Uses of Interface
org.biojavax.bio.alignment.RemotePairwiseAlignmentProperties

Packages that use RemotePairwiseAlignmentProperties

Package	Description
org.biojavax.bio.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast	This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.

Uses of RemotePairwiseAlignmentProperties in org.biojavax.bio.alignment

Methods in org.biojavax.bio.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(RichSequence rs, RemotePairwiseAlignmentProperties rpa)	Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

Uses of RemotePairwiseAlignmentProperties in org.biojavax.bio.alignment.blast

Classes in org.biojavax.bio.alignment.blast that implement RemotePairwiseAlignmentProperties

Modifier and Type	Class	Description
class	RemoteQBlastAlignmentProperties	This class implements RemotePairwiseAlignmentProperties by specifying several convenient methods used to wrap the addition of Blast alignment parameters.

Methods in org.biojavax.bio.alignment.blast with parameters of type RemotePairwiseAlignmentProperties

Modifier and Type	Method	Description
String	RemoteQBlastService.sendAlignmentRequest(int gid, RemotePairwiseAlignmentProperties rpa)	This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a GenBank GID.
String	RemoteQBlastService.sendAlignmentRequest(String str, RemotePairwiseAlignmentProperties rpa)	This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a string representing the sequence.
String	RemoteQBlastService.sendAlignmentRequest(RichSequence rs, RemotePairwiseAlignmentProperties rpa)	This method is a wrapper that executes the Blast request via the Put command of the CGI-BIN interface with the specified parameters and a RichSequence.