001/* 
002 * Copyright 2018 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
003 *
004 * Licensed under the Apache License, Version 2.0 (the "License");
005 * you may not use this file except in compliance with the License.
006 * You may obtain a copy of the License at
007 *
008 *      http://www.apache.org/licenses/LICENSE-2.0
009 *
010 * Unless required by applicable law or agreed to in writing, software
011 * distributed under the License is distributed on an "AS IS" BASIS,
012 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
013 * See the License for the specific language governing permissions and
014 * limitations under the License.
015 */
016package uk.ac.ebi.pride.jmztab2.model;
017
018import de.isas.mztab2.model.IndexedElement;
019import de.isas.mztab2.model.SmallMoleculeFeature;
020import static de.isas.mztab2.model.SmallMoleculeFeature.Properties.*;
021import de.isas.mztab2.model.StringList;
022import java.util.Arrays;
023import java.util.List;
024import java.util.stream.Collectors;
025
026/**
027 * Define the stable columns which have stable order in the small molecule
028 * feature header line.
029 *
030 * To create optional column mappings, see
031 * {@link uk.ac.ebi.pride.jmztab2.model.OptColumnMappingBuilder}.
032 *
033 * @author nilshoffmann
034 * @since 11/09/17
035 *
036 */
037public class SmallMoleculeFeatureColumn implements ISmallMoleculeFeatureColumn {
038
039    private final IMZTabColumn column;
040
041    SmallMoleculeFeatureColumn(String name, Class dataType, boolean optional,
042        String order) {
043        this.column = new MZTabColumn(name, dataType, optional, order);
044    }
045
046    SmallMoleculeFeatureColumn(String name, Class dataType, boolean optional,
047        String order, Integer id) {
048        this.column = new MZTabColumn(name, dataType, optional, order, id);
049    }
050
051    /**
052     * Stable {@link SmallMoleculeFeatureColumn} definition templates.
053     */
054    public static enum Stable {
055        SMF_ID(smfId.toUpper(), Integer.class, false, "01"),
056        SME_ID_REFS(smeIdRefs.toUpper(), StringList.class, true, "02"),
057        SME_ID_REF_AMBIGUITY_CODE("SME_ID_REF_ambiguity_code", Integer.class,
058            true, "03"),
059        ADDUCT_ION(
060            adductIon, String.class, true, "04"),
061        ISOTOPOMER(isotopomer, String.class, true, "05"),
062        EXP_MASS_TO_CHARGE(
063            expMassToCharge, Double.class, false, "06"),
064        CHARGE(charge, Integer.class, false, "07"),
065        RETENTION_TIME_IN_SECONDS(retentionTimeInSeconds, Double.class, true,
066            "08"),
067        RETENTION_TIME_IN_SECONDS_START(retentionTimeInSecondsStart,
068            Double.class, true, "09"),
069        RETENTION_TIME_IN_SECONDS_END(retentionTimeInSecondsEnd, Double.class,
070            true, "10");
071
072        private final ISmallMoleculeFeatureColumn column;
073
074        private Stable(SmallMoleculeFeature.Properties property,
075            Class columnType, boolean optional,
076            String order) {
077            this.column = new SmallMoleculeFeatureColumn(property.
078                getPropertyName(), columnType, optional,
079                order);
080        }
081
082        private Stable(String name, Class columnType, boolean optional,
083            String order) {
084            this.column = new SmallMoleculeFeatureColumn(name, columnType,
085                optional,
086                order);
087        }
088
089        private Stable(String name, Class columnType, boolean optional,
090            String order, Integer id) {
091            this.column = new SmallMoleculeFeatureColumn(name, columnType,
092                optional,
093                order, id);
094        }
095
096        /**
097         * Returns a stable column instance template.
098         *
099         * @param name the column name (lower case).
100         * @return the stable column instance template.
101         * @throws IllegalArgumentException for unknown column names.
102         */
103        public static Stable forName(String name) throws IllegalArgumentException {
104            Stable s = Arrays.stream(Stable.values()).
105                filter((v) ->
106                    v.column.
107                        getName().
108                        equals(name)).
109                findFirst().
110                orElseThrow(() ->
111                    new IllegalArgumentException("Unknown key:" + name));
112            return s;
113        }
114
115        /**
116         * Returns a new {@link ISmallMoleculeFeatureColumn} instance for the
117         * given stable column template.
118         *
119         * @param s the small molecule feature stable column template.
120         * @return a new small molecule feature column instance
121         * {@link SmallMoleculeFeatureColumn}.
122         */
123        public static ISmallMoleculeFeatureColumn columnFor(
124            SmallMoleculeFeatureColumn.Stable s) {
125            return new SmallMoleculeFeatureColumn(s.column.getName(), s.column.
126                getDataType(), s.column.isOptional(), s.column.getOrder());
127        }
128
129        /**
130         * Returns a new {@link ISmallMoleculeFeatureColumn} instance for the
131         * given stable column name.
132         *
133         * @param name the small molecule feature stable column template name
134         * (lower case).
135         * @return a new small molecule feature column instance
136         * {@link SmallMoleculeFeatureColumn}.
137         * @throws IllegalArgumentException for unknown column names.
138         */
139        public static ISmallMoleculeFeatureColumn columnFor(String name) throws IllegalArgumentException {
140            return columnFor(forName(name));
141        }
142
143        /**
144         * Returns all stable {@link ISmallMoleculeFeatureColumn} templates.
145         *
146         * @return the stable small molecule feature columns templates.
147         */
148        public static List<ISmallMoleculeFeatureColumn> columns() {
149            return Arrays.stream(Stable.values()).
150                map((s) ->
151                {
152                    return new SmallMoleculeFeatureColumn(s.column.getName(),
153                        s.column.getDataType(), s.column.isOptional(), s.column.
154                        getOrder());
155                }).
156                collect(Collectors.toList());
157        }
158
159    };
160
161    /**
162     * {@inheritDoc}
163     */
164    @Override
165    public Class<?> getDataType() {
166        return this.column.getDataType();
167    }
168
169    /**
170     * {@inheritDoc}
171     */
172    @Override
173    public IndexedElement getElement() {
174        return this.column.getElement();
175    }
176
177    /**
178     * {@inheritDoc}
179     */
180    @Override
181    public String getHeader() {
182        return this.column.getHeader();
183    }
184
185    /**
186     * {@inheritDoc}
187     */
188    @Override
189    public String getLogicPosition() {
190        return this.column.getLogicPosition();
191    }
192
193    /**
194     * {@inheritDoc}
195     */
196    @Override
197    public String getName() {
198        return this.column.getName();
199    }
200
201    /**
202     * {@inheritDoc}
203     */
204    @Override
205    public String getOrder() {
206        return this.column.getOrder();
207    }
208
209    /**
210     * {@inheritDoc}
211     */
212    @Override
213    public boolean isOptional() {
214        return this.column.isOptional();
215    }
216
217    /**
218     * {@inheritDoc}
219     */
220    @Override
221    public void setHeader(String header) {
222        this.column.setHeader(header);
223    }
224
225    /**
226     * {@inheritDoc}
227     */
228    @Override
229    public void setLogicPosition(String logicPosition) {
230        this.column.setLogicPosition(logicPosition);
231    }
232
233    /**
234     * {@inheritDoc}
235     */
236    @Override
237    public void setOrder(String order) {
238        this.column.setOrder(order);
239    }
240
241    /**
242     * {@inheritDoc}
243     */
244    @Override
245    public void setElement(IndexedElement element) {
246        this.column.setElement(element);
247    }
248}