|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface RemotePairwiseAlignmentService
This interface specifies minimal information needed to execute a pairwise alignment on a remote service. Example of service: QBlast service at NCBI Web Service at EBI
Method Summary | |
---|---|
InputStream |
getAlignmentResults(String rid,
RemotePairwiseAlignmentOutputProperties out)
Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object. |
boolean |
isReady(String id,
long present)
Simple method to check if the specified request has been completed by the service used. |
String |
sendAlignmentRequest(Sequence<Compound> seq,
RemotePairwiseAlignmentProperties rpa)
Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object |
String |
sendAlignmentRequest(String str,
RemotePairwiseAlignmentProperties rpa)
Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object |
Method Detail |
---|
String sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) throws Exception
Exception
String sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa) throws Exception
Exception
boolean isReady(String id, long present) throws Exception
id
- :an ID for an alignment requestpresent
- :a long integer value representing the actual time
Exception
- if the ID does not exist.InputStream getAlignmentResults(String rid, RemotePairwiseAlignmentOutputProperties out) throws Exception
rid
- :a String with the request ID for this single alignment runout
- :a RemotePairwiseAlignmentOutputProperties with the specific output instructions.
InputStream
with the actual alignment results
Exception
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |