edu.umn.msi.tropix.proteomics.FileDTAListImpl.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.FileDTAListImpl.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;

import com.google.common.collect.Iterables;

import edu.umn.msi.tropix.common.collect.StringPredicates;
import edu.umn.msi.tropix.common.io.Directory;
import edu.umn.msi.tropix.common.io.InputContext;
import edu.umn.msi.tropix.common.io.InputContexts;
import edu.umn.msi.tropix.common.io.OutputContext;

public class FileDTAListImpl extends GenericDTAListImpl<String> {
    private Directory parentDirectory = null;

    public FileDTAListImpl(final Directory directory) {
        this.parentDirectory = directory;
    }

    public void populate() {
        populate(null);
    }

    public void populate(final String baseName) {
        final Iterable<String> dtaResources = Iterables.filter(parentDirectory.getResourceNames(null),
                StringPredicates.matches(".*\\.[dD][tT][aA]"));
        for (final String dtaResource : dtaResources) {
            addContents(dtaResource);
            final String fileName = dtaResource;
            if (baseName == null) {
                addName(fileName);
            } else {
                addName(baseName + fileName.substring(fileName.indexOf('.')));
            }
        }
    }

    public String getKey(final byte[] contents, final String name) {
        final OutputContext context = parentDirectory.getOutputContext(name);
        context.put(contents);
        return name;
    }

    public byte[] getValue(final String key, final String name) {
        final InputContext context = parentDirectory.getInputContext(key);
        return InputContexts.getAsByteArray(context);
    }

}