X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fws%2Fserver%2FDisemblWS.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fws%2Fserver%2FDisemblWS.html;h=e4ca353e3869a85886e6bd95710c2c12202497c9;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/ws/server/DisemblWS.html b/website/full_javadoc/compbio/ws/server/DisemblWS.html new file mode 100644 index 0000000..e4ca353 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/DisemblWS.html @@ -0,0 +1,414 @@ + + + + + + +DisemblWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+ + + +
+ +

+ +compbio.ws.server +
+Class DisemblWS

+
+java.lang.Object
+  extended by compbio.ws.server.GenericMetadataService
+      extended by compbio.ws.server.SequenceAnnotationService<Disembl>
+          extended by compbio.ws.server.DisemblWS
+
+
+
All Implemented Interfaces:
JABAService, JManagement, Metadata<Disembl>, SequenceAnnotation<Disembl>
+
+
+
+
public class DisemblWS
extends SequenceAnnotationService<Disembl>
implements SequenceAnnotation<Disembl>
+ + +

+

+ +

+ + + + + + + +
+Field Summary
+  + + + + + + + +
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
+  + + + + + + + + + + +
+Constructor Summary
DisemblWS() + +
+           
+  + + + + + + + + + + + + + + + +
+Method Summary
+ StringcustomAnalize(List<FastaSequence> sequences, + List<Option<Disembl>> options) + +
+          Analyse the sequences according to custom settings defined in options + list.
+ StringpresetAnalize(List<FastaSequence> sequences, + Preset<Disembl> preset) + +
+          Analyse the sequences according to the preset settings.
+  + + + + + + + +
Methods inherited from class compbio.ws.server.SequenceAnnotationService
analize, getAnnotation
+  + + + + + + + +
Methods inherited from class compbio.ws.server.GenericMetadataService
cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
+  + + + + + + + +
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.SequenceAnnotation
analize, getAnnotation
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+DisemblWS

+
+public DisemblWS()
+
+
+ + + + + + + + +
+Method Detail
+ +

+customAnalize

+
+public String customAnalize(List<FastaSequence> sequences,
+                            List<Option<Disembl>> 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<Disembl>
Overrides:
customAnalize in class SequenceAnnotationService<Disembl>
+
+
+
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 String presetAnalize(List<FastaSequence> sequences,
+                            Preset<Disembl> 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<Disembl>
Overrides:
presetAnalize in class SequenceAnnotationService<Disembl>
+
+
+
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.
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
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+ + + +
+ + +