loci.common

Class Location

java.lang.Object

loci.common.Location

Direct Known Subclasses:

CaseInsensitiveLocation

public class Location
extends Object

Pseudo-extension of File that supports reading over HTTP (among other things). It is strongly recommended to use this instead of java.io.File.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	Location.ListingsResult
protected static class	Location.UrlType

Constructor Summary

Constructors

Constructor and Description
Location(File file) Construct a Location using the given file on disk.
Location(Location parent, String child) Construct a Location using the given directory and relative path.
Location(String pathname) Construct a Location using the given path.
Location(String parent, String child) Construct a Location using the given directory and relative path.

Method Summary

Modifier and Type	Method and Description
static void	cacheDirectoryListings(boolean cache) Turn cacheing of directory listings on or off.
boolean	canRead() If the underlying location is a URL, this method will return true if the URL exists.
boolean	canWrite() If the underlying location is a URL, this method will always return false.
static void	checkValidId(String id) Checks that the given id points at a valid data stream.
static void	cleanStaleCacheEntries() Remove any cached directory listings that have expired.
static void	clearDirectoryListingsCache() Clear the directory listings cache.
boolean	createNewFile() Creates a new empty file named by this Location's path name iff a file with this name does not already exist.
boolean	delete() Deletes this file.
void	deleteOnExit() Request that this file be deleted when the JVM terminates.
boolean	equals(Object obj)
boolean	exists() Returns whether or not the pathname exists.
Location	getAbsoluteFile() Return the absolute form of this abstract location.
String	getAbsolutePath() Return the absolute form of this abstract location.
Location	getCanonicalFile() Returns the canonical path to this file.
String	getCanonicalPath() Returns the canonical path to this file.
static IRandomAccess	getHandle(String id) Gets an IRandomAccess object that can read from the given file.
static IRandomAccess	getHandle(String id, boolean writable) Gets an IRandomAccess object that can read from or write to the given file.
static IRandomAccess	getHandle(String id, boolean writable, boolean allowArchiveHandles) Gets an IRandomAccess object that can read from or write to the given file.
static IRandomAccess	getHandle(String id, boolean writable, boolean allowArchiveHandles, int bufferSize) Gets an IRandomAccess object that can read from or write to the given file.
static HashMap<String,Object>	getIdMap() Return the id mapping.
static IRandomAccess	getMappedFile(String id) Gets the random access handle for the given id.
static String	getMappedId(String id) Gets the actual filename on disk for the given id.
String	getName() Returns the name of this file, i.e.
String	getParent() Returns the pathname string of this abstract pathname's parent, or null if this pathname does not have a parent directory.
Location	getParentFile() Returns the abstract pathname of this abstract pathname's parent, or null if this pathname does not name a parent directory.
String	getPath() Returns the file's path.
int	hashCode()
boolean	isAbsolute() Returns whether or not this file's path is absolute.
boolean	isDirectory() Returns whether or not this file is a directory.
boolean	isFile() Returns whether or not this file is a regular file (i.e.
boolean	isHidden() Returns whether or not this file is marked hidden by the filesystem.
long	lastModified() Return the last modification time of the file.
long	length() Return the file length in bytes.
String[]	list() Return a list of relative file names in this directory, or null if this file is not a directory.
String[]	list(boolean noHiddenFiles) Return a list of all of the files in this directory.
Location[]	listFiles() Return a list of files in this directory, or null if this file is not a directory.
static void	mapFile(String id, IRandomAccess ira) Maps the given id to the given IRandomAccess object.
static void	mapId(String id, String filename) Maps the given id to an actual filename on disk.
boolean	mkdirs() Creates a directory structures described by this Location's internal File instance.
static void	reset() Clear all caches and reset cache-related bookkeeping variables to their original values.
static void	setCacheDirectoryTimeout(double sec) Cache directory listings for this many seconds before relisting.
static void	setIdMap(HashMap<String,Object> map) Set the id mapping using the given HashMap.
String	toString()
URL	toURL() Return a URL corresponding to this file.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Location

public Location(String pathname)

Construct a Location using the given path.

