gov.nih.nlm.util
Class SystemToolkit

java.lang.Object
  gov.nih.nlm.util.SystemToolkit

public class SystemToolkit
extends Object

Utility toolkit.

Author:

MEME Group

Constructor Summary

SystemToolkit()

Method Summary

static void	copy(File in, File out) Copies the input file to the output file.
static void	copy(File in, File out, ProgressMonitor pm) Copies the input file to the output file.
static String[]	getIndexWords(String[] words) Lowercases words and returns the list sorted and uniqed.
static String[]	getZipEntries(String zip_file_name) Returns a list of zip entry file names.
static InputStream	getZipInputStream(String zf, String ze) Returns an InputStream for the ZipEntry in the specified ZipFile.
static boolean	isStopWord(String word) Checks whether the word is one of the stop words.
static void	main(String[] s) main method
static String	md5(File file) Returns the MD5 value for the given File.
static String	md5(File file, ProgressMonitor pm) Returns the MD5 value for the given File.
static String	md5(String text) Compute the MD5 hash of a string.
static String	md5(String text, String char_encoding) Compute the MD5 hash of a string using the specified character encoding.
static String	md5CrossPlatform(File file) Returns the MD5 value for the given File.
static String	md5CrossPlatform(File file, ProgressMonitor pm) Returns the MD5 value for the given File.
static String[][]	readFieldedFile(File file, String delim) Reads the fielded file into a two-dimensional string array.
static String[][]	readFieldedReader(BufferedReader in, String delim) Reads the fielded file into a two-dimensional string array.
static String	readLine(RandomAccessFile raf, String char_set) Reads and returns a line from the RandomAccessFile using the specified character set.
static String	removeLinks(String html) Removes any links within a specified HTML document.
static String	removeTags(String html) Returns an HTML document stripped of its tags.
static long	seekstr(RandomAccessFile raf, String search_string, String char_set) Seek to the location in the RandomAccessFile where the first line of text starts with the search string.
static void	sort(String filename) Sort the specified file.
static void	sort(String filename, boolean unique) Sort the specified file (optionally uniquely).
static void	sort(String filename, boolean unique, ProgressMonitor pm) Sort the specified file (optionally uniquely).
static void	sort(String filename, Comparator comp) Sort the specified file using the specified Comparator.
static void	sort(String filename, Comparator comp, boolean unique) Sort the specified file using the specified Comparator and optionally sort uniquely.
static void	sort(String filename, Comparator comp, boolean unique, ProgressMonitor pm) Sort the specified file using the specified Comparator and optionally sort uniquely.
static void	sort(String filename, ProgressMonitor pm) Sort the specified file.
static String	toHexString(byte[] v) Converts a byte[] to a hex string.
static void	unzip(String zip_file, String output_dir, String archive_subdir, ProgressMonitor pm) Unzips the specified file into the specified directory using.
static void	unzip(String unzip_cmd, String zip_file, String output_dir, String archive_subdir, ProgressMonitor pm) Unzips the specified file into the specified directory using the specified operating system command.
static void	unzipInternal(String zip_file, String output_dir, String archive_subdir) Unzips the specified file into the specified directory using pure java.
static void	unzipInternal(String zip_file, String output_dir, String archive_subdir, ProgressMonitor pm) Unzips the specified file into the specified directory using pure java.

Methods inherited from class java.lang.Object

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

Constructor Detail

SystemToolkit

public SystemToolkit()

Method Detail

isStopWord

public static boolean isStopWord(String word)

Checks whether the word is one of the stop words. Assumes the word is lowercased

Parameters:

word - lowercase string

Returns:

true if the word is a stop word, false otherwise

getIndexWords

public static String[] getIndexWords(String[] words)

Lowercases words and returns the list sorted and uniqed. Also removes stop words.

Parameters:

words - words from a string

Returns:

sorted uniqued, lowercased word list

copy

public static void copy(File in,
                        File out)
                 throws IOException

Copies the input file to the output file.

