001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package demo;
022
023import org.biojava.nbio.core.sequence.ProteinSequence;
024import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
025import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
026import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
027import org.biojava.nbio.ws.hmmer.HmmerDomain;
028import org.biojava.nbio.ws.hmmer.HmmerResult;
029import org.biojava.nbio.ws.hmmer.RemoteHmmerScan;
030
031import java.util.SortedSet;
032
033/** The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
034 *
035 * @author Andreas Prlic
036 * @since 3.0.3
037 */
038public class HmmerDemo {
039
040        public static void main(String[] args){
041
042                try {
043                        // first we get a UniProt sequence
044                        String uniProtID = "P08487";
045                        ProteinSequence seq = getUniprot(uniProtID);
046
047
048                        // now we submit this sequence to the Hmmer web site
049                        RemoteHmmerScan hmmer = new RemoteHmmerScan();
050
051                        SortedSet<HmmerResult> results = hmmer.scan(seq);
052
053                        // and now let's print out the obtained annotations
054
055                        System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s",
056                                        "Domain","ACC", "Start","End","eValue","Description"));
057
058                        int counter = 0;
059                        for (HmmerResult hmmerResult : results) {
060                                //System.out.println(hmmerResult);
061
062                                for ( HmmerDomain domain : hmmerResult.getDomains()) {
063                                        counter++;
064                                        System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s",
065                                                        counter,
066                                                        hmmerResult.getName(), domain.getHmmAcc(),
067                                                        domain.getSqFrom(),domain.getSqTo(),
068                                                        domain.getEvalue(), hmmerResult.getDesc()
069                                                        ));
070
071                                }
072
073                        }
074
075                } catch (Exception e) {
076                        // TODO Auto-generated catch block
077                        e.printStackTrace();
078                }
079        }
080
081        /** Fetch a protein sequence from the UniProt web site
082         *
083         * @param uniProtID
084         * @return a Protein Sequence
085         * @throws Exception
086         */
087        private static ProteinSequence getUniprot(String uniProtID) throws Exception {
088
089                AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
090                UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
091
092                ProteinSequence seq = new ProteinSequence(uniprotSequence);
093
094                return seq;
095        }
096}