Uses of Package
compbio.metadata

Packages that use compbio.metadata

Package	Description
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.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.runner.structure
compbio.stat.collector
compbio.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.
compbio.ws.server

Classes in compbio.metadata used by compbio.data.msa

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
JobSubmissionException Exception for generic problems with JobSubmission it is often thrown as a wrapper for the lower level exceptions like IOException or DrmaaException.
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.conservation

Class and Description
ResultNotAvailableException ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.

Classes in compbio.metadata used by compbio.runner.disorder

Class and Description
ResultNotAvailableException ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.

Classes in compbio.metadata used by compbio.runner.msa

Class and Description
ResultNotAvailableException ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.

Classes in compbio.metadata used by compbio.runner.structure

Class and Description
ResultNotAvailableException ResultNotAvailableException is thrown wherever the results of the calculation cannot be obtained.

Classes in compbio.metadata used by compbio.stat.collector

Class and Description
JobStatus The status of the job.

Classes in compbio.metadata used by compbio.ws.client

Class and Description
Limit A value object containing a maximum number of sequences and a maximum average sequence length for a preset.
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.
UnsupportedRuntimeException Indicates that the server could not execute native executables.

Classes in compbio.metadata used by compbio.ws.server

Class and Description
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.