htsjdk.tribble.Tribble Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2013 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.tribble;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.tribble.util.ParsingUtils;
import htsjdk.tribble.util.TabixUtils;
import java.io.File;
import java.nio.file.Path;
/**
* Common, tribble wide constants and static functions
*/
public class Tribble {
private Tribble() { } // can't be instantiated
/**
* @deprecated since June 2019 Use {@link FileExtensions#TRIBBLE_INDEX} instead.
*/
@Deprecated
public final static String STANDARD_INDEX_EXTENSION = FileExtensions.TRIBBLE_INDEX;
/**
* Return the name of the index file for the provided {@code filename}
* Does not actually create an index
* @param filename name of the file
* @return non-null String representing the index filename
*/
public static String indexFile(final String filename) {
return indexFile(filename, FileExtensions.TRIBBLE_INDEX);
}
/**
* Return the File of the index file for the provided {@code file}
* Does not actually create an index
* @param file the file
* @return a non-null File representing the index
*/
public static File indexFile(final File file) {
return indexFile(file.getAbsoluteFile(), FileExtensions.TRIBBLE_INDEX);
}
/**
* Return the name of the index file for the provided {@code path}
* Does not actually create an index
* @param path the path
* @return Path representing the index filename
*/
public static Path indexPath(final Path path) {
return path.getFileSystem().getPath(indexFile(path.toAbsolutePath().toString()));
}
/**
* Return the name of the tabix index file for the provided {@code filename}
* Does not actually create an index
* @param filename name of the file
* @return non-null String representing the index filename
*/
public static String tabixIndexFile(final String filename) {
return indexFile(filename, FileExtensions.TABIX_INDEX);
}
/**
* Return the File of the tabix index file for the provided {@code file}
* Does not actually create an index
* @param file the file
* @return a non-null File representing the index
*/
public static File tabixIndexFile(final File file) {
return indexFile(file.getAbsoluteFile(), FileExtensions.TABIX_INDEX);
}
/**
* Return the name of the tabix index file for the provided {@code path}
* Does not actually create an index
* @param path the path
* @return Path representing the index filename
*/
public static Path tabixIndexPath(final Path path) {
return path.getFileSystem().getPath(tabixIndexFile(path.toAbsolutePath().toString()));
}
/**
* Return the name of the index file for the provided {@code filename} and {@code extension}
* Does not actually create an index
* @param filename name of the file
* @param extension the extension to use for the index
* @return non-null String representing the index filename
*/
private static String indexFile(final String filename, final String extension) {
return ParsingUtils.appendToPath(filename, extension);
}
/**
* Return the File of the index file for the provided {@code file} and {@code extension}
* Does not actually create an index
* @param file the file
* @param extension the extension to use for the index
* @return a non-null File representing the index
*/
private static File indexFile(final File file, final String extension) {
return new File(file.getAbsoluteFile() + extension);
}
}