Package htsjdk.io

Interface IOPath

  • All Known Implementing Classes:
    HtsPath
    public interface IOPath
    Interface for htsjdk input/output paths/URIs.

    • Method Detail

      • getURI

        URI getURI()
        Get a java.net.URI object for this IOPath. Will not be null.
        Returns:
        The URI object for this IOPath.

      • getURIString

        String getURIString()
        Returns the string from which this IOPath was originally created. This string may differ from the normalized string returned from a java.nio.file.Path that has been object resolved from this IOPath.
        Returns:
        string from which this URI as originally created. Will not be null.

      • getRawInputString

        String getRawInputString()
        Return the raw input string that was provided to the constructor.

      • hasFileSystemProvider

        boolean hasFileSystemProvider()
        Returns:
        true if this URI has a scheme that has an installed java.nio file system provider (). This does not guarantee the URI can be converted into a java.nio.file.Path, since the URI can be syntactically valid, and specify a valid file system provider, but still fail to be semantically meaningful.

      • isPath

        boolean isPath()
        Return true if this {code IOPath} can be resolved to an java.nio Path. If true, #toPath() can be safely called. There are cases where a valid URI with a valid scheme backed by an installed {@code java.nio File System still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid authority "namenode": hdfs://namenode/to/file The current implementation returns false for these cases (toPath will fail, getInvalidPathReason returns the reason code).

      • toPath

        Path toPath()
        Resolve this IOPath to an NIO java.nio.file.Path. Can be safely called only if #isPath() returns true.

      • getToPathFailureReason

        String getToPathFailureReason()
        Return a string message describing why this URI cannot be converted to a java.nio.file.Path (#isPath() returns false).
        Returns:
        Message explaining toPath failure reason, since it can fail for various reasons.

      • getScheme

        default String getScheme()
        Return the scheme for this IOPath. For file URIs (URIs that have no explicit scheme), this will return the scheme "file".
        Returns:
        the scheme String or this URI, if any. May be null.

      • getExtension

        default Optional<String> getExtension()
        Returns:
        an Optional containing the extension of the last component of the hierarchical part of the scheme-specific part of the URI, if any, including the ".", or Optional.empty() if the hierarchical name ends with the default file system separator, (i.e. "/"), or if the hierarchical name ends with a last component that does not contain a ".". Note that this only returns the part of the last component after the last ".", ie. it will return ".gz" for a name that ends in ".fasta.gz" (the hasExtension(String) method can be used to test for the presence of multi-part extensions such as this).

      • hasExtension

        default boolean hasExtension​(String extension)
        Return true if the path component (the hierarchical part of the scheme specific part of the underlying URI) ends with the provided extension string. This method can be used to test for both single and multi-part extensions (ie. for a name that ends in ".fasta.gz", it will return true for both ".gz" and ".fasta.gz".
        Parameters:
        extension - the target extension to test, INCLUDING the leading ".". May not be null.
        Returns:
        true if the path component of this specifier ends with the extension, otherwise false.

      • getBaseName

        default Optional<String> getBaseName()
        Returns:
        an Optional containing the base name (the last component of the hierarchical part of the scheme-specific part of the URI, after the last "/"), up to but not including the extension (the last "."), or Optional.empty() if the last component is empty (ie, the component ends in "/"), or the last component exists but starts with "."

      • isSam

        default boolean isSam()
        Returns true if the file's extension is ".sam"".

      • isBam

        default boolean isBam()
        Returns true if the file's extension is ".bam"".

      • isCram

        default boolean isCram()
        Returns true if the GATKPath's extension is ".cram".

      • isFasta

        default boolean isFasta()
        Returns:
        true if this path spec has a FASTA file extension

      • getInputStream

        InputStream getInputStream()
        Get a InputStream for this URI if a provider is for the URI's scheme is available.
        Returns:
        InputStream for this URI.

      • getOutputStream

        OutputStream getOutputStream()
        Get an OutputStream for this URI if a provider is for the URI's scheme.
        Returns:
        OutputStream for this URI.