PathSpecifier (gatk 4.1.7.0 API)

java.lang.Object
- org.broadinstitute.hellbender.engine.PathSpecifier

All Implemented Interfaces:

java.io.Serializable, PathURI

Direct Known Subclasses:

GATKPathSpecifier
```
public class PathSpecifier
extends java.lang.Object
implements PathURI, java.io.Serializable
```
Default implementation for PathURI. This class takes a raw string that is to be interpreted as a path specifier, and converts it internally to a URI and/or Path object. If no scheme is provided as part of the raw string used in the constructor(s), the input is assumed to represent a file on the local file system, and will be backed by a URI with a "file:/" scheme and a path part that is automatically encoded/escaped to ensure it is a valid URI. If the raw string contains a scheme, it will be backed by a URI formed from the raw string as presented, with no further encoding/escaping. For example, a URI that contains a scheme and has an embedded "#" in the path will be treated as a URI having a fragment delimiter. If the URI contains an scheme, the "#" will be escaped and the encoded "#" will be interpreted as part of the URI path. There are 3 succeeding levels of input validation/conversion: 1) PathSpecifier constructor: requires a syntactically valid URI, possibly containing a scheme (if no scheme is present the path part will be escaped/encoded), or a valid local file reference 2) hasFileSystemProvider: true if the input string is an identifier that is syntactically valid, and is backed by an installed java.nio file system provider that matches the URI scheme 3) isPath: syntactically valid URI that can be resolved to a java.io.Path by the associated provider Definitions taken from RFC 2396 "Uniform Resource Identifiers (URI): Generic Syntax" (https://www.ietf.org/rfc/rfc2396.txt): "absolute" URI - specifies a scheme "relative" URI - does not specify a scheme "opaque" URI - an "absolute" URI whose scheme-specific part does not begin with a slash character "hierarchical" URI - either an "absolute" URI whose scheme-specific part begins with a slash character, or a "relative" URI (no scheme) URIs that do not make use of the slash "/" character for separating hierarchical components are considered "opaque" by the generic URI parser. General syntax for an "absolute" URI: : Many "hierarchical" URI schemes use this syntax: ://? More specifically: absoluteURI = scheme ":" ( hier_part | opaque_part ) hier_part = ( net_path | abs_path ) [ "?" query ] net_path = "//" authority [ abs_path ] abs_path = "/" path_segments opaque_part = uric_no_slash *uric uric_no_slash = unreserved | escaped | ";" | "?" | ":" | "@" | "&" | "=" | "+" | "$" | ","

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`PathSpecifier(java.lang.String rawInputString)` If the raw input string already contains a scheme (including a "file" scheme), assume its already properly escape/encoded.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`equals(java.lang.Object o)`
`protected java.nio.file.Path`	`getCachedPath()`
`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 provided to the constructor.
`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 `PathURI`.
`java.lang.String`	`getURIString()` Returns the string from which this `PathURI` was originally created.
`boolean`	`hasFileSystemProvider()`
`int`	`hashCode()`
`boolean`	`isPath()` Return true if this {code PathURI} can be resolved to an `java.nio` Path.
`protected void`	`setCachedPath(java.nio.file.Path path)`
`java.nio.file.Path`	`toPath()` Resolve the URI to a `Path` object.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.broadinstitute.hellbender.engine.PathURI
getScheme

- Constructor Detail
  - PathSpecifier
```
public PathSpecifier(java.lang.String rawInputString)
```
    If the raw input string already contains a scheme (including a "file" scheme), assume its already properly escape/encoded. If no scheme component is present, assume it referencess a raw path on the local file system, so try to get a Path first, and then retrieve the URI from the resulting Path. This ensures that input strings that are local file references without a scheme component and contain embedded characters are valid in file names, but which would otherwise be interpreted as excluded URI characters (such as the URI fragment delimiter "#") are properly escape/encoded.
    
    Parameters:
    
    rawInputString -
- Method Detail
  - getURI
```
public java.net.URI getURI()
```
    Description copied from interface: PathURI
    
    Get a java.net.URI object for this PathURI. Will not be null.
    
    Specified by:
    
    getURI in interface PathURI
    
    Returns:
    
    The URI object for this PathURI.
  - getURIString
```
public java.lang.String getURIString()
```
    Description copied from interface: PathURI
    
    Returns the string from which this PathURI 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 PathURI.
    
    Specified by:
    
    getURIString in interface PathURI
    
    Returns:
    
    string from which this URI as originally created. Will not be null.
  - getRawInputString
```
public java.lang.String getRawInputString()
```
    Return the raw input string provided to the constructor.
    
    Specified by:
    
    getRawInputString in interface PathURI
  - hasFileSystemProvider
```
public boolean hasFileSystemProvider()
```
    Specified by:
    
    hasFileSystemProvider in interface PathURI
    
    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
```
public boolean isPath()
```
    Description copied from interface: PathURI
    
    Return true if this {code PathURI} 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).
    
    Specified by:
    
    isPath in interface PathURI
  - toPath
```
public java.nio.file.Path toPath()
```
    Resolve the URI to a Path object.
    
    Specified by:
    
    toPath in interface PathURI
    
    Returns:
    
    the resulting Path
    
    Throws:
    
    UserException - if an I/O error occurs when creating the file system
  - getToPathFailureReason
```
public java.lang.String getToPathFailureReason()
```
    Description copied from interface: PathURI
    
    Return a string message describing why this URI cannot be converted to a java.nio.file.Path (#isPath() returns false).
    
    Specified by:
    
    getToPathFailureReason in interface PathURI
    
    Returns:
    
    Message explaining toPath failure reason, since it can fail for various reasons.
  - getInputStream
```
public java.io.InputStream getInputStream()
```
    Description copied from interface: PathURI
    
    Get a InputStream for this URI if a provider is for the URI's scheme is available.
    
    Specified by:
    
    getInputStream in interface PathURI
    
    Returns:
    
    InputStream for this URI.
  - getOutputStream
```
public java.io.OutputStream getOutputStream()
```
    Description copied from interface: PathURI
    
    Get an OutputStream for this URI if a provider is for the URI's scheme.
    
    Specified by:
    
    getOutputStream in interface PathURI
    
    Returns:
    
    OutputStream for this URI.
  - getCachedPath
```
protected java.nio.file.Path getCachedPath()
```
  - setCachedPath
```
protected void setCachedPath(java.nio.file.Path path)
```
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object

Class PathSpecifier

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.broadinstitute.hellbender.engine.PathURI

Constructor Detail

PathSpecifier

Method Detail

getURI

getURIString

getRawInputString

hasFileSystemProvider

isPath

toPath

getToPathFailureReason

getInputStream

getOutputStream

getCachedPath

setCachedPath

toString

equals

hashCode