Parameters:

pathname - a URL, a file on disk, or a mapped name

See Also:

getMappedId(String), getMappedFile(String)

Location

public Location(File file)

Construct a Location using the given file on disk.

Parameters:

file - a file on disk

Location

public Location(String parent,
                String child)

Construct a Location using the given directory and relative path. The two parameters are joined with a file separator and passed to #Location(String)

Parameters:

parent - the directory path name

child - the relative path name

Location

public Location(Location parent,
                String child)

Construct a Location using the given directory and relative path.

Parameters:

parent - a Location representing the directory name

child - the relative path name

See Also:

Location(String, String)

Method Detail

reset

public static void reset()

Clear all caches and reset cache-related bookkeeping variables to their original values.

cacheDirectoryListings

public static void cacheDirectoryListings(boolean cache)

Turn cacheing of directory listings on or off. Cacheing is turned off by default. Reasons to cache - directory listings over network shares can be very expensive, especially in HCS experiments with thousands of files in the same directory. Technically, if you use a directory listing and then go and access the file, you are using stale information. Unlike a database, there's no transactional integrity to file system operations, so the directory could change by the time you access the file. Reasons not to cache - the contents of the directories might change during the program invocation.

Parameters:

cache - - true to turn cacheing on, false to leave it off.

setCacheDirectoryTimeout

public static void setCacheDirectoryTimeout(double sec)

Cache directory listings for this many seconds before relisting.

Parameters:

sec - - use the cache if a directory list was done within this many seconds.

clearDirectoryListingsCache

public static void clearDirectoryListingsCache()

Clear the directory listings cache. Do this if directory contents might have changed in a significant way.

cleanStaleCacheEntries

public static void cleanStaleCacheEntries()

Remove any cached directory listings that have expired.

mapId

public static void mapId(String id,
                         String filename)

Maps the given id to an actual filename on disk. Typically actual filenames are used for ids, making this step unnecessary, but in some cases it is useful; e.g., if the file has been renamed to conform to a standard naming scheme and the original file extension is lost, then using the original filename as the id assists format handlers with type identification and pattern matching, and the id can be mapped to the actual filename for reading the file's contents.

Parameters:

id - the mapped name

filename - the actual filename on disk. If null, any existing mapping for id will be cleared.

See Also:

getMappedId(String)

mapFile

public static void mapFile(String id,
                           IRandomAccess ira)

Maps the given id to the given IRandomAccess object.

Parameters:

id - the mapped name

ira - the IRandomAccess object that will be referenced by id. If null, any existing mapping for id will be cleared.

See Also:

getMappedFile(String)

getMappedId

public static String getMappedId(String id)

Gets the actual filename on disk for the given id. Typically the id itself is the filename, but in some cases may not be; e.g., if OMEIS has renamed a file from its original name to a standard location such as Files/101, the original filename is useful for checking the file extension and doing pattern matching, but the renamed filename is required to read its contents.

Parameters:

id - the mapped name

Returns:

the corresponding file name on disk, or null if there is no mapping

See Also:

mapId(String, String)

getMappedFile

public static IRandomAccess getMappedFile(String id)

Gets the random access handle for the given id.

Parameters:

id - the mapped name

Returns:

the corresponding IRandomAccess, or null if there is no mapping

See Also:

mapFile(String, IRandomAccess)

getIdMap

public static HashMap<String,Object> getIdMap()

Return the id mapping.

Returns:

the map from names to filesystem paths and IRandomAccess objects

See Also:

mapId(String, String), mapFile(String, IRandomAccess)

setIdMap

public static void setIdMap(HashMap<String,Object> map)

Set the id mapping using the given HashMap.

Parameters:

map - the new mapping from names to filesystem paths and IRandomAccess objects

Throws:

IllegalArgumentException - if the given HashMap is null.

getHandle

public static IRandomAccess getHandle(String id)
                               throws IOException

Gets an IRandomAccess object that can read from the given file.

Parameters:

id - the name for which to locate an IRandomAccess

Returns:

a previously mapped IRandomAccess, or a new IRandomAccess according to the name's type (URL, filesystem path, etc.)

