Uses of Interface
org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties

Packages that use RemotePairwiseAlignmentProperties

Package	Description
org.biojava.nbio.ws.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast

Uses of RemotePairwiseAlignmentProperties in org.biojava.nbio.ws.alignment

Methods in org.biojava.nbio.ws.alignment with parameters of type RemotePairwiseAlignmentProperties

Modifier and Type	Method	Description
String	RemotePairwiseAlignmentService.sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
String	RemotePairwiseAlignmentService.sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

Uses of RemotePairwiseAlignmentProperties in org.biojava.nbio.ws.alignment.qblast

Classes in org.biojava.nbio.ws.alignment.qblast that implement RemotePairwiseAlignmentProperties

Modifier and Type	Class	Description
class	NCBIQBlastAlignmentProperties	This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.

Methods in org.biojava.nbio.ws.alignment.qblast with parameters of type RemotePairwiseAlignmentProperties

Modifier and Type	Method	Description
String	NCBIQBlastService.sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rpa)	Converts given GenBank GID to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
String	NCBIQBlastService.sendAlignmentRequest(String query, RemotePairwiseAlignmentProperties alignmentProperties)	Sends the Blast request via the Put command of the CGI-BIN interface.
String	NCBIQBlastService.sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa)	Converts given sequence to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)