compbio.ws.server

Class RNAalifoldWS

java.lang.Object

compbio.ws.server.GenericMetadataService

compbio.ws.server.SequenceAnnotationService<RNAalifold>

compbio.ws.server.RNAalifoldWS

All Implemented Interfaces:

JABAService, JManagement, Metadata<RNAalifold>, SequenceAnnotation<RNAalifold>

public class RNAalifoldWS
extends SequenceAnnotationService<RNAalifold>
implements SequenceAnnotation<RNAalifold>

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	log

Fields inherited from interface compbio.data.msa.JABAService

JABAWS_VERSION, SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE, V3_SERVICE_NAMESPACE

Constructor Summary

Constructors

Constructor and Description
RNAalifoldWS()

Method Summary

Modifier and Type	Method and Description
java.lang.String	analize(java.util.List<FastaSequence> sequences) Analyse the sequences.
java.lang.String	customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<RNAalifold>> options) Analyse the sequences according to custom settings defined in options list.
java.lang.String	presetAnalize(java.util.List<FastaSequence> sequences, Preset<RNAalifold> preset) Analyse the sequences according to the preset settings.

Methods inherited from class compbio.ws.server.SequenceAnnotationService

getAnnotation

Methods inherited from class compbio.ws.server.GenericMetadataService

cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, init, pullExecStatistics

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface compbio.data.msa.SequenceAnnotation

getAnnotation

Methods inherited from interface compbio.data.msa.JManagement

cancelJob, getJobStatus, pullExecStatistics

Methods inherited from interface compbio.data.msa.Metadata

getLimit, getLimits, getPresets, getRunnerOptions

Field Detail

log

private static org.apache.log4j.Logger log

Constructor Detail

RNAalifoldWS

public RNAalifoldWS()

Method Detail

analize

public java.lang.String analize(java.util.List<FastaSequence> sequences)
                         throws UnsupportedRuntimeException,
                                LimitExceededException,
                                JobSubmissionException

Description copied from interface: SequenceAnnotation

Analyse the sequences. The actual analysis algorithm is defined by the type T. Any dataset containing a greater number of sequences or the average length of the sequences are greater then defined in the default Limit will not be accepted for an alignment operation and JobSubmissionException will be thrown.

Specified by:

analize in interface SequenceAnnotation<RNAalifold>

Overrides:

analize in class SequenceAnnotationService<RNAalifold>

Parameters:

sequences - List of FastaSequence objects. The programme does not perform any sequence validity checks. Nor does it checks whether the sequences names are unique. It is responsibility of the caller to validate this information

Returns:

jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or average length exceeds what is defined by the limit

JobSubmissionException - is thrown when the job could not be submitted due to the following reasons: 1) The number of sequences in the submission or their average length is greater then defined by the default Limit. 2) Any problems on the server side e.g. it is misconfigured or malfunction, is reported via this exception. In the first case the information on the limit could be obtained from an exception.

customAnalize

public java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
                                      java.util.List<Option<RNAalifold>> options)
                               throws UnsupportedRuntimeException,
                                      LimitExceededException,
                                      JobSubmissionException,
                                      WrongParameterException

Description copied from interface: SequenceAnnotation

Analyse the sequences according to custom settings defined in options list. The actual analysis algorithm is defined by the type T. Default Limit is used to decide whether the calculation will be permitted or denied

Specified by:

customAnalize in interface SequenceAnnotation<RNAalifold>

Overrides:

customAnalize in class SequenceAnnotationService<RNAalifold>

Parameters:

sequences - List of FastaSequence objects. The programme does not perform any sequence validity checks. Nor does it checks whether the sequences names are unique. It is responsibility of the caller to validate this information

options - A list of Options

Returns:

jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or average length exceeds what is defined by the limit

JobSubmissionException - is thrown when the job could not be submitted due to the following reasons: 1) The number of sequences in the submission or their average length is greater then defined by the default Limit. 2) Any problems on the server side e.g. it is misconfigured or malfunction, is reported via this exception. In the first case the information on the limit could be obtained from an exception.

WrongParameterException - is throws when 1) One of the Options provided is not supported, 2) The value of the option is defined outside the boundaries. In both cases exception object contain the information on the violating Option.

See Also:

Option

presetAnalize

public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
                                      Preset<RNAalifold> preset)
                               throws UnsupportedRuntimeException,
                                      LimitExceededException,
                                      JobSubmissionException,
                                      WrongParameterException

Description copied from interface: SequenceAnnotation

Analyse the sequences according to the preset settings. The actual analysis algorithm is defined by the type T. Limit for a presetName is used whether the calculation will be permitted or denied. If no Limit was defined for a presetName, than default limit is used.

Specified by:

presetAnalize in interface SequenceAnnotation<RNAalifold>

Overrides:

presetAnalize in class SequenceAnnotationService<RNAalifold>

Parameters:

sequences - List of FastaSequence objects. The programme does not perform any sequence validity checks. Nor does it checks whether the sequences names are unique. It is responsibility of the caller to validate this information

preset - A list of Options

Returns:

String - jobId - unique identifier for the job

Throws:

UnsupportedRuntimeException - thrown if server OS does not support native executables for a given web service, e.g. JABAWS is deployed on Windows and Mafft service is called

LimitExceededException - is throw if the input sequences number or average length exceeds what is defined by the limit

JobSubmissionException - is thrown when the job could not be submitted due to the following reasons: 1) The number of sequences in the submission or their average length is greater then defined by the default Limit. 2) Any problems on the server side e.g. it is misconfigured or malfunction, is reported via this exception. In the first case the information on the limit could be obtained from an exception.

WrongParameterException - is throws when 1) One of the Options provided is not supported, 2) The value of the option is defined outside the boundaries. In both cases exception object contain the information on the violating Option.