// Path: biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
// public static enum FetchBehavior {
// 	/** Never fetch from the server; Throw errors for missing files */
// 	LOCAL_ONLY,
// 	/** Fetch missing files from the server. Don't check for outdated files */
// 	FETCH_FILES,
// 	/**
// 	 * Fetch missing files from the server, also fetch if file present but older than the
// 	 * server file.
// 	 * This requires always querying the server for the last modified time of the file, thus
// 	 * it adds an overhead to getting files from cache.
// 	 */
// 	FETCH_IF_OUTDATED,
// 	/**
// 	 * Fetch missing files from the server.
// 	 * Also force the download of files older than {@value #LAST_REMEDIATION_DATE_STRING}.
// 	 */
// 	FETCH_REMEDIATED,
// 	/** For every file, force downloading from the server */
// 	FORCE_DOWNLOAD;
// 
// 	public static final FetchBehavior DEFAULT = FETCH_REMEDIATED;
// }


import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on May 11, 2010
 * Author: Andreas Prlic
 *
 */

package org.biojava.nbio.protmod.structure;


public class TmpAtomCache
{
	static String tmpDir = System.getProperty("java.io.tmpdir");
	public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
	static {
		FileParsingParameters params = new FileParsingParameters();
		params.setAlignSeqRes(true);
		params.setParseSecStruc(false);
		params.setCreateAtomBonds(true);
// Path: biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
// public static enum FetchBehavior {
// 	/** Never fetch from the server; Throw errors for missing files */
// 	LOCAL_ONLY,
// 	/** Fetch missing files from the server. Don't check for outdated files */
// 	FETCH_FILES,
// 	/**
// 	 * Fetch missing files from the server, also fetch if file present but older than the
// 	 * server file.
// 	 * This requires always querying the server for the last modified time of the file, thus
// 	 * it adds an overhead to getting files from cache.
// 	 */
// 	FETCH_IF_OUTDATED,
// 	/**
// 	 * Fetch missing files from the server.
// 	 * Also force the download of files older than {@value #LAST_REMEDIATION_DATE_STRING}.
// 	 */
// 	FETCH_REMEDIATED,
// 	/** For every file, force downloading from the server */
// 	FORCE_DOWNLOAD;
// 
// 	public static final FetchBehavior DEFAULT = FETCH_REMEDIATED;
// }


// Path: biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/TmpAtomCache.java
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on May 11, 2010
 * Author: Andreas Prlic
 *
 */

package org.biojava.nbio.protmod.structure;


public class TmpAtomCache
{
	static String tmpDir = System.getProperty("java.io.tmpdir");
	public static AtomCache cache = new AtomCache(tmpDir, tmpDir);
	static {
		FileParsingParameters params = new FileParsingParameters();
		params.setAlignSeqRes(true);
		params.setParseSecStruc(false);
		params.setCreateAtomBonds(true);
		cache.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);