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+ + + +
+ +

+ +compbio.data.msa +
+Interface MsaWS<T>

+
+
Type Parameters:
T - executable type / web service type
+
+
All Superinterfaces:
JABAService, JManagement, Metadata<T>
+
+
+
+
public interface MsaWS<T>
extends JABAService, JManagement, Metadata<T>
+ + +

+Multiple Sequence Alignment (MSA) Web Services Interface +

+ +

+

+
Author:
+
pvtroshin + + Date November 2010
+
+
+ +

+ + + + + + + +
+Field Summary
+  + + + + + + + +
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
+          Align a list of sequences with options.
+ AlignmentgetResult(java.lang.String jobId) + +
+          Return the result of the job.
+ java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
+  + + + + + + + +
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
+  +

+ + + + + + + + +
+Method Detail
+ +

+align

+
+java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws UnsupportedRuntimeException,
+                              LimitExceededException,
+                              JobSubmissionException
+
+
Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when 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. +

+

+
+
+
+
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 make sure of this +
Returns:
jobId - unique identifier for the job +
Throws: +
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. +
java.security.InvalidParameterException - thrown if input list of FASTA sequences is null or empty +
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 their average + length exceeds what is defined by the limit
+
+
+
+ +

+customAlign

+
+java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                             java.util.List<Option<T>> options)
+                             throws UnsupportedRuntimeException,
+                                    LimitExceededException,
+                                    JobSubmissionException,
+                                    WrongParameterException
+
+
Align a list of sequences with options. +

+

+
+
+
+
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: +
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. +
java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
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 their average + length exceeds what is defined by the limit
See Also:
Default Limit is used to decide whether the calculation will be + permitted or denied
+
+
+
+ +

+presetAlign

+
+java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                             Preset<T> preset)
+                             throws UnsupportedRuntimeException,
+                                    LimitExceededException,
+                                    JobSubmissionException,
+                                    WrongParameterException
+
+
Align a list of sequences with preset. + + 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. +

+

+
+
+
+
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: +
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. +
java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
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
See Also:
Preset
+
+
+
+ +

+getResult

+
+Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
+
+
Return the result of the job. This method waits for the job + jobId to complete before return. +

+

+
+
+
+
Parameters:
jobId - a unique job identifier +
Returns:
Alignment +
Throws: +
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 due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
java.security.InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid + format
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + +