Package uk.ac.ebi.utils.opt.io

Class IOUtils

java.lang.Object

uk.ac.ebi.utils.opt.io.IOUtils

public class IOUtils
extends Object

Miscellanea of small IO utilities. TODO: complete the migration to unchecked exceptions. TODO: does it need to be an *.opt.* package?

date

July 29, 2007, 1:03 PM

Author:

brandizi

Method Summary

Modifier and Type	Method	Description
static String	getHash(File f, String algorithm)	A wrapper to getHash(InputStream, String) that opens a file.
static String	getHash(InputStream is, String algorithm)	Reads the input stream and returns an hash for it, based on the algorithm passed as parameter. algorithm is passed to MessageDigest
static String	getHash(String string, String algorithm)	Hashes a string, using getHash(InputStream, String).
static String	getMD5(File f)	A wrapper of #getHash(InputStream, File) that uses the MD5 algorithm.
static String	getMD5(InputStream is)	A wrapper of getHash(InputStream, String) that uses the MD5 algorithm.
static String	getMD5(String string)	A wrapper for getHash(String, String) that uses MD5.
static Reader	openResourceReader(Class<?> clazz, String path)	Defaults to "UTF-8"
static Reader	openResourceReader(Class<?> clazz, String path, Charset charset)	Facility to get a reader from a resource, uses Resources.getResource(Class, String) and URL.openStream().
static Reader	openResourceReader(String path)	Defaults to UTF-8
static Reader	openResourceReader(String path, Charset charset)
static Stream<String>	processIOItems(Stream<String> ioItemsStrm)	Defaults to ioItemsStrm = true
static Stream<String>	processIOItems(Stream<String> ioItemsStrm, boolean doTrim)	Returns a new stream assuming that the input comes from some I/O describing one item per line.
static String	readFile(String path)	Defaults to UTF-8
static String	readFile(String path, String charSet)
static String	readFile(String path, Charset charSet)	Opens an input stream from a file path.
static String[]	readFiles(String dirPath)	Defaults to any file, ignoreMissingDir = false, UTF-8
static String[]	readFiles(String dirPath, boolean ignoreMissingDir)	Defaults to any file, UTF-8
static String[]	readFiles(String dirPath, boolean ignoreMissingDir, Charset charSet)	Defaults to any file
static String[]	readFiles(String dirPath, FilenameFilter filter)	Defaults to missingDir = false, `UTF-8`.
static String[]	readFiles(String dirPath, FilenameFilter filter, boolean ignoreMissingDir)	Defaults to `UTF-8`.
static String[]	readFiles(String dirPath, FilenameFilter filter, boolean ignoreMissingDir, Charset charSet)	Invokes readFile(String, Charset) upon all the files in a directory and return an array of file contents.
static String[]	readFiles(String dirPath, FilenameFilter filter, Charset charSet)	Defaults to missingDir = false
static String[]	readFiles(String dirPath, Charset charSet)	Defaults to any file, ignoreMissingDir = false
static String	readResource(Class<?> clazz, String path)	WARNING: after 5.0 this uses UTF-8 as default and not the system default!
static String	readResource(Class<?> clazz, String path, Charset charset)	Facility to read a resource from the class loader associated to a class.
static String	readResource(ClassLoader classLoader, String path)	Defaults to UTF-8
static String	readResource(ClassLoader classLoader, String path, Charset charset)	Facility to read a resource from a class loader.
static String	readResource(String path)	Defaults to UTF-8
static String	readResource(String path, Charset charset)	Uses the class loader in the current thread, or the one in Resources.
static URI	uri(String uriStr)	Creates a URI and intercepts URISyntaxException, throwing IllegalArgumentException if such an exception occurs.
static URL	url(String urlStr)
static void	writeFile(String path, String string)	Defaults to UTF8, append = false
static void	writeFile(String path, String string, boolean append)	Defaults to UTF8
static void	writeFile(String path, String string, Charset charSet, boolean append)	Writes the string to the file and then closes it

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

readFile

public static String readFile(String path,
 String charSet)
                       throws UncheckedIOException

Throws:

UncheckedIOException

See Also:

• readFile(String, Charset)

readFile

public static String readFile(String path,
 Charset charSet)
                       throws UncheckedIOException

Opens an input stream from a file path.

Throws:

UncheckedIOException

readFile

public static String readFile(String path)
                       throws UncheckedIOException

Defaults to UTF-8

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 FilenameFilter filter,
 boolean ignoreMissingDir,
 Charset charSet)
                          throws UncheckedFileNotFoundException,
UncheckedIOException

Invokes readFile(String, Charset) upon all the files in a directory and return an array of file contents.

Throws:

UncheckedFileNotFoundException

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 FilenameFilter filter,
 Charset charSet)
                          throws UncheckedIOException

Defaults to missingDir = false

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 FilenameFilter filter,
 boolean ignoreMissingDir)
                          throws UncheckedIOException

Defaults to `UTF-8`.

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 FilenameFilter filter)
                          throws UncheckedIOException

Defaults to missingDir = false, `UTF-8`.

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 boolean ignoreMissingDir,
 Charset charSet)
                          throws UncheckedIOException

Defaults to any file

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 boolean ignoreMissingDir)
                          throws UncheckedIOException

Defaults to any file, UTF-8

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath,
 Charset charSet)
                          throws UncheckedIOException

Defaults to any file, ignoreMissingDir = false

Throws:

UncheckedIOException

readFiles

public static String[] readFiles(String dirPath)
                          throws UncheckedIOException

Defaults to any file, ignoreMissingDir = false, UTF-8

Throws:

UncheckedIOException

processIOItems

public static Stream<String> processIOItems(Stream<String> ioItemsStrm,
 boolean doTrim)

Returns a new stream assuming that the input comes from some I/O describing one item per line. Currently,

• if doTrim, trims to null and then passes the result downstream
• it removes blank lines (empty and space-like only lines)
• it removes lines starting with '#', ie, comments (spaces before are allowed)

TODO: write unit tests (it's being used in KnetMiner)

processIOItems

public static Stream<String> processIOItems(Stream<String> ioItemsStrm)

Defaults to ioItemsStrm = true

openResourceReader

public static Reader openResourceReader(Class<?> clazz,
 String path,
 Charset charset)
                                 throws IOException

Facility to get a reader from a resource, uses Resources.getResource(Class, String) and URL.openStream().

Throws:

IOException

openResourceReader

public static Reader openResourceReader(Class<?> clazz,
 String path)
                                 throws IOException

Defaults to "UTF-8"

Throws:

IOException

openResourceReader

public static Reader openResourceReader(String path,
 Charset charset)
                                 throws IOException

Throws:

IOException

openResourceReader

public static Reader openResourceReader(String path)
                                 throws IOException

Defaults to UTF-8

Throws:

IOException

readResource

public static String readResource(Class<?> clazz,
 String path,
 Charset charset)
                           throws IOException

Facility to read a resource from the class loader associated to a class.

Throws:

IOException

readResource

public static String readResource(Class<?> clazz,
 String path)
                           throws IOException

WARNING: after 5.0 this uses UTF-8 as default and not the system default!

Throws:

IOException

readResource

public static String readResource(String path,
 Charset charset)
                           throws IOException

Uses the class loader in the current thread, or the one in Resources.

Throws:

IOException

readResource

public static String readResource(String path)
                           throws IOException

Defaults to UTF-8

Throws:

IOException

readResource

public static String readResource(ClassLoader classLoader,
 String path,
 Charset charset)
                           throws IOException

Facility to read a resource from a class loader.

Throws:

IOException

See Also:

• ClassLoader.getResource(String)

readResource

public static String readResource(ClassLoader classLoader,
 String path)
                           throws IOException

Defaults to UTF-8

Throws:

IOException

writeFile

public static void writeFile(String path,
 String string,
 Charset charSet,
 boolean append)
                      throws IOException

Writes the string to the file and then closes it

Throws:

IOException

writeFile

public static void writeFile(String path,
 String string,
 boolean append)
                      throws IOException

Defaults to UTF8

Throws:

IOException

writeFile

public static void writeFile(String path,
 String string)
                      throws IOException

Defaults to UTF8, append = false

Throws:

IOException

getHash

public static String getHash(InputStream is,
 String algorithm)
                      throws IOException,
NoSuchAlgorithmException

Reads the input stream and returns an hash for it, based on the algorithm passed as parameter. algorithm is passed to MessageDigest

Throws:

IOException

NoSuchAlgorithmException

getHash

public static String getHash(File f,
 String algorithm)
                      throws IOException,
NoSuchAlgorithmException

A wrapper to getHash(InputStream, String) that opens a file.

Throws:

IOException

NoSuchAlgorithmException

getHash

public static String getHash(String string,
 String algorithm)
                      throws NoSuchAlgorithmException

Hashes a string, using getHash(InputStream, String).

Throws:

NoSuchAlgorithmException

getMD5

public static String getMD5(InputStream is)
                     throws IOException

A wrapper of getHash(InputStream, String) that uses the MD5 algorithm.

Throws:

IOException

getMD5

public static String getMD5(File f)
                     throws IOException

A wrapper of #getHash(InputStream, File) that uses the MD5 algorithm.

Throws:

IOException

getMD5

public static String getMD5(String string)

A wrapper for getHash(String, String) that uses MD5.

uri

public static URI uri(String uriStr)

Creates a URI and intercepts URISyntaxException, throwing IllegalArgumentException if such an exception occurs. I've created this method because it's often very annoying to have a checked exception here.

url

public static URL url(String urlStr)

See Also:

• uri(String)