org.biojava3.ws.hmmer
Class RemoteHmmerScan
java.lang.Object
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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HMMER_SERVICE
public static String HMMER_SERVICE
DEFAULT_SEARCH_CUT_GA
public boolean DEFAULT_SEARCH_CUT_GA
RemoteHmmerScan
public RemoteHmmerScan()
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