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Score
- Class in
compbio.data.sequence
A value class for AACon annotation results storage.
Score(Enum<?>, ArrayList<Float>)
- Constructor for class compbio.data.sequence.
Score
Instantiate the Score
Score(Enum<?>, ArrayList<Float>, TreeSet<Range>)
- Constructor for class compbio.data.sequence.
Score
Score(Enum<?>, TreeSet<Range>)
- Constructor for class compbio.data.sequence.
Score
Score(Enum<?>, float[])
- Constructor for class compbio.data.sequence.
Score
ScoreManager
- Class in
compbio.data.sequence
ScoreManager.ScoreHolder
- Class in
compbio.data.sequence
scores
- Variable in class compbio.data.sequence.
ScoreManager.ScoreHolder
SequenceAnnotation
<
T
> - Interface in
compbio.data.msa
Interface for tools that results to one or more annotation to sequence(s) Single, multiple sequences their groups or alignments can be annotated
SequenceUtil
- Class in
compbio.data.sequence
Utility class for operations on sequences
SERVICE_NAMESPACE
- Static variable in interface compbio.data.msa.
JABAService
Services
- Enum in
compbio.ws.client
List of web services currently supported by JABAWS version 2
ServicesUtil
- Class in
compbio.ws.client
ServicesUtil()
- Constructor for class compbio.ws.client.
ServicesUtil
setActualNumberofSequences(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setArg0(Services)
- Method in class compbio.data.msa.jaxws.
GetLastTested
setArg0(Services)
- Method in class compbio.data.msa.jaxws.
GetLastTestedOn
setArg0(Services)
- Method in class compbio.data.msa.jaxws.
GetServiceDescription
setArg0(Services)
- Method in class compbio.data.msa.jaxws.
IsOperating
setArg0(Services)
- Method in class compbio.data.msa.jaxws.
TestService
setDefaultValue(String)
- Method in class compbio.metadata.
Option
Sets one of the values defined in optionList as default.
setDefaultValue(String)
- Method in class compbio.metadata.
Parameter
setDescription(String)
- Method in class compbio.metadata.
Option
setDescription(String)
- Method in class compbio.metadata.
Preset
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
Align
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
Analize
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
CustomAlign
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
CustomAnalize
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
PresetAlign
setFastaSequences(List<FastaSequence>)
- Method in class compbio.data.msa.jaxws.
PresetAnalize
setFurtherDetails(URL)
- Method in class compbio.metadata.
Option
setJobId(String)
- Method in class compbio.data.msa.jaxws.
CancelJob
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetAnnotation
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetJobStatus
setJobId(String)
- Method in class compbio.data.msa.jaxws.
GetResult
setJobId(String)
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
setMax(String)
- Method in class compbio.metadata.
ValueConstrain
setMessage(String)
- Method in class compbio.data.msa.jaxws.
JobSubmissionExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
ResultNotAvailableExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
UnsupportedRuntimeExceptionBean
setMessage(String)
- Method in class compbio.data.msa.jaxws.
WrongParameterExceptionBean
setMin(String)
- Method in class compbio.metadata.
ValueConstrain
setName(String)
- Method in class compbio.metadata.
Option
setName(String)
- Method in class compbio.metadata.
Preset
setNumberOfSequencesAllowed(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setOptionName(String)
- Method in class compbio.metadata.
Parameter
setOptionNames(Set<String>)
- Method in class compbio.metadata.
Option
setOptionNames(Set<String>)
- Method in class compbio.metadata.
Parameter
setOptions(List<Option>)
- Method in class compbio.data.msa.jaxws.
CustomAlign
setOptions(List<Option>)
- Method in class compbio.data.msa.jaxws.
CustomAnalize
setOptions(List<String>)
- Method in class compbio.metadata.
Preset
setOptions(List<Option<T>>)
- Method in class compbio.metadata.
RunnerConfig
Adds the list of options or parameters to the internal list of options
setParameters(List<Parameter<T>>)
- Method in class compbio.metadata.
RunnerConfig
Sets the list of parameters as internal list
setPosition(long)
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
setPossibleValues(Set<String>)
- Method in class compbio.metadata.
Parameter
setPreset(Preset)
- Method in class compbio.data.msa.jaxws.
PresetAlign
setPreset(Preset)
- Method in class compbio.data.msa.jaxws.
PresetAnalize
setPresetName(String)
- Method in class compbio.data.msa.jaxws.
GetLimit
setPresets(List<Preset<T>>)
- Method in class compbio.metadata.
PresetManager
setPrmSeparator(String)
- Method in class compbio.metadata.
RunnerConfig
Sets name value separator character
setRanges(TreeSet<Range>)
- Method in class compbio.data.sequence.
Score
setRequired(boolean)
- Method in class compbio.metadata.
Option
setReturn(String)
- Method in class compbio.data.msa.jaxws.
AlignResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
AnalizeResponse
setReturn(boolean)
- Method in class compbio.data.msa.jaxws.
CancelJobResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
CustomAlignResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
CustomAnalizeResponse
setReturn(ScoreManager)
- Method in class compbio.data.msa.jaxws.
GetAnnotationResponse
setReturn(JobStatus)
- Method in class compbio.data.msa.jaxws.
GetJobStatusResponse
setReturn(Date)
- Method in class compbio.data.msa.jaxws.
GetLastTestedOnResponse
setReturn(int)
- Method in class compbio.data.msa.jaxws.
GetLastTestedResponse
setReturn(Limit)
- Method in class compbio.data.msa.jaxws.
GetLimitResponse
setReturn(LimitsManager)
- Method in class compbio.data.msa.jaxws.
GetLimitsResponse
setReturn(PresetManager)
- Method in class compbio.data.msa.jaxws.
GetPresetsResponse
setReturn(Alignment)
- Method in class compbio.data.msa.jaxws.
GetResultResponse
setReturn(RunnerConfig)
- Method in class compbio.data.msa.jaxws.
GetRunnerOptionsResponse
setReturn(Set<Category>)
- Method in class compbio.data.msa.jaxws.
GetServiceCategoriesResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
GetServiceDescriptionResponse
setReturn(Set<Services>)
- Method in class compbio.data.msa.jaxws.
GetSupportedServicesResponse
setReturn(boolean)
- Method in class compbio.data.msa.jaxws.
IsOperatingResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
PresetAlignResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
PresetAnalizeResponse
setReturn(ChunkHolder)
- Method in class compbio.data.msa.jaxws.
PullExecStatisticsResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
TestAllServicesResponse
setReturn(String)
- Method in class compbio.data.msa.jaxws.
TestServiceResponse
setRunnerClassName(String)
- Method in class compbio.metadata.
PresetManager
setRunnerClassName(String)
- Method in class compbio.metadata.
RunnerConfig
Set the name of a runner class
setSequenceLenghtActual(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setSequenceLenghtAllowed(int)
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
setType(ValueConstrain.Type)
- Method in class compbio.metadata.
ValueConstrain
setValidValue(ValueConstrain)
- Method in class compbio.metadata.
Parameter
setValue(String)
- Method in interface compbio.metadata.
Argument
Set default values for the parameter or an option
setValue(String)
- Method in class compbio.metadata.
Option
SINGLE_ENTRY_KEY
- Static variable in class compbio.data.sequence.
ScoreManager
SMERFSConstraints
- Enum in
compbio.data.sequence
Enumeration defining two constraints for SMERFS columns score calculation.
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