apollo.analysis
Class RemotePrimerBlastNCBI

java.lang.Object
  apollo.analysis.RemotePrimerBlastNCBI

public class RemotePrimerBlastNCBI
extends java.lang.Object

Sends and retrieves a request to NCBI's Primer-BLAST CGI.

Author:

elee

Nested Class Summary

static class

RemotePrimerBlastNCBI.PrimerBlastOptions Options for running Primer-BLAST.

Constructor Summary

RemotePrimerBlastNCBI(RemotePrimerBlastNCBI.PrimerBlastOptions opts)
Constructor.

Method Summary

java.lang.String	runAnalysis(CurationSet cs, SequenceI seq, int offset) Run Primer-BLAST analysis.
java.lang.String	runAnalysis(CurationSet cs, SequenceI seq, int offset, FeatureList fl) Run Primer-BLAST analysis.

Methods inherited from class java.lang.Object

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

Constructor Detail

RemotePrimerBlastNCBI

public RemotePrimerBlastNCBI(RemotePrimerBlastNCBI.PrimerBlastOptions opts)

Constructor.

Parameters:

opts - - Primer-BLAST options

Method Detail

runAnalysis

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

Run Primer-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

Returns:

name of the analysis run

Throws:

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

runAnalysis

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

Run Primer-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

fl - - FeatureList of selected features to filter against

Returns:

name of the analysis run

Throws:

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