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/*
* Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
* All Rights Reserved.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
* is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
* ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
* OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
* RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
* ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
* DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
* BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
* FOREGOING.
*/
package htsjdk.tribble;
import htsjdk.samtools.util.FileExtensions;
import htsjdk.samtools.util.IOUtil;
import htsjdk.tribble.index.Index;
import htsjdk.tribble.util.ParsingUtils;
import htsjdk.tribble.util.TabixUtils;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.nio.channels.SeekableByteChannel;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import java.util.function.Function;
/**
* jrobinso
*
* the feature reader class, which uses indices and codecs to read in Tribble file formats.
*/
public abstract class AbstractFeatureReader implements FeatureReader {
// the logging destination for this source
//private final static Logger log = Logger.getLogger("BasicFeatureSource");
/**
* The path to underlying data file, this must be the input path converted with {@link FeatureCodec#getPathToDataFile(String)}
*/
String path;
// a wrapper to apply to the raw stream of the Feature file to allow features like prefetching and caching to be injected
final Function wrapper;
// a wrapper to apply to the raw stream of the index file
final Function indexWrapper;
// the query source, codec, and header
// protected final QuerySource querySource;
protected final FeatureCodec codec;
protected FeatureCodecHeader header;
private static ComponentMethods methods = new ComponentMethods();
/** @deprecated since June 2019 use {@link FileExtensions#BLOCK_COMPRESSED} instead. */
@Deprecated
public static final Set BLOCK_COMPRESSED_EXTENSIONS = FileExtensions.BLOCK_COMPRESSED;
/**
* Calls {@link #getFeatureReader(String, FeatureCodec, boolean)} with {@code requireIndex} = true
*/
public static AbstractFeatureReader getFeatureReader(final String featureFile, final FeatureCodec codec) throws TribbleException {
return getFeatureReader(featureFile, codec, true);
}
/**
* {@link #getFeatureReader(String, String, FeatureCodec, boolean, Function, Function)} with {@code null} for indexResource, wrapper, and indexWrapper
* @throws TribbleException
*/
public static AbstractFeatureReader getFeatureReader(final String featureResource, final FeatureCodec codec, final boolean requireIndex) throws TribbleException {
return getFeatureReader(featureResource, null, codec, requireIndex, null, null);
}
/**
* {@link #getFeatureReader(String, String, FeatureCodec, boolean, Function, Function)} with {@code null} for wrapper, and indexWrapper
* @throws TribbleException
*/
public static AbstractFeatureReader getFeatureReader(final String featureResource, String indexResource, final FeatureCodec codec, final boolean requireIndex) throws TribbleException {
return getFeatureReader(featureResource, indexResource, codec, requireIndex, null, null);
}
/**
*
* @param featureResource the feature file to create from
* @param indexResource the index for the feature file. If null, will auto-generate (if necessary)
* @param codec the codec to use to decode the individual features
* @param requireIndex whether an index is required for this file
* @param wrapper a wrapper to apply to the byte stream from the featureResource allowing injecting features
* like caching and prefetching of the stream, may be null, will only be applied if featureResource
* is a uri representing a {@link java.nio.file.Path}
* @param indexWrapper a wrapper to apply to the byte stream from the indexResource, may be null, will only be
* applied if indexResource is a uri representing a {@link java.nio.file.Path}
*
* @throws TribbleException
*/
public static AbstractFeatureReader getFeatureReader(final String featureResource, String indexResource, final FeatureCodec codec, final boolean requireIndex, Function wrapper, Function indexWrapper) throws TribbleException {
try {
// Test for tabix index.
// Note that we use pathToDataFile here when determining the file type, but featureResource when constructing the readers.
// This is because the reader's constructor will convert the path and it needs to be converted exactly once.
final String pathToDataFile = codec.getPathToDataFile(featureResource);
if (methods.isTabix(pathToDataFile, indexResource)) {
if ( ! (codec instanceof AsciiFeatureCodec) )
throw new TribbleException("Tabix indexed files only work with ASCII codecs, but received non-Ascii codec " + codec.getClass().getSimpleName());
return new TabixFeatureReader<>(featureResource, indexResource, (AsciiFeatureCodec) codec, wrapper, indexWrapper);
}
// Not tabix => tribble index file (might be gzipped, but not block gzipped)
else {
return new TribbleIndexedFeatureReader<>(featureResource, indexResource, codec, requireIndex, wrapper, indexWrapper);
}
} catch (final IOException e) {
throw new TribbleException.MalformedFeatureFile("Unable to create BasicFeatureReader using feature file ", featureResource, e);
} catch (final TribbleException e) {
e.setSource(featureResource);
throw e;
}
}
/**
* Return a reader with a supplied index.
*
* @param featureResource the path to the source file containing the features
* @param codec used to decode the features
* @param index index of featureResource
* @return a reader for this data
* @throws TribbleException
*/
public static AbstractFeatureReader getFeatureReader(final String featureResource, final FeatureCodec codec, final Index index) throws TribbleException {
try {
return new TribbleIndexedFeatureReader<>(featureResource, codec, index);
} catch (final IOException e) {
throw new TribbleException.MalformedFeatureFile("Unable to create AbstractFeatureReader using feature file ", featureResource, e);
}
}
protected AbstractFeatureReader(final String path, final FeatureCodec codec) {
this(path, codec, null, null);
}
protected AbstractFeatureReader(final String path, final FeatureCodec codec,
final Function wrapper,
final Function indexWrapper) {
this.path = codec.getPathToDataFile(path);
this.codec = codec;
this.wrapper = wrapper;
this.indexWrapper = indexWrapper;
}
/**
* Whether the reader has an index or not
* Default implementation returns false
* @return false
*/
public boolean hasIndex() {
return false;
}
/**
* @return true if the reader has an index, which means that it can be queried.
*/
@Override
public boolean isQueryable(){
return hasIndex();
}
public static void setComponentMethods(ComponentMethods methods){
AbstractFeatureReader.methods = methods;
}
/**
* @deprecated use {@link IOUtil#hasBlockCompressedExtension(String)}.
*/
@Deprecated
public static boolean hasBlockCompressedExtension (final String fileName) {
return IOUtil.hasBlockCompressedExtension(fileName);
}
/**
* @deprecated use {@link IOUtil#hasBlockCompressedExtension(File)}.
*/
@Deprecated
public static boolean hasBlockCompressedExtension (final File file) {
return IOUtil.hasBlockCompressedExtension(file.getName());
}
/**
* @deprecated use {@link IOUtil#hasBlockCompressedExtension(URI)}.
*/
@Deprecated
public static boolean hasBlockCompressedExtension (final URI uri) {
String path = uri.getPath();
return IOUtil.hasBlockCompressedExtension(path);
}
/**
* get the header
*
* @return the header object we've read-in
*/
@Override
public Object getHeader() {
return header.getHeaderValue();
}
static class EmptyIterator implements CloseableTribbleIterator {
@Override public Iterator iterator() { return this; }
@Override public boolean hasNext() { return false; }
@Override public T next() { return null; }
@Override public void remove() { }
@Override public void close() { }
}
public static boolean isTabix(String resourcePath, String indexPath) throws IOException {
if(indexPath == null){
indexPath = ParsingUtils.appendToPath(resourcePath, FileExtensions.TABIX_INDEX);
}
return IOUtil.hasBlockCompressedExtension(resourcePath) && ParsingUtils.resourceExists(indexPath);
}
public static class ComponentMethods{
public boolean isTabix(String resourcePath, String indexPath) throws IOException{
return AbstractFeatureReader.isTabix(resourcePath, indexPath);
}
}
}
