Uses of Package
compbio.metadata

Packages that use compbio.metadata

compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
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.

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.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.