Package org.biojava.nbio.ws.hmmer

Class RemoteHmmerScan

java.lang.Object

org.biojava.nbio.ws.hmmer.RemoteHmmerScan

All Implemented Interfaces:

HmmerScan

public class RemoteHmmerScan
extends 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	Description
static final String	HMMER_SERVICE

Constructor Summary

Constructors

Constructor	Description
RemoteHmmerScan()

Method Summary

Modifier and Type	Method	Description
SortedSet<HmmerResult>	scan(ProteinSequence sequence)
SortedSet<HmmerResult>	scan(ProteinSequence sequence, 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 Details

HMMER_SERVICE

public static final String HMMER_SERVICE

See Also:

• Constant Field Values

Constructor Details

RemoteHmmerScan

public RemoteHmmerScan()

Method Details

scan

public SortedSet<HmmerResult> scan(ProteinSequence sequence)
                            throws IOException

Specified by:

scan in interface HmmerScan

Throws:

IOException

scan

public SortedSet<HmmerResult> scan(ProteinSequence sequence,
 URL serviceLocation)
                            throws IOException

Scans a protein sequence for Pfam profile matches.

Parameters:

sequence -

serviceLocation -

Returns:

Throws:

IOException