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+Uses of Package
compbio.metadata

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+Packages that use compbio.metadata
compbio.data.msaWeb 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.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.conservation  
compbio.runner.disorder  
compbio.runner.msaWrappers 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.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
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