Package picard.nio
Class PicardHtsPath
- java.lang.Object
-
- htsjdk.io.HtsPath
-
- picard.nio.PicardHtsPath
-
- All Implemented Interfaces:
htsjdk.io.IOPath
,Serializable
public class PicardHtsPath extends htsjdk.io.HtsPath
- See Also:
- Serialized Form
-
-
Constructor Summary
Constructors Constructor Description PicardHtsPath(htsjdk.io.HtsPath htsPath)
Create a PicardHtsPath from an existingHtsPath
or subclass.PicardHtsPath(File file)
Create a PicardHtsPath from aFile
reference.PicardHtsPath(String rawInputString)
Create a PicardHtsPath from a raw input path string.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static PicardHtsPath
fromPath(Path path)
Construct aPicardHtsPath
from aPath
static List<PicardHtsPath>
fromPaths(Collection<String> paths)
Create aList
from path representations.Path
toPath()
Resolve the URI of this object to aPath
object.static List<Path>
toPaths(Collection<PicardHtsPath> picardHtsPaths)
Create aList
fromPicardHtsPath
s-
Methods inherited from class htsjdk.io.HtsPath
equals, getCachedPath, getInputStream, getOutputStream, getRawInputString, getToPathFailureReason, getURI, getURIString, hasFileSystemProvider, hashCode, isPath, setCachedPath, toString
-
-
-
-
Constructor Detail
-
PicardHtsPath
public PicardHtsPath(String rawInputString)
Create a PicardHtsPath from a raw input path string.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 references 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
- a string specifying an input path. May not be null.
-
PicardHtsPath
public PicardHtsPath(htsjdk.io.HtsPath htsPath)
Create a PicardHtsPath from an existingHtsPath
or subclass.- Parameters:
htsPath
- an existing PathSpecifier. May not be null.
-
-
Method Detail
-
fromPaths
public static List<PicardHtsPath> fromPaths(Collection<String> paths)
Create aList
from path representations.- Parameters:
paths
- URIs or local paths. May not be null but may be empty.- Returns:
- the converted
List
-
toPath
public Path toPath()
Resolve the URI of this object to aPath
object.- Specified by:
toPath
in interfacehtsjdk.io.IOPath
- Overrides:
toPath
in classhtsjdk.io.HtsPath
- Returns:
- the resulting
Path
- Throws:
RuntimeException
- if an I/O error occurs when creating the file system
-
fromPath
public static PicardHtsPath fromPath(Path path)
Construct aPicardHtsPath
from aPath
- Parameters:
path
- may NOT be null- Returns:
- a new object representing path
-
toPaths
public static List<Path> toPaths(Collection<PicardHtsPath> picardHtsPaths)
Create aList
fromPicardHtsPath
s- Parameters:
picardHtsPaths
- may NOT be null- Returns:
- Path representations of the input picardHtsPaths
-
-