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

getAnnotation(String) - Method in interface compbio.data.msa.SequenceAnnotation

Return the result of the job.

getAnnotationForSequence(String) - Method in class compbio.data.sequence.ScoreManager

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

Returns list of Parameter and Option supported by current runner

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

getCategories() - Static method in class compbio.data.msa.Category

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

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

Gets the value of id

getJobStatus(String) - Method in interface compbio.data.msa.JManagement

Return the status of the job.

getLastTested(Services) - Method in interface compbio.data.msa.RegistryWS

Number of seconds since the last test.

getLastTestedOn(Services) - Method in interface compbio.data.msa.RegistryWS

The date and time the service has been verified to work last time

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

getLimit(String) - Method in interface compbio.data.msa.Metadata

Get a Limit for a preset.

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

getLimits() - Method in interface compbio.data.msa.Metadata

List Limits supported by a web service.

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

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

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

getMethod(String) - Static method in enum compbio.data.sequence.ConservationMethod

getMethod() - Method in class compbio.data.sequence.Score

Returns the ConservationMethod

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

getNumberOfScores() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder

getNumberOfSeq() - Method in class compbio.data.sequence.ScoreManager

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

Returns the list of the Options supported by the executable of type T

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

Returns the list of parameters supported executable of type T.

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 interface compbio.data.msa.Metadata

Get presets supported by a web service

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

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

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

getRanges() - Method in class compbio.data.sequence.Score

Return Ranges if any Collections.EMPTY_SET otherwise

getResult(String) - Method in interface compbio.data.msa.MsaWS

Return the result of the job.

getRunnerByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil

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

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

getRunnerOptions() - Method in interface compbio.data.msa.Metadata

Get options supported by a web service

getScoreByMethod(Enum<?>) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder

getScoreByMethod(String) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder

getScores() - Method in class compbio.data.sequence.Score

The column scores for the alignment

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

getService(String) - Static method in enum compbio.ws.client.Services

getServiceByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil

getServiceByRunner(Class<? extends Executable>) - Static method in class compbio.ws.client.ServicesUtil

getServiceCategories() - Method in interface compbio.data.msa.RegistryWS

Gets the list of services per category.

getServiceDescription(Services) - Method in interface compbio.data.msa.RegistryWS

Gives the description of the service.

getServiceImpl(Services) - Static method in class compbio.ws.client.ServicesUtil

getServiceInfo() - Method in enum compbio.ws.client.Services

getServices() - Method in class compbio.data.msa.Category

getServices(String) - Static method in class compbio.ws.client.Jws2Client

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

getSMERFSColumnScore(String) - Static method in enum compbio.data.sequence.SMERFSConstraints

getSupportedServices() - Method in interface compbio.data.msa.RegistryWS

List of services that are functioning on the server.

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

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

GLOBPLOT_INFO - Static variable in enum compbio.ws.client.Services