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+ + + +
+ +

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

+
+
Type Parameters:
T - executable type / web service type
+
+
All Superinterfaces:
JABAService, JManagement, Metadata<T>
+
+
+
All Known Implementing Classes:
AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS
+
+
+
+
public interface SequenceAnnotation<T>
extends JABAService, JManagement, Metadata<T>
+ + +

+Interface for tools that results to one or more annotation to sequence(s) + + Single, multiple sequences their groups or alignments can be annotated +

+ +

+

+
Version:
+
1.0 November 2010
+
Author:
+
Peter Troshin
+
+
+ +

+ + + + + + + +
+Field Summary
+  + + + + + + + +
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Stringanalize(List<FastaSequence> sequences) + +
+          Analyse the sequences.
+ StringcustomAnalize(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Analyse the sequences according to custom settings defined in options + list.
+ ScoreManagergetAnnotation(String jobId) + +
+          Return the result of the job.
+ StringpresetAnalize(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Analyse the sequences according to the preset settings.
+  + + + + + + + +
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
+ +

+analize

+
+String analize(List<FastaSequence> sequences)
+               throws UnsupportedRuntimeException,
+                      LimitExceededException,
+                      JobSubmissionException
+
+
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. +

+

+
+
+
+
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: +
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. +
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
+
+
+
+ +

+customAnalize

+
+String customAnalize(List<FastaSequence> sequences,
+                     List<Option<T>> options)
+                     throws UnsupportedRuntimeException,
+                            LimitExceededException,
+                            JobSubmissionException,
+                            WrongParameterException
+
+
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 +

+

+
+
+
+
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. +
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:
Option
+
+
+
+ +

+presetAnalize

+
+String presetAnalize(List<FastaSequence> sequences,
+                     Preset<T> preset)
+                     throws UnsupportedRuntimeException,
+                            LimitExceededException,
+                            JobSubmissionException,
+                            WrongParameterException
+
+
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. +

+

+
+
+
+
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. +
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
+
+
+
+ +

+getAnnotation

+
+ScoreManager getAnnotation(String jobId)
+                           throws ResultNotAvailableException
+
+
Return the result of the job. +

+

+
+
+
+
Parameters:
jobId - a unique job identifier +
Returns:
the Map with the sequence names, sequence group names or the word + 'Alignment' in case of alignments and values the represented by a + Set of Score objects. The alignment can be represented in as + little as one key->value pair in this map, the list of sequences + will be represented by multiple key->value mappings. If multiple + annotations were calculated, then they are represented as a Set + of Scores. +
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 is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +