IOPath (htsjdk 2.24.1 API)

All Known Implementing Classes:

HtsPath
```
public interface IOPath
```
Interface for htsjdk input/output paths/URIs.

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`default java.util.Optional<java.lang.String>`	`getBaseName()`
`default java.util.Optional<java.lang.String>`	`getExtension()`
`java.io.InputStream`	`getInputStream()` Get a `InputStream` for this URI if a provider is for the URI's scheme is available.
`java.io.OutputStream`	`getOutputStream()` Get an `OutputStream` for this URI if a provider is for the URI's scheme.
`java.lang.String`	`getRawInputString()` Return the raw input string that was provided to the constructor.
`default java.lang.String`	`getScheme()` Return the scheme for this `IOPath`.
`java.lang.String`	`getToPathFailureReason()` Return a string message describing why this URI cannot be converted to a `java.nio.file.Path` (`#isPath()` returns false).
`java.net.URI`	`getURI()` Get a `java.net.URI` object for this `IOPath`.
`java.lang.String`	`getURIString()` Returns the string from which this `IOPath` was originally created.
`default boolean`	`hasExtension(java.lang.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.
`boolean`	`hasFileSystemProvider()`
`default boolean`	`isBam()` Returns true if the file's extension is ".bam"".
`default boolean`	`isCram()` Returns true if the GATKPath's extension is ".cram".
`default boolean`	`isFasta()`
`boolean`	`isPath()` Return true if this {code IOPath} can be resolved to an `java.nio` Path.
`default boolean`	`isSam()` Returns true if the file's extension is ".sam"".
`java.nio.file.Path`	`toPath()` Resolve this `IOPath` to an NIO `java.nio.file.Path`.

- Method Detail
  - getURI
```
java.net.URI getURI()
```
    Get a java.net.URI object for this IOPath. Will not be null.
    
    Returns:
    
    The URI object for this IOPath.
  - getURIString
```
java.lang.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
```
java.lang.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 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
```
java.nio.file.Path toPath()
```
    Resolve this IOPath to an NIO java.nio.file.Path. Can be safely called only if #isPath() returns true.
  - getToPathFailureReason
```
java.lang.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 java.lang.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 java.util.Optional<java.lang.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(java.lang.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 java.util.Optional<java.lang.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
```
java.io.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
```
java.io.OutputStream getOutputStream()
```
    Get an OutputStream for this URI if a provider is for the URI's scheme.
    
    Returns:
    
    OutputStream for this URI.

Interface IOPath

Method Summary

Method Detail

getURI

getURIString

getRawInputString

hasFileSystemProvider

isPath

toPath

getToPathFailureReason

getScheme

getExtension

hasExtension

getBaseName

isSam

isBam

isCram

isFasta

getInputStream

getOutputStream