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| Packages that use compbio.metadata | |
|---|---|
| compbio.data.msa | Web Service interfaces for JAva Bioinformatics Analysis Web Services. |
| compbio.data.msa.jaxws | |
| compbio.engine | |
| compbio.engine.client | |
| compbio.engine.cluster.drmaa | |
| compbio.engine.local | |
| compbio.metadata | A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project. |
| compbio.runner | Utilities commonly used by all runners. |
| compbio.runner._impl | |
| compbio.runner.conservation | |
| compbio.runner.disorder | |
| compbio.runner.msa | Wrappers for native executables for multiple sequence alignment (msa) |
| compbio.ws.server | |
| Classes in compbio.metadata used by compbio.data.msa | |
|---|---|
| ChunkHolder
Represents a chunk of a string data together with the position in a file for the next read operation. |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitExceededException
This exception is thrown if the task larger in size that the limit that applies to the calculation. |
|
| LimitsManager
A collection of Limits |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| Preset
Collection of Options and Parameters with their values |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| UnsupportedRuntimeException
Indicates that the server could not execute native executables. |
|
| WrongParameterException
WrongParameterException is thrown wherever the RunnerConfig object
does not match the actual runnable or then attempting to set the value of
Argument to invalid value. |
|
| Classes in compbio.metadata used by compbio.data.msa.jaxws | |
|---|---|
| ChunkHolder
Represents a chunk of a string data together with the position in a file for the next read operation. |
|
| JobStatus
The status of the job. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitsManager
A collection of Limits |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| Preset
Collection of Options and Parameters with their values |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| Classes in compbio.metadata used by compbio.engine | |
|---|---|
| ChunkHolder
Represents a chunk of a string data together with the position in a file for the next read operation. |
|
| JobExecutionException
JobExecutionException is thrown wherever the results of the calculation cannot be obtained. |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.engine.client | |
|---|---|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitsManager
A collection of Limits |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| UnsupportedRuntimeException
Indicates that the server could not execute native executables. |
|
| Classes in compbio.metadata used by compbio.engine.cluster.drmaa | |
|---|---|
| JobExecutionException
JobExecutionException is thrown wherever the results of the calculation cannot be obtained. |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.engine.local | |
|---|---|
| JobExecutionException
JobExecutionException is thrown wherever the results of the calculation cannot be obtained. |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.metadata | |
|---|---|
| Argument
An unmodifiable view for the options and parameters, with one exception - it allows to set a value |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitExceededException
This exception is thrown if the task larger in size that the limit that applies to the calculation. |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| Parameter
A single value containing an option supported by the web service e.g. |
|
| Preset
Collection of Options and Parameters with their values |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| ValueConstrain
The type and the lower and upper boundaries for numerical value. |
|
| ValueConstrain.Type
|
|
| WrongParameterException
WrongParameterException is thrown wherever the RunnerConfig object
does not match the actual runnable or then attempting to set the value of
Argument to invalid value. |
|
| Classes in compbio.metadata used by compbio.runner | |
|---|---|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitsManager
A collection of Limits |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| Parameter
A single value containing an option supported by the web service e.g. |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| Classes in compbio.metadata used by compbio.runner._impl | |
|---|---|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitsManager
A collection of Limits |
|
| Classes in compbio.metadata used by compbio.runner.conservation | |
|---|---|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.runner.disorder | |
|---|---|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.runner.msa | |
|---|---|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| Classes in compbio.metadata used by compbio.ws.server | |
|---|---|
| ChunkHolder
Represents a chunk of a string data together with the position in a file for the next read operation. |
|
| JobStatus
The status of the job. |
|
| JobSubmissionException
Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException. |
|
| Limit
A value object containing a maximum number of sequences and a maximum average sequence length for a preset. |
|
| LimitExceededException
This exception is thrown if the task larger in size that the limit that applies to the calculation. |
|
| LimitsManager
A collection of Limits |
|
| Option
Command line option/flag or multiple exclusive options with no value. |
|
| Preset
Collection of Options and Parameters with their values |
|
| PresetManager
Collection of presets and methods to manipulate them @see Preset |
|
| ResultNotAvailableException
ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained. |
|
| RunnerConfig
The list of Parameters and Options supported by executable. |
|
| UnsupportedRuntimeException
Indicates that the server could not execute native executables. |
|
| WrongParameterException
WrongParameterException is thrown wherever the RunnerConfig object
does not match the actual runnable or then attempting to set the value of
Argument to invalid value. |
|
|
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