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java.lang.Object compbio.ws.server.MafftWS
public class MafftWS
Constructor Summary | |
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MafftWS()
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Method Summary | |
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java.lang.String |
align(java.util.List<FastaSequence> sequences)
Align a list of sequences with default settings. |
boolean |
cancelJob(java.lang.String jobId)
Stop running job but leave its output untouched |
java.lang.String |
customAlign(java.util.List<FastaSequence> sequences,
java.util.List<Option<Mafft>> options)
Align a list of sequences with options. |
JobStatus |
getJobStatus(java.lang.String jobId)
Return the status of the job. |
Limit<Mafft> |
getLimit(java.lang.String presetName)
Get a Limit for a preset. |
LimitsManager<Mafft> |
getLimits()
List Limits supported by a web service. |
PresetManager<Mafft> |
getPresets()
Get presets supported by a web service |
Alignment |
getResult(java.lang.String jobId)
Return the result of the job. |
RunnerConfig<Mafft> |
getRunnerOptions()
Get options supported by a web service |
java.lang.String |
presetAlign(java.util.List<FastaSequence> sequences,
Preset<Mafft> preset)
Align a list of sequences with preset. |
ChunkHolder |
pullExecStatistics(java.lang.String jobId,
long position)
Reads 1kb chunk from the statistics file which is specific to a given web service from the position. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MafftWS()
Method Detail |
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public java.lang.String align(java.util.List<FastaSequence> sequences) throws JobSubmissionException
MsaWS
align
in interface MsaWS<Mafft>
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
UnsupportedRuntimeException
- thrown if server OS does not support native executables for a
given web service, e.g. JWS2 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
public java.lang.String customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options) throws JobSubmissionException, WrongParameterException
MsaWS
customAlign
in interface MsaWS<Mafft>
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 informationoptions
- A list of Options
UnsupportedRuntimeException
- thrown if server OS does not support native executables for a
given web service, e.g. JWS2 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
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.
JobSubmissionException
Default Limit is used to decide whether the calculation will be
permitted or denied
public java.lang.String presetAlign(java.util.List<FastaSequence> sequences, Preset<Mafft> preset) throws JobSubmissionException, WrongParameterException
MsaWS
presetAlign
in interface MsaWS<Mafft>
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 informationpreset
- A list of Options
UnsupportedRuntimeException
- thrown if server OS does not support native executables for a
given web service, e.g. JWS2 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
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.
JobSubmissionException
public Alignment getResult(java.lang.String jobId) throws ResultNotAvailableException
MsaWS
getResult
in interface MsaWS<Mafft>
jobId
- a unique job identifier
ResultNotAvailableException
- this exception is throw if the job execution was not
successful or the result of the execution could not be found.
(e.g. removed). Exception could also be thrown is dues to the
lower level problems on the server i.e. IOException,
FileNotFoundException problems as well as
UnknownFileFormatException.public Limit<Mafft> getLimit(java.lang.String presetName)
MsaWS
getLimit
in interface MsaWS<Mafft>
presetName
- the name of the preset. if no name is provided, then the
default preset is returned. If no limit for a particular
preset is defined then the default preset is returned
public LimitsManager<Mafft> getLimits()
MsaWS
getLimits
in interface MsaWS<Mafft>
public ChunkHolder pullExecStatistics(java.lang.String jobId, long position)
MsaWS
pullExecStatistics
in interface MsaWS<Mafft>
jobId
- - unique job identifierposition
- - next position within the file to read
public boolean cancelJob(java.lang.String jobId)
MsaWS
cancelJob
in interface MsaWS<Mafft>
public JobStatus getJobStatus(java.lang.String jobId)
MsaWS
getJobStatus
in interface MsaWS<Mafft>
jobId
- - unique job identifier
public PresetManager<Mafft> getPresets()
MsaWS
getPresets
in interface MsaWS<Mafft>
public RunnerConfig<Mafft> getRunnerOptions()
MsaWS
getRunnerOptions
in interface MsaWS<Mafft>
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