org.biojava3.ws.hmmer
Class RemoteHmmerScan

java.lang.Object
  extended by org.biojava3.ws.hmmer.RemoteHmmerScan
All Implemented Interfaces:
HmmerScan

public class RemoteHmmerScan
extends Object
implements HmmerScan

Makes remote calls to the Hmmer3 web site and returns Pfam domain annotations for an input protein sequence.

Since:
3.0.3
Author:
Andreas Prlic

Field Summary
 boolean DEFAULT_SEARCH_CUT_GA
           
static String HMMER_SERVICE
           
 
Constructor Summary
RemoteHmmerScan()
           
 
Method Summary
 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 Detail

HMMER_SERVICE

public static String HMMER_SERVICE

DEFAULT_SEARCH_CUT_GA

public boolean DEFAULT_SEARCH_CUT_GA
Constructor Detail

RemoteHmmerScan

public RemoteHmmerScan()
Method Detail

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