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