uk.ac.ebi.embl.flatfile.reader.QualifierMatcher.java Source code

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Here is the source code for uk.ac.ebi.embl.flatfile.reader.QualifierMatcher.java

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/*******************************************************************************
 * Copyright 2012 EMBL-EBI, Hinxton outstation
 * 
 * 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.embl.flatfile.reader;

import java.util.regex.Pattern;

import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.embl.flatfile.FlatFileUtils;
import uk.ac.ebi.embl.api.entry.qualifier.Qualifier;
import uk.ac.ebi.embl.api.entry.qualifier.QualifierFactory;

public class QualifierMatcher extends FlatFileMatcher {

    public QualifierMatcher(FlatFileLineReader reader) {
        super(reader, PATTERN);
    }

    private static final Pattern PATTERN = Pattern.compile("\\/([a-zA-Z1-9-_]+)\\s*=?(.*)?");

    private static final int GROUP_QUALIFIER_NAME = 1;
    private static final int GROUP_QUALIFIER_VALUE = 2;

    public Qualifier getQualifier() {
        QualifierFactory qualifierFactory = new QualifierFactory();
        String qualifierName = getString(GROUP_QUALIFIER_NAME);
        String qualifierValue = getString(GROUP_QUALIFIER_VALUE);
        int nofQuotes = StringUtils.countMatches(qualifierValue, "\"");
        Qualifier qualifier = qualifierFactory.createQualifier(qualifierName);
        if (qualifierValue != null) {
            if (!qualifier.isValueQuoted() && nofQuotes != 0) {
                if ((!qualifier.getName().equals(Qualifier.ANTICODON_QUALIFIER_NAME)
                        && !qualifier.getName().equals(Qualifier.COMPARE_QUALIFIER_NAME)))
                    error("FT.10", qualifierName, qualifierValue);
            } else if (qualifier.isValueQuoted()) {
                if (nofQuotes == 0) {
                    error("FT.10", qualifierName, qualifierValue);
                } else {
                    if (qualifierValue.indexOf('"') != 0
                            && qualifierValue.lastIndexOf('"') != qualifierValue.length() - 1)

                    {
                        error("FT.10", qualifierName, qualifierValue);
                    } else if (nofQuotes % 2 != 0) {
                        error("FT.10", qualifierName, qualifierValue);
                    }
                }
            }
            qualifierValue = FlatFileUtils.trimLeft(qualifierValue, '"');
            qualifierValue = FlatFileUtils.trimRight(qualifierValue, '"');
            qualifier.setValue(qualifierValue);
            return qualifier;
        } else {
            return qualifier;
        }
    }
}