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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service.molecular;
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import java.util.Collection;
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import java.util.Map;
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import java.util.UUID;
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import eu.etaxonomy.cdm.api.service.DeleteResult;
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import eu.etaxonomy.cdm.api.service.IAnnotatableService;
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import eu.etaxonomy.cdm.api.service.UpdateResult;
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import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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/**
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* @author pplitzner
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* @since 11.03.2014
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*
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*/
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public interface ISequenceService extends IAnnotatableService<Sequence>{
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/**
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* Moves the given {@link SingleRead} from one {@link Sequence} to another.
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* @param from the Sequence from which the SingleRead will be removed
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* @param to the Sequence to which the SingleRead will be added
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* @param singleRead the SingleRead to move
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* @return <code>true</code> if successfully moved, <code>false</code> otherwise
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*/
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public UpdateResult moveSingleRead(Sequence from, Sequence to, SingleRead singleRead);
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/**
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* @param fromUuid
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* @param toUuid
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* @param singleReadUuid
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* @return
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*/
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public UpdateResult moveSingleRead(UUID fromUuid, UUID toUuid, UUID singleReadUuid);
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/**
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* Creates and returns a map with {@link SingleRead}s as keys.
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* The value for each key is a list of those {@link Sequence}s that link to this SingleRead.
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* @return a map of SingleReads as keys and the Sequences linking to them
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*/
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public Map<SingleRead, Collection<Sequence>> getSingleReadSequencesMap();
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/**
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* Deletes a {@link SingleRead} from the given {@link Sequence} and its {@link AmplificationResult}.
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* @param singleRead the single read to delete
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* @param sequence the sequence to which the single read belongs
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* @return the {@link DeleteResult} which holds information about the outcome of this operation
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*/
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public DeleteResult deleteSingleRead(SingleRead singleRead, Sequence sequence);
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/**
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* Deletes a {@link SingleRead} from the given {@link Sequence} and its {@link AmplificationResult},
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* by first loading the corresponding uuids and then calling {@link #deleteSingleRead(SingleRead, Sequence) deleteSingleRead}
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* @param singleReadUuid uuid of the single read to delete
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* @param sequenceUuid uuid of the sequence to which the single read belongs
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* @return the {@link DeleteResult} which holds information about the outcome of this operation
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*/
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public DeleteResult deleteSingleRead(UUID singleReadUuid, UUID sequenceUuid);
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}
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