apollo.analysis
Class RemoteBlastNCBI

java.lang.Object
  apollo.analysis.RemoteBlastNCBI

public class RemoteBlastNCBI
extends java.lang.Object

Sends and retrieves a BLAST request to NCBI's qBLAST service.

Author:

elee

Nested Class Summary

static class	RemoteBlastNCBI.BlastOptions Options for running qBLAST.
static class	RemoteBlastNCBI.BlastType Type of BLAST analysis to run.

Constructor Summary

RemoteBlastNCBI(RemoteBlastNCBI.BlastType type, RemoteBlastNCBI.BlastOptions opts)
Constructor.

Method Summary

java.lang.String

runAnalysis(CurationSet cs, SequenceI seq, int strand, int offset) Run BLAST analysis.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RemoteBlastNCBI

public RemoteBlastNCBI(RemoteBlastNCBI.BlastType type,
                       RemoteBlastNCBI.BlastOptions opts)

Constructor.

Parameters:

type - - BLAST type to run

opts - - BLAST options

Method Detail

runAnalysis

public java.lang.String runAnalysis(CurationSet cs,
                                    SequenceI seq,
                                    int strand,
                                    int offset)
                             throws java.lang.Exception

Run BLAST analysis.

Parameters:

cs - - CurationSet which will hold the BLAST results

seq - - genomic sequence that will be blasted

offset - - genomic position of the start of segment

strand - - genomic strand (1 for plus, -1 for minus)

Returns:

name of the type of BLAST and database run

Throws:

java.lang.Exception - - All encompassing exception should something go wrong