edu.umn.msi.tropix.proteomics.client.EnzymeUtils.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.client.EnzymeUtils.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.client;

import java.io.InputStream;

import javax.annotation.ManagedBean;

import com.google.common.base.Function;
import com.google.common.collect.Iterables;

import edu.umn.msi.tropix.common.io.IOUtils;
import edu.umn.msi.tropix.common.io.IOUtilsFactory;
import edu.umn.msi.tropix.proteomics.enzyme.Enzyme;
import edu.umn.msi.tropix.proteomics.enzyme.EnzymeSet;
import edu.umn.msi.tropix.proteomics.enzyme.TermInfo;
import edu.umn.msi.tropix.proteomics.xml.EnzymeSetUtility;

@ManagedBean
public class EnzymeUtils {
    private static final IOUtils IO_UTILS = IOUtilsFactory.getInstance();
    private static final EnzymeSetUtility ENZYME_SET_UTILITY = new EnzymeSetUtility();
    private static final Function<Enzyme, String> ENZYME_NAME_FUNCTION = new Function<Enzyme, String>() {
        public String apply(final Enzyme enzyme) {
            return enzyme.getName();
        }
    };
    private final EnzymeSet enzymes;

    public EnzymeUtils() {
        final InputStream enzymesStream = EnzymeUtils.class.getResourceAsStream("enzymes.xml");
        try {
            this.enzymes = ENZYME_SET_UTILITY.deserialize(enzymesStream);
        } finally {
            IO_UTILS.closeQuietly(enzymesStream);
        }
    }

    public Iterable<String> getEnzymeNames() {
        return Iterables.transform(enzymes.getEnzymes(), ENZYME_NAME_FUNCTION);
    }

    public Enzyme getEnzyme(final String enzymeName) {
        Enzyme enzyme = null;
        for (final Enzyme curEnzyme : enzymes.getEnzymes()) {
            if (curEnzyme.getName().equals(enzymeName)) {
                enzyme = curEnzyme;
                break;
            }
        }
        return enzyme;
    }

    // Return "n" or "c"
    public String getTerm(final String enzymeName) {
        if (getEnzyme(enzymeName).getTerm().equals(TermInfo.CTERM)) {
            return "c";
        } else {
            return "n";
        }
    }

    public String getCleaveResidues(final String enzymeName) {
        return getEnzyme(enzymeName).getDoCleave();
    }

    public String getNotCleaveResidues(final String enzymeName) {
        return getEnzyme(enzymeName).getDoNotCleave();
    }

}