001 /**
002 * Copyright (c) 2010, SIB. All rights reserved.
003 *
004 * SIB (Swiss Institute of Bioinformatics) - http://www.isb-sib.ch Host -
005 * https://sourceforge.net/projects/javaprotlib/
006 *
007 * Redistribution and use in source and binary forms, with or without
008 * modification, are permitted provided that the following conditions are met:
009 * Redistributions of source code must retain the above copyright notice, this
010 * list of conditions and the following disclaimer. Redistributions in binary
011 * form must reproduce the above copyright notice, this list of conditions and
012 * the following disclaimer in the documentation and/or other materials provided
013 * with the distribution. Neither the name of the SIB/GENEBIO nor the names of
014 * its contributors may be used to endorse or promote products derived from this
015 * software without specific prior written permission.
016 *
017 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
018 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
019 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
020 * ARE DISCLAIMED. IN NO EVENT SHALL SIB/GENEBIO BE LIABLE FOR ANY DIRECT,
021 * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
022 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
023 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
024 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
025 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
026 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
027 */
028 package org.expasy.jpl.commons.base.io;
029
030
031 import java.io.File;
032 import java.io.FileNotFoundException;
033 import java.util.ArrayList;
034 import java.util.List;
035 import java.util.regex.Matcher;
036 import java.util.regex.Pattern;
037
038
039 /**
040 * Class to find all files matching a regular expression in a directory tree.
041 *
042 * @author Markus Muller
043 *
044 * @version 1.0
045 *
046 */
047 public final class FileFinder {
048
049 public static List<File> getFiles(final String root, final String regex)
050 throws FileNotFoundException {
051 return getFiles(root, regex, true);
052 }
053
054 /**
055 * Find all files in the directory sub-tree under root
056 *
057 * @param root Root directory for search
058 * @param regex Regular expression to match file name
059 * @param recurse recursive search if true
060 * @return List of matched files throws FileNotFoundException if root does
061 * not exist or is not a directory
062 */
063 public static List<File> getFiles(final String root, final String regex,
064 final boolean recurse) throws FileNotFoundException {
065
066 final File rootDir = new File(root);
067
068 if (!rootDir.isDirectory()) {
069 throw new FileNotFoundException(root
070 + " does not exist or is not a directory!");
071 }
072
073 final List<File> files =
074 listFilesAndDirs(rootDir, Pattern.compile(regex), recurse);
075
076 return files;
077 }
078
079 public static List<File> getFiles(final String root, final Pattern pattern)
080 throws FileNotFoundException {
081 return getFiles(root, pattern, true);
082 }
083
084 /**
085 * Find all files in the directory sub-tree under root
086 *
087 * @param root Root directory for search
088 * @param pattern Regular expression pattern to match file name
089 * @param recurse recursive search if true
090 * @return List of matched files throws FileNotFoundException if root does
091 * not exist or is not a directory
092 */
093 public static List<File> getFiles(final String root, final Pattern pattern,
094 final boolean recurse) throws FileNotFoundException {
095
096 final File rootDir = new File(root);
097
098 if (!rootDir.isDirectory()) {
099 throw new FileNotFoundException(root
100 + " does not exist or is not a directory!");
101 }
102
103 final List<File> files = listFilesAndDirs(rootDir, pattern, recurse);
104
105 return files;
106 }
107
108 /**
109 * List all files and directories under root
110 *
111 * @param root Root directory
112 * @param regex Regular expression for file names
113 * @param filter Filter object implementing regex
114 * @param recurse if true, the search is extended to subdirectories
115 * @return
116 */
117 private static List<File> listFilesAndDirs(final File root,
118 final Pattern pattern, final boolean recurse) {
119 // List of files / directories
120 final List<File> files = new ArrayList<File>();
121
122 // Get files / directories in the directory
123 final File[] entries = root.listFiles();
124
125 Matcher matcher;
126
127 // Go over entries
128 for (final File entry : entries) {
129
130 // If there is no filter or the filter accepts the
131 // file / directory, add it to the list
132 if (pattern != null) {
133 matcher = pattern.matcher(entry.getName());
134
135 if (matcher.matches()) {
136 files.add(entry);
137 }
138 }
139
140 // If the file is a directory and the recurse flag
141 // is set, recurse into the directory
142 if (recurse && entry.isDirectory()) {
143 files.addAll(listFilesAndDirs(entry, pattern, recurse));
144 }
145 }
146
147 // Return collection of files
148 return files;
149 }
150 }