eu.eubrazilcc.lvl.storage.SequenceKey.java Source code

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Here is the source code for eu.eubrazilcc.lvl.storage.SequenceKey.java

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/*
 * Copyright 2014 EUBrazilCC (EU?Brazil Cloud Connect)
 * 
 * Licensed under the EUPL, Version 1.1 or - as soon they will be approved by 
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at:
 * 
 *   http://ec.europa.eu/idabc/eupl
 * 
 * Unless required by applicable law or agreed to in writing, software 
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing permissions and 
 * limitations under the Licence.
 * 
 * This product combines work with different licenses. See the "NOTICE" text
 * file for details on the various modules and licenses.
 * The "NOTICE" text file is part of the distribution. Any derivative works
 * that you distribute must include a readable copy of the "NOTICE" text file.
 */

package eu.eubrazilcc.lvl.storage;

import static com.google.common.base.MoreObjects.toStringHelper;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkState;
import static com.google.common.base.Splitter.on;
import static eu.eubrazilcc.lvl.core.DataSource.toLongNotation;
import static eu.eubrazilcc.lvl.core.DataSource.toShortNotation;
import static eu.eubrazilcc.lvl.core.DataSource.Notation.NOTATION_SHORT;
import static org.apache.commons.lang.StringUtils.isNotBlank;

import java.util.List;
import java.util.Objects;

import eu.eubrazilcc.lvl.core.DataSource;
import eu.eubrazilcc.lvl.core.DataSource.Notation;
import eu.eubrazilcc.lvl.core.util.NamingUtils;

/**
 * Stores a sequence key that can be used to transmit over the network and to store it in the database.
 * @author Erik Torres <ertorser@upv.es>
 */
public class SequenceKey {

    private String dataSource;
    private String accession;

    public String getDataSource() {
        return dataSource;
    }

    public void setDataSource(final String dataSource) {
        this.dataSource = dataSource;
    }

    public String getAccession() {
        return accession;
    }

    public void setAccession(final String accession) {
        this.accession = accession;
    }

    @Override
    public boolean equals(final Object obj) {
        if (obj == null || !(obj instanceof SequenceKey)) {
            return false;
        }
        final SequenceKey other = SequenceKey.class.cast(obj);
        return Objects.equals(dataSource, other.dataSource) && Objects.equals(accession, other.accession);
    }

    @Override
    public int hashCode() {
        return Objects.hash(dataSource, accession);
    }

    @Override
    public String toString() {
        return toStringHelper(this).add("dataSource", dataSource).add("accession", accession).toString();
    }

    /**
     * Creates an identifier that uniquely identifies the sequence in the LVL. This identifier 
     * is computed from the data source and the accession fields. This method uses the default
     * character {@link NamingUtils#ID_FRAGMENT_SEPARATOR} to separate these particles in the 
     * created identifier and the default notation {@link DataSource.Notation#NOTATION_SHORT}.
     * @return an identifier that uniquely identifies the sequence in the LVL.
     */
    public String toId() {
        return NamingUtils.toId(dataSource, accession, NOTATION_SHORT);
    }

    /* Fluent API */

    public static Builder builder() {
        return new Builder();
    }

    public static class Builder {

        private final SequenceKey instance = new SequenceKey();

        public Builder dataSource(final String dataSource) {
            instance.setDataSource(dataSource);
            return this;
        }

        public Builder accession(final String accession) {
            instance.setAccession(accession);
            return this;
        }

        public SequenceKey build() {
            return instance;
        }

        /**
         * Parses the input identifier, extracting the parts of a {@link SequenceKey}. In addition, the data source of the generated sequence key is
         * converted to the specified notation.
         * @param id - the identifier to be parsed
         * @param separator - the separator the identifier uses to separate its different parts
         * @param notation - the notation the data source of the generated sequence key is converted to
         * @return a sequence key.
         */
        public SequenceKey parse(final String id, final char separator, final Notation notation) {
            checkArgument(notation != null, "Uninitialized notation");
            final SequenceKey sequenceKey = parse(id, separator);
            switch (notation) {
            case NOTATION_SHORT:
                sequenceKey.setDataSource(toShortNotation(sequenceKey.getDataSource()));
                break;
            case NOTATION_LONG:
                sequenceKey.setDataSource(toLongNotation(sequenceKey.getDataSource()));
                break;
            default:
                break;
            }
            return sequenceKey;
        }

        /**
         * Parses the input identifier, extracting the parts of a {@link SequenceKey}.
         * @param id - the identifier to be parsed
         * @param separator - the separator the identifier uses to separate its different parts
         * @return a sequence key.
         */
        public SequenceKey parse(final String id, final char separator) {
            checkArgument(isNotBlank(id) && id.matches("[a-zA-Z_0-9]+" + separator + "[a-zA-Z_0-9]+"),
                    "Uninitialized or invalid id");
            final List<String> tokens = on(separator).omitEmptyStrings().trimResults().splitToList(id);
            checkState(tokens != null && tokens.size() == 2, "Invalid id or separator");
            return dataSource(tokens.get(0)).accession(tokens.get(1)).build();
        }

    }

}