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 class compbio.data.msa.jaxws.LimitExceededExceptionBean

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

GetAnnotation - Class in compbio.data.msa.jaxws

GetAnnotation() - Constructor for class compbio.data.msa.jaxws.GetAnnotation

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

Return the result of the job.

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

GetAnnotationResponse - Class in compbio.data.msa.jaxws

GetAnnotationResponse() - Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse

getArg0() - Method in class compbio.data.msa.jaxws.GetLastTested

getArg0() - Method in class compbio.data.msa.jaxws.GetLastTestedOn

getArg0() - Method in class compbio.data.msa.jaxws.IsOperating

getArg0() - Method in class compbio.data.msa.jaxws.TestService

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

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

getFastaSequences() - Method in class compbio.data.msa.jaxws.Align

getFastaSequences() - Method in class compbio.data.msa.jaxws.Analize

getFastaSequences() - Method in class compbio.data.msa.jaxws.CustomAlign

getFastaSequences() - Method in class compbio.data.msa.jaxws.CustomAnalize

getFastaSequences() - Method in class compbio.data.msa.jaxws.PresetAlign

getFastaSequences() - Method in class compbio.data.msa.jaxws.PresetAnalize

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

getJobId() - Method in class compbio.data.msa.jaxws.CancelJob

getJobId() - Method in class compbio.data.msa.jaxws.GetAnnotation

getJobId() - Method in class compbio.data.msa.jaxws.GetJobStatus

getJobId() - Method in class compbio.data.msa.jaxws.GetResult

getJobId() - Method in class compbio.data.msa.jaxws.PullExecStatistics

GetJobStatus - Class in compbio.data.msa.jaxws

GetJobStatus() - Constructor for class compbio.data.msa.jaxws.GetJobStatus

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

Return the status of the job.

GetJobStatusResponse - Class in compbio.data.msa.jaxws

GetJobStatusResponse() - Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse

GetLastTested - Class in compbio.data.msa.jaxws

GetLastTested() - Constructor for class compbio.data.msa.jaxws.GetLastTested

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

Number of seconds since the last test.

GetLastTestedOn - Class in compbio.data.msa.jaxws

GetLastTestedOn() - Constructor for class compbio.data.msa.jaxws.GetLastTestedOn

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

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

GetLastTestedOnResponse - Class in compbio.data.msa.jaxws

GetLastTestedOnResponse() - Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse

GetLastTestedResponse - Class in compbio.data.msa.jaxws

GetLastTestedResponse() - Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse

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

GetLimit - Class in compbio.data.msa.jaxws

GetLimit() - Constructor for class compbio.data.msa.jaxws.GetLimit

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

Get a Limit for a preset.

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

GetLimitResponse - Class in compbio.data.msa.jaxws

GetLimitResponse() - Constructor for class compbio.data.msa.jaxws.GetLimitResponse

GetLimits - Class in compbio.data.msa.jaxws

GetLimits() - Constructor for class compbio.data.msa.jaxws.GetLimits

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

List Limits supported by a web service.

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

GetLimitsResponse - Class in compbio.data.msa.jaxws

GetLimitsResponse() - Constructor for class compbio.data.msa.jaxws.GetLimitsResponse

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

getMessage() - Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean

getMessage() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean

getMessage() - Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean

getMessage() - Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean

getMessage() - Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean

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 class compbio.data.msa.jaxws.LimitExceededExceptionBean

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.data.msa.jaxws.CustomAlign

getOptions() - Method in class compbio.data.msa.jaxws.CustomAnalize

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.

getPosition() - Method in class compbio.data.msa.jaxws.PullExecStatistics

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.data.msa.jaxws.PresetAlign

getPreset() - Method in class compbio.data.msa.jaxws.PresetAnalize

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

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

getPresetName() - Method in class compbio.data.msa.jaxws.GetLimit

GetPresets - Class in compbio.data.msa.jaxws

GetPresets() - Constructor for class compbio.data.msa.jaxws.GetPresets

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

Get presets supported by a web service

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

GetPresetsResponse - Class in compbio.data.msa.jaxws

GetPresetsResponse() - Constructor for class compbio.data.msa.jaxws.GetPresetsResponse

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 - Class in compbio.data.msa.jaxws

GetResult() - Constructor for class compbio.data.msa.jaxws.GetResult

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

Return the result of the job.

GetResultResponse - Class in compbio.data.msa.jaxws

GetResultResponse() - Constructor for class compbio.data.msa.jaxws.GetResultResponse

getReturn() - Method in class compbio.data.msa.jaxws.AlignResponse

getReturn() - Method in class compbio.data.msa.jaxws.AnalizeResponse

getReturn() - Method in class compbio.data.msa.jaxws.CustomAlignResponse

getReturn() - Method in class compbio.data.msa.jaxws.CustomAnalizeResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetAnnotationResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetJobStatusResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetLastTestedResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetLimitResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetLimitsResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetPresetsResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetResultResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse

getReturn() - Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse

getReturn() - Method in class compbio.data.msa.jaxws.PresetAlignResponse

getReturn() - Method in class compbio.data.msa.jaxws.PresetAnalizeResponse

getReturn() - Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse

getReturn() - Method in class compbio.data.msa.jaxws.TestAllServicesResponse

getReturn() - Method in class compbio.data.msa.jaxws.TestServiceResponse

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 - Class in compbio.data.msa.jaxws

GetRunnerOptions() - Constructor for class compbio.data.msa.jaxws.GetRunnerOptions

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

Get options supported by a web service

GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws

GetRunnerOptionsResponse() - Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse

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 class compbio.data.msa.jaxws.LimitExceededExceptionBean

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

getSequenceLenghtAllowed() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean

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<Executable<?>>) - Static method in class compbio.ws.client.ServicesUtil

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

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 - Class in compbio.data.msa.jaxws

GetSupportedServices() - Constructor for class compbio.data.msa.jaxws.GetSupportedServices

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

List of services that are functioning on the server.

GetSupportedServicesResponse - Class in compbio.data.msa.jaxws

GetSupportedServicesResponse() - Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse

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

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