Parameters:

in - the input File

out - the output File

Throws:

IOException

copy

public static void copy(File in,
                        File out,
                        ProgressMonitor pm)
                 throws IOException

Copies the input file to the output file. Supports ability to monitor progress

Parameters:

in - the input File

out - the output File

pm - the ProgressMonitor

Throws:

IOException

md5

public static String md5(String text)
                  throws NoSuchAlgorithmException,
                         UnsupportedEncodingException

Compute the MD5 hash of a string.

Parameters:

text - the value to compute a hash for

Returns:

the MD5 hash value of the string

Throws:

NoSuchAlgorithmException - if failed due to no such algorithm

UnsupportedEncodingException - if failed due to unsupported encoding

md5

public static String md5(String text,
                         String char_encoding)
                  throws NoSuchAlgorithmException,
                         UnsupportedEncodingException

Compute the MD5 hash of a string using the specified character encoding.

Parameters:

text - the value to compute a hash for

char_encoding - a character encoding (e.g. "UTF-8")

Returns:

the MD5 hash value of the string

Throws:

NoSuchAlgorithmException - if failed due to no such algorithm

UnsupportedEncodingException - if failed due to unsupported encoding

md5

public static String md5(File file)
                  throws IOException,
                         NoSuchAlgorithmException

Returns the MD5 value for the given File.

Parameters:

file - for which to determine the MD5

Returns:

MD5 string

Throws:

IOException

NoSuchAlgorithmException

md5

public static String md5(File file,
                         ProgressMonitor pm)
                  throws IOException,
                         NoSuchAlgorithmException

Returns the MD5 value for the given File.

Parameters:

file - for which to determine the MD5

pm - an optional progress monitor to track whether operation should be cancelled

Returns:

MD5 string

Throws:

IOException

NoSuchAlgorithmException

md5CrossPlatform

public static String md5CrossPlatform(File file)
                               throws IOException,
                                      NoSuchAlgorithmException

Returns the MD5 value for the given File.

Parameters:

file - for which to determine the MD5

Returns:

MD5 string

Throws:

IOException

NoSuchAlgorithmException

md5CrossPlatform

public static String md5CrossPlatform(File file,
                                      ProgressMonitor pm)
                               throws IOException,
                                      NoSuchAlgorithmException

Returns the MD5 value for the given File.

Parameters:

file - for which to determine the MD5

pm - an optional progress monitor to track whether operation should be cancelled

Returns:

MD5 string

Throws:

IOException

NoSuchAlgorithmException

toHexString

public static String toHexString(byte[] v)

Converts a byte[] to a hex string.

Parameters:

v - the byte[]

Returns:

the hex string

removeTags

public static String removeTags(String html)

Returns an HTML document stripped of its tags.

Parameters:

html - an html document

Returns:

plain text document

removeLinks

public static String removeLinks(String html)

Removes any links within a specified HTML document.

Parameters:

html - an html document

Returns:

document without any links

unzip

public static void unzip(String zip_file,
                         String output_dir,
                         String archive_subdir,
                         ProgressMonitor pm)
                  throws IOException

Unzips the specified file into the specified directory using. Makes use of the system unzip.native property to determine whether to use the unzip program stored in unzip.path system property or to use a pure java solution.

Parameters:

zip_file - the zip file name

output_dir - the directory to unzip to

archive_subdir - the portion of the archive to extract

pm - the progrss monitor

Throws:

IOException

unzip

public static void unzip(String unzip_cmd,
                         String zip_file,
                         String output_dir,
                         String archive_subdir,
                         ProgressMonitor pm)
                  throws IOException

Unzips the specified file into the specified directory using the specified operating system command. This method makes use of a progress monitor (if usingView() returns true).

Parameters:

unzip_cmd - the OS command to use to unzip

zip_file - the zip file name

output_dir - the directory to unzip to

archive_subdir - the portion of the archive to extract

pm - the progrss monitor

Throws:

IOException

unzipInternal

public static void unzipInternal(String zip_file,
                                 String output_dir,
                                 String archive_subdir)
                          throws IOException

Unzips the specified file into the specified directory using pure java.

