htsjdk CloseableIterator接口介绍

CloseableIterator接口是Java中一种特殊类型的迭代器,它结合了IteratorAutoCloseable接口的特性。CloseableIterator不仅允许你像普通的Iterator一样遍历集合,还提供了一个close()方法,用于在不再需要时释放资源。这在处理诸如文件、数据库连接等需要手动释放资源的场景中特别有用。

通常情况下,CloseableIterator用于那些需要在遍历完成后进行资源清理的迭代器。实现CloseableIterator接口的类不仅需要实现Iterator接口的方法,还需要实现AutoCloseable接口的方法,即close()

htsjdk.samtools.util.CloseableIterator源码

/*
 * The MIT License
 *
 * Copyright (c) 2009 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.samtools.util;

import java.io.Closeable;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;

/**
 * This interface is used by iterators that use releasable resources during iteration.
 * 
 * The consumer of a CloseableIterator should ensure that the close() method is always called,
 * for example by putting such a call in a finally block.  Two conventions should be followed
 * by all implementors of CloseableIterator:
 * 1) The close() method should be idempotent: calling close() twice should have no effect.
 * 2) When hasNext() returns false, the iterator implementation should automatically close itself.
 *    The latter makes it somewhat safer for consumers to use the for loop syntax for iteration:
 *    for (Type obj : getCloseableIterator()) { ... }
 */
public interface CloseableIterator<T> extends Iterator<T>, Closeable {
    /** Should be implemented to close/release any underlying resources. */
    @Override
    void close();

    /** Consumes the contents of the iterator and returns it as a List. */
    default List<T> toList() {
        final List<T> list = new ArrayList<>();
        while (hasNext()) list.add(next());
        close();
        return list;
    }

    /** Returns a Stream that will consume from the underlying iterator. */
    default Stream<T> stream() {
        final Spliterator<T> s = Spliterators.spliteratorUnknownSize(this, Spliterator.ORDERED);
        return StreamSupport.stream(s, false).onClose(this::close);
    }
}

示例代码

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Iterator;

public class CloseableIteratorExample {

    public static void main(String[] args) {
        try (LineIterator iterator = new LineIterator("example.txt")) {
            while (iterator.hasNext()) {
                String line = iterator.next();
                System.out.println(line);
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    static class LineIterator implements Iterator<String>, AutoCloseable {

        private BufferedReader reader;
        private String nextLine;

        public LineIterator(String filePath) throws IOException {
            this.reader = new BufferedReader(new FileReader(filePath));
            this.nextLine = reader.readLine();
        }

        @Override
        public boolean hasNext() {
            return nextLine != null;
        }

        @Override
        public String next() {
            String line = nextLine;
            try {
                nextLine = reader.readLine();
            } catch (IOException e) {
                throw new RuntimeException(e);
            }
            return line;
        }

        @Override
        public void close() throws IOException {
            reader.close();
        }
    }
}

代码解释

  • LineIterator类实现了Iterator<String>AutoCloseable接口。LineIterator通过BufferedReader逐行读取文件内容。

  • hasNext()方法检查是否还有未读取的行。

  • next()方法返回当前行,并读取下一行内容。

  • close()方法在遍历完成或异常发生时关闭BufferedReader,释放资源。

  • try-with-resources块中使用LineIterator时,即使在遍历过程中出现异常,也会自动调用close()方法。

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使用GATK的combinegvcf模块合并gvcf文件,可是到了这一步Using GATK jar /stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar CombineGVCFs -R /stor9000/apps/users/NWSUAF/2008115251/genomes/ARS-UCD1.2_Btau5.0.1Y.fa --variant /stor9000/apps/users/NWSUAF/2020055419/home/xncattle/03.GVCF/01_out_GVCF/XN_22/1_XN_22.g.vcf.gz --variant /stor9000/apps/users/NWSUAF/2020055419/home/xncattle/03.GVCF/01_out_GVCF/XN_18/1_XN_18.g.vcf.gz -O /stor9000/apps/users/NWSUAF/2022050469/candy/bwa/gatk/Combine/chr1.g.vcf.gz 09:10:40.524 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/stor9000/apps/users/NWSUAF/2022050434/biosoft/gatk4.3/gatk-4.3.0.0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 09:10:50.696 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.697 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.3.0.0 09:10:50.697 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 09:10:50.698 INFO CombineGVCFs - Executing as 2022050469@node54 on Linux v3.10.0-1127.el7.x86_64 amd64 09:10:50.698 INFO CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_72-b15 09:10:50.698 INFO CombineGVCFs - Start Date/Time: July 21, 2023 9:10:40 AM CST 09:10:50.698 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.698 INFO CombineGVCFs - ------------------------------------------------------------ 09:10:50.698 INFO CombineGVCFs - HTSJDK Version: 3.0.1 09:10:50.699 INFO CombineGVCFs - Picard Version: 2.27.5 09:10:50.699 INFO CombineGVCFs - Built for Spark Version: 2.4.5 09:10:50.699 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 09:10:50.699 INFO CombineGVCFs - HTSJDK Defa就停止了,没有输出文件,也没有报错文件
07-22
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