Class 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 Description
      static java.lang.String HMMER_SERVICE  
    • Constructor Summary

      Constructors 
      Constructor Description
      RemoteHmmerScan()  
    • Constructor Detail

      • RemoteHmmerScan

        public RemoteHmmerScan()
    • Method Detail

      • 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