cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/molecular/SequenceServiceImpl.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.api.service.molecular;
  11
  12 import java.util.ArrayList;
  13 import java.util.Collection;
  14 import java.util.HashMap;
  15 import java.util.Map;
  16
  17 import org.apache.log4j.Logger;
  18 import org.springframework.beans.factory.annotation.Autowired;
  19 import org.springframework.stereotype.Service;
  20 import org.springframework.transaction.annotation.Transactional;
  21
  22 import eu.etaxonomy.cdm.api.service.AnnotatableServiceBase;
  23 import eu.etaxonomy.cdm.api.service.PreferenceServiceImpl;
  24 import eu.etaxonomy.cdm.model.molecular.Sequence;
  25 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  26 import eu.etaxonomy.cdm.persistence.dao.molecular.ISequenceDao;
  27
  28 /**
  29  * @author pplitzner
  30  * @date 11.03.2014
  31  *
  32  */
  33 @Service
  34 @Transactional(readOnly = true)
  35 public class SequenceServiceImpl extends AnnotatableServiceBase<Sequence, ISequenceDao> implements ISequenceService{
  36     private static final Logger logger = Logger.getLogger(PreferenceServiceImpl.class);
  37
  38     /* (non-Javadoc)
  39      * @see eu.etaxonomy.cdm.api.service.ServiceBase#setDao(eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao)
  40      */
  41     @Override
  42     @Autowired
  43     protected void setDao(ISequenceDao dao) {
  44         this.dao = dao;
  45     }
  46
  47     /* (non-Javadoc)
  48      * @see eu.etaxonomy.cdm.api.service.ISequenceService#moveSingleRead(eu.etaxonomy.cdm.model.molecular.Sequence, eu.etaxonomy.cdm.model.molecular.Sequence, eu.etaxonomy.cdm.model.molecular.SingleRead)
  49      */
  50     @Override
  51     public boolean moveSingleRead(Sequence from, Sequence to, SingleRead singleRead) {
  52         from.removeSingleRead(singleRead);
  53         saveOrUpdate(from);
  54         to.addSingleRead(singleRead);
  55         saveOrUpdate(to);
  56         return true;
  57     }
  58
  59     /* (non-Javadoc)
  60      * @see eu.etaxonomy.cdm.api.service.molecular.ISequenceService#getSingleReadSequenceMap()
  61      */
  62     @Override
  63     public Map<SingleRead, Collection<Sequence>> getSingleReadSequencesMap() {
  64         Map<SingleRead, Collection<Sequence>> singleReadToSequences = new HashMap<SingleRead, Collection<Sequence>>();
  65         for(Sequence sequence:list(Sequence.class, null, null, null, null)){
  66             for(SingleRead singleRead:sequence.getSingleReads()){
  67                 Collection<Sequence> sequences = singleReadToSequences.get(singleRead);
  68                 if(sequences==null){
  69                     sequences = new ArrayList<Sequence>();
  70                 }
  71                 sequences.add(sequence);
  72                 singleReadToSequences.put(singleRead, sequences);
  73             }
  74         }
  75         return singleReadToSequences;
  76     }
  77 }