OptionColumn.java

/* 
 * Copyright 2018 Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V..
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.pride.jmztab2.model;

import de.isas.mztab2.io.serialization.Serializers;
import de.isas.mztab2.model.IndexedElement;

/**
 * Additional columns can be added to the end of the protein table. These column
 * headers MUST start with the prefix "opt_". Column names MUST only contain the
 * following characters: 'A'-'Z', 'a'-'z', '0'-'9', '_', '-', '[', ']', and ':'.
 *
 * @author qingwei
 * @since 28/05/13
 *
 */
public class OptionColumn extends MZTabColumn {

    /**
     * Constant <code>OPT="opt"</code>
     */
    public static final String OPT = "opt";
    /**
     * Constant <code>GLOBAL="global"</code>
     */
    public static final String GLOBAL = "global";

    /**
     * Get the optional column header, which start with the prefix "opt_". the
     * format: opt_{indexedElement[id]}_{name}. Spaces within the parameter's
     * name MUST be replaced by '_'.
     *
     * @param element if the name relates to all replicates, we use "global" in
     * header. Here, if user set element to null, the definition applies for all
     * replicates.
     * @param name SHOULD NOT be empty.
     * @return a {@link java.lang.String} object.
     */
    public static String getHeader(IndexedElement element, String name) {
        if (MZTabStringUtils.isEmpty(name)) {
            throw new IllegalArgumentException(
                    "Optional column's name should not be empty.");
        }

        return OPT + "_" + (element == null ? GLOBAL : Serializers.
                getElementName(element).
                orElseThrow(()
                        -> {
                    return new IllegalArgumentException(
                            "Could not retrieve element name for " + element.toString());
                }))
                + "_" + name.replaceAll(" ", "_");
    }

    /**
     * Create a optional column. Which header start with the prefix "opt_",
     * logical position always stay the end of table.
     *
     * @see #getHeader() generate optional column header.
     * @param element if the value relates to all replicates, we use "global" in
     * header. Here, if user set element is null for define for all replicates.
     * @param value SHOULD NOT be empty.
     * @param columnType SHOULD NOT be empty.
     * @param offset SHOULD be positive integer.
     */
    public OptionColumn(IndexedElement element, String value, Class columnType,
            int offset) {
        super(getHeader(element, value), columnType, true, offset + 1 + "");
    }
}