be used as gap char in the alignments

getActualNumberofSequences() - Method in exception compbio.metadata.LimitExceededException

getArgument(String) - Method in class compbio.metadata.RunnerConfig

Returns the argument by its name if found, NULL otherwise

getArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig

Returns the argument by option name, NULL if the argument is not found

getArguments(RunnerConfig<T>) - Method in class compbio.metadata.Preset

Converts list of options as String to type Option

getArguments() - Method in class compbio.metadata.RunnerConfig

getAvgSeqLength() - Method in class compbio.metadata.Limit

getAvgSequenceLength(List<FastaSequence>) - Static method in class compbio.metadata.Limit

Calculates an average sequence length of the dataset

getChunk() - Method in class compbio.metadata.ChunkHolder

getDefaultLimit() - Method in class compbio.metadata.LimitsManager

getDefaultValue() - Method in interface compbio.metadata.Argument

getDefaultValue() - Method in class compbio.metadata.Option

A default value of the option.

getDescription() - Method in interface compbio.metadata.Argument

getDescription() - Method in class compbio.metadata.Option

A long description of the Option

getDescription() - Method in class compbio.metadata.Preset

getFormatedSequence(int) - Method in class compbio.data.sequence.FastaSequence

Format sequence per width letter in one string.

getFormattedFasta() - Method in class compbio.data.sequence.FastaSequence

getFurtherDetails() - Method in interface compbio.metadata.Argument

getFurtherDetails() - Method in class compbio.metadata.Option

The URL where further details about the option can be found

getGapchar() - Method in class compbio.data.sequence.AlignmentMetadata

getHost(String[]) - Static method in class compbio.ws.client.Jws2Client

Extracts host name from the command line

getId() - Method in class compbio.data.sequence.FastaSequence

Gets the value of id

getLength() - Method in class compbio.data.sequence.FastaSequence

getLimitByName(String) - Method in class compbio.metadata.LimitsManager

getLimits() - Method in class compbio.metadata.LimitsManager

getMax() - Method in class compbio.metadata.ValueConstrain

getMetadata() - Method in class compbio.data.sequence.Alignment

getMin() - Method in class compbio.metadata.ValueConstrain

getName() - Method in interface compbio.metadata.Argument

getName() - Method in class compbio.metadata.Option

Human readable name of the option

getName() - Method in class compbio.metadata.Preset

getNextPosition() - Method in class compbio.metadata.ChunkHolder

getNumberOfSequencesAllowed() - Method in exception compbio.metadata.LimitExceededException

getOnelineFasta() - Method in class compbio.data.sequence.FastaSequence

getOptionName() - Method in class compbio.metadata.Parameter

getOptionNames() - Method in class compbio.metadata.Option

getOptions() - Method in class compbio.metadata.Preset

getOptions() - Method in class compbio.metadata.RunnerConfig

getParameters() - Method in class compbio.metadata.RunnerConfig

getPossibleValues() - Method in interface compbio.metadata.Argument

getPossibleValues() - Method in class compbio.metadata.Option

List of possible optionNames

getPossibleValues() - Method in class compbio.metadata.Parameter

List is more convenient to work with

getPreset() - Method in class compbio.metadata.Limit

getPresetByName(String) - Method in class compbio.metadata.PresetManager

getPresets() - Method in class compbio.metadata.PresetManager

getPrmSeparator() - Method in class compbio.metadata.RunnerConfig

getProgram() - Method in class compbio.data.sequence.AlignmentMetadata

getRunnerClassName() - Method in class compbio.metadata.PresetManager

getRunnerClassName() - Method in class compbio.metadata.RunnerConfig

getSeqNumber() - Method in class compbio.metadata.Limit

getSequence() - Method in class compbio.data.sequence.FastaSequence

Gets the value of sequence

getSequenceLenghtActual() - Method in exception compbio.metadata.LimitExceededException

getSequenceLenghtAllowed() - Method in exception compbio.metadata.LimitExceededException

getSequences() - Method in class compbio.data.sequence.Alignment

getServiceName(String[]) - Static method in class compbio.ws.client.Jws2Client

Extracts service name from the command line

getSize() - Method in class compbio.data.sequence.Alignment

getType() - Method in class compbio.metadata.ValueConstrain

getValidValue() - Method in class compbio.metadata.Parameter