Throws:

IOException - if a valid IRandomAccess cannot be created

See Also:

getHandle(String, boolean, boolean, int), IRandomAccess

getHandle

public static IRandomAccess getHandle(String id,
                                      boolean writable)
                               throws IOException

Gets an IRandomAccess object that can read from or write to the given file.

Parameters:

id - the name for which to locate an IRandomAccess

writable - true if the returned IRandomAccess should have write permission

Returns:

a previously mapped IRandomAccess, or a new IRandomAccess according to the name's type (URL, filesystem path, etc.)

Throws:

IOException - if a valid IRandomAccess cannot be created

See Also:

getHandle(String, boolean, boolean, int), IRandomAccess

getHandle

public static IRandomAccess getHandle(String id,
                                      boolean writable,
                                      boolean allowArchiveHandles)
                               throws IOException

Gets an IRandomAccess object that can read from or write to the given file.

Parameters:

id - the name for which to locate an IRandomAccess

writable - true if the returned IRandomAccess should have write permission

allowArchiveHandles - true if checks for compressed/archive file types (e.g. Zip, GZip, BZip2) should be enabled

Returns:

a previously mapped IRandomAccess, or a new IRandomAccess according to the name's type (URL, filesystem path, etc.)

Throws:

IOException - if a valid IRandomAccess cannot be created

See Also:

getHandle(String, boolean, boolean, int), IRandomAccess

getHandle

public static IRandomAccess getHandle(String id,
                                      boolean writable,
                                      boolean allowArchiveHandles,
                                      int bufferSize)
                               throws IOException

Gets an IRandomAccess object that can read from or write to the given file.

Parameters:

id - the name for which to locate an IRandomAccess

writable - true if the returned IRandomAccess should have write permission

allowArchiveHandles - true if checks for compressed/archive file types (e.g. Zip, GZip, BZip2) should be enabled

bufferSize - the buffer size to use when constructing a NIOFileHandle. Ignored when non-positive.

Returns:

a previously mapped IRandomAccess, or a new IRandomAccess according to the name's type (URL, filesystem path, etc.)

Throws:

IOException - if a valid IRandomAccess cannot be created

See Also:

IRandomAccess

checkValidId

public static void checkValidId(String id)
                         throws IOException

Checks that the given id points at a valid data stream.

Parameters:

id - The id string to validate.

Throws:

IOException - if the id is not valid.

list

public String[] list(boolean noHiddenFiles)

Return a list of all of the files in this directory. If 'noHiddenFiles' is set to true, then hidden files are omitted.

Parameters:

noHiddenFiles - true if hidden files should be omitted

Returns:

an unsorted list of all relative files in the directory represented by this Location

See Also:

File.list()

canRead

public boolean canRead()

If the underlying location is a URL, this method will return true if the URL exists. Otherwise, it will return true iff the file exists and is readable.

Returns:

see above

See Also:

File.canRead()

canWrite

public boolean canWrite()

If the underlying location is a URL, this method will always return false. Otherwise, it will return true iff the file exists and is writable.

Returns:

see above

See Also:

File.canWrite()

createNewFile

public boolean createNewFile()
                      throws IOException

Creates a new empty file named by this Location's path name iff a file with this name does not already exist. Note that this operation is only supported if the path name can be interpreted as a path to a file on disk (i.e. is not a URL).

Returns:

true if the file was created successfully

Throws:

IOException - if an I/O error occurred, or the abstract pathname is a URL

See Also:

File.createNewFile()

mkdirs

public boolean mkdirs()

Creates a directory structures described by this Location's internal File instance.

Returns:

true if the directory structure was created successfully.

See Also:

File.mkdirs()

delete

public boolean delete()

Deletes this file. If isDirectory() returns true, then the directory must be empty in order to be deleted. URLs cannot be deleted.

Returns:

true if the file was successfully deleted

See Also:

File.delete()

deleteOnExit

public void deleteOnExit()

Request that this file be deleted when the JVM terminates. This method will do nothing if the pathname represents a URL.

See Also:

File.deleteOnExit()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

See Also:

File.equals(Object), URL.equals(Object)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

exists

public boolean exists()

Returns whether or not the pathname exists. If the pathname is a URL, then existence is determined based on whether or not we can successfully read content from the URL.

