org.biojava.nbio.ws.hmmer

Class RemoteHmmerScan

java.lang.Object

org.biojava.nbio.ws.hmmer.RemoteHmmerScan

All Implemented Interfaces:

HmmerScan

public class RemoteHmmerScan
extends java.lang.Object
implements HmmerScan

Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.

Since:

3.0.3

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	HMMER_SERVICE

Constructor Summary

Constructors

Constructor and Description
RemoteHmmerScan()

Method Summary

Modifier and Type	Method and Description
java.util.SortedSet<HmmerResult>	scan(ProteinSequence sequence)
java.util.SortedSet<HmmerResult>	scan(ProteinSequence sequence, java.net.URL serviceLocation) Scans a protein sequence for Pfam profile matches.

Methods inherited from class java.lang.Object

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

Field Detail

HMMER_SERVICE

public static final java.lang.String HMMER_SERVICE

See Also:

Constant Field Values

Constructor Detail

RemoteHmmerScan

public RemoteHmmerScan()

Method Detail

scan

public java.util.SortedSet<HmmerResult> scan(ProteinSequence sequence)
                                      throws java.io.IOException

Specified by:

scan in interface HmmerScan

Throws:

java.io.IOException

scan

public java.util.SortedSet<HmmerResult> scan(ProteinSequence sequence,
                                             java.net.URL serviceLocation)
                                      throws java.io.IOException

Scans a protein sequence for Pfam profile matches.

Parameters:

sequence -

serviceLocation -

Returns:

Throws:

java.io.IOException