Parameters:

zip_file - the ZipFile name to unzip

output_dir - the output directory

archive_subdir - indicates what to unzip, (use * for everything)

Throws:

IOException - if anything goes wrong manipulating the files.

unzipInternal

public static void unzipInternal(String zip_file,
                                 String output_dir,
                                 String archive_subdir,
                                 ProgressMonitor pm)
                          throws IOException

Unzips the specified file into the specified directory using pure java.

Parameters:

zip_file - the ZipFile name to unzip

output_dir - the output directory

archive_subdir - indicates what to unzip, (use * for everything)

pm - the ProgressMonitor used to track progress.

Throws:

IOException - if anything goes wrong manipulating the files.

seekstr

public static long seekstr(RandomAccessFile raf,
                           String search_string,
                           String char_set)
                    throws IOException

Seek to the location in the RandomAccessFile where the first line of text starts with the search string. This implements a binary search function in a file (like the UNIX look command).

Parameters:

raf - the RandomAccessFile to search

search_string - the search string

char_set - the character set to use for the search_string

Returns:

the index into the file where to start looking

Throws:

IOException - if anything goes wrong

readLine

public static String readLine(RandomAccessFile raf,
                              String char_set)
                       throws IOException

Reads and returns a line from the RandomAccessFile using the specified character set.

Parameters:

raf - the RandomAccessFile

char_set - the character set

Returns:

a line from the RandomAccessFile in the specified character set

Throws:

IOException

getZipInputStream

public static InputStream getZipInputStream(String zf,
                                            String ze)
                                     throws IOException

Returns an InputStream for the ZipEntry in the specified ZipFile. Uses the native unzip program found in the system "unzip.path" property.

Parameters:

zf - the ZipFile

ze - the ZipEntry

Returns:

the InputStream

Throws:

IOException - if anything goes wrong

getZipEntries

public static String[] getZipEntries(String zip_file_name)
                              throws IOException

Returns a list of zip entry file names. Uses the native unzip program found in the system "unzip.path" property.

Parameters:

zip_file_name - the zip file name

Returns:

a list of zip entry file names

Throws:

IOException

main

public static void main(String[] s)

main method

Parameters:

s -

sort

public static void sort(String filename)
                 throws IOException

Sort the specified file.

Parameters:

filename - the file to sort

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        ProgressMonitor pm)
                 throws IOException

Sort the specified file.

Parameters:

filename - the file to sort

pm - ProgressMonitor

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        boolean unique)
                 throws IOException

Sort the specified file (optionally uniquely).

Parameters:

filename - the file to sort

unique - a boolean which detemine duplicate lines

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        boolean unique,
                        ProgressMonitor pm)
                 throws IOException

Sort the specified file (optionally uniquely).

Parameters:

filename - the file to sort

unique - a boolean which detemine duplicate lines

pm - ProgressMonitor

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        Comparator comp)
                 throws IOException

Sort the specified file using the specified Comparator.

Parameters:

filename - the file to sort

comp - the Comparator

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        Comparator comp,
                        boolean unique)
                 throws IOException

Sort the specified file using the specified Comparator and optionally sort uniquely.

Parameters:

filename - the file to sort

comp - the Comparator

unique - a boolean which detemine duplicate lines

Throws:

IOException - if failed to sort

sort

public static void sort(String filename,
                        Comparator comp,
                        boolean unique,
                        ProgressMonitor pm)
                 throws IOException

Sort the specified file using the specified Comparator and optionally sort uniquely.

Parameters:

filename - the file to sort

comp - the Comparator

unique - a boolean which detemine duplicate lines

pm - a ProgressMonitor

Throws:

IOException - if failed to sort

readFieldedFile

public static String[][] readFieldedFile(File file,
                                         String delim)
                                  throws IOException

Reads the fielded file into a two-dimensional string array.

Parameters:

file - the file to read

delim - the field separator in the file

Returns:

a String[][] of the lines/fields

Throws:

IOException - if anything goes wrong

readFieldedReader

public static String[][] readFieldedReader(BufferedReader in,
                                           String delim)
                                    throws IOException

Reads the fielded file into a two-dimensional string array.

Parameters:

in - the BufferedReader input

delim - the field separator in the file

Returns:

a String[][] of the lines/fields

Throws:

IOException - if anything goes wrong