Returns:

true if there is a way to read bytes from this Location's name

See Also:

File.exists()

getAbsoluteFile

public Location getAbsoluteFile()

Return the absolute form of this abstract location.

Returns:

a Location representing @see #getAbsolutePath

See Also:

File.getAbsoluteFile()

getAbsolutePath

public String getAbsolutePath()

Return the absolute form of this abstract location.

Returns:

a string representing the absolute path

See Also:

File.getAbsolutePath()

getCanonicalFile

public Location getCanonicalFile()
                          throws IOException

Returns the canonical path to this file. If the file is a URL, then the canonical path is equivalent to the absolute file (getAbsoluteFile()). Otherwise, this method will delegate to File.getCanonicalFile().

Returns:

see above

Throws:

IOException - if the canonical path cannot be constructed

See Also:

File.getCanonicalFile()

getCanonicalPath

public String getCanonicalPath()
                        throws IOException

Returns the canonical path to this file. If the file is a URL, then the canonical path is equivalent to the absolute path (getAbsolutePath()). Otherwise, this method will delegate to File.getCanonicalPath().

Returns:

see above

Throws:

IOException - if the path cannot be retrieved

getName

public String getName()

Returns the name of this file, i.e. the last name in the path name sequence.

Returns:

the relative path name

See Also:

File.getName()

getParent

public String getParent()

Returns the pathname string of this abstract pathname's parent, or null if this pathname does not have a parent directory. The parent of an abstract pathname consists of the pathname's prefix, if any, and each name in the pathname's name sequence except for the last. If the name sequence is empty then the pathname does not name a parent directory.

Returns:

see above

See Also:

File.getParent()

getParentFile

public Location getParentFile()

Returns the abstract pathname of this abstract pathname's parent, or null if this pathname does not name a parent directory. The parent of an abstract pathname consists of the pathname's prefix, if any, and each name in the pathname's name sequence except for the last. If the name sequence is empty then the pathname does not name a parent directory.

Returns:

The abstract pathname of the parent directory named by this abstract pathname, or null if this pathname does not name a parent

See Also:

File.getParentFile()

getPath

public String getPath()

Returns the file's path.

Returns:

this file's path name

See Also:

File.getPath()

isAbsolute

public boolean isAbsolute()

Returns whether or not this file's path is absolute.

Returns:

true if this path name is absolute. If the path name is a URL, this method will always return true.

See Also:

File.isAbsolute()

isDirectory

public boolean isDirectory()

Returns whether or not this file is a directory.

Returns:

true if this pathname exists and represents a directory.

See Also:

File.isDirectory()

isFile

public boolean isFile()

Returns whether or not this file is a regular file (i.e. not a directory).

Returns:

true if this pathname exists and represents a regular file.

See Also:

File.exists()

isHidden

public boolean isHidden()

Returns whether or not this file is marked hidden by the filesystem.

Returns:

true if the pathname is 'hidden'. This method will always return false if the pathname corresponds to a URL.

See Also:

File.isHidden()

lastModified

public long lastModified()

Return the last modification time of the file.

Returns:

the last modification time of this file, in milliseconds since the UNIX epoch. If the file does not exist, 0 is returned.

See Also:

File.lastModified(), URLConnection.getLastModified()

length

public long length()

Return the file length in bytes.

Returns:

the length of the file or stream in bytes

See Also:

File.length(), URLConnection.getContentLength()

list

public String[] list()

Return a list of relative file names in this directory, or null if this file is not a directory.

Returns:

a list of file names in this directory. Hidden files will be included in the list. If this is not a directory, return null.

See Also:

list(boolean)

listFiles

public Location[] listFiles()

Return a list of files in this directory, or null if this file is not a directory.

Returns:

a list of absolute files in this directory. Hidden files will be included in the list. If this is not a directory, return null.

See Also:

list()

toURL

public URL toURL()
          throws MalformedURLException

Return a URL corresponding to this file.

Returns:

the URL corresponding to this pathname.

Throws:

MalformedURLException - if the pathname is not a valid URL

See Also:

File.toURL()

toString

public String toString()

Overrides:

toString in class Object

See Also:

File.toString(), URL.toString()