/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MISO is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.tools.run;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.integration.file.DefaultDirectoryScanner;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* uk.ac.bbsrc.tgac.miso.tools.run
* <p/>
* Info
*
* @author Rob Davey
* @date 26/10/11
* @since 0.1.2
*/
public class RunFolderScanner extends DefaultDirectoryScanner {
private static final Log log = LogFactory.getLog(RunFolderScanner.class);
private Pattern runDirPattern;
public RunFolderScanner(String runDirRegex) {
runDirPattern = Pattern.compile(runDirRegex);
}
@Override
protected File[] listEligibleFiles(File directory) throws IllegalArgumentException {
File[] rootFiles = directory.listFiles();
List<File> files = new ArrayList<File>(rootFiles.length);
for (File rootFile : rootFiles) {
if (rootFile.isDirectory()) {
Matcher rm = runDirPattern.matcher(rootFile.getAbsolutePath());
if (rm.matches()) {
files.add(rootFile);
}
else {
if (rm.find()) {
files.addAll(Arrays.asList(listEligibleFiles(rootFile)));
}
}
}
}
return files.toArray(new File[files.size()]);
}
}