util.gen
Class IO

java.lang.Object
  util.gen.IO

public class IO

extends java.lang.Object

Static methods for Input Output related tasks.

Constructor Summary

IO()

Method Summary

static java.util.LinkedHashMap	buildDirectoryFileGroups(java.lang.String map) Converts a String of "grp1=/my/Dir1,grp2=/my/Dir2, etc that contains directories into a LinkedHashMap.
static java.util.ArrayList	buildFileGroups(java.lang.String map, java.lang.String directoryFileExtensionFilter) Converts a String of "grp1=/my/file1,grp1=/my/old/file2,grp2=/my/file2, grp2=/my/new/file3,grp3=/my/new/dir/,/my/default etc" to a File[][] where the files have been broken by grouping into different File[].
static java.lang.String[]	bunZip2(java.io.File bunZip2App, java.io.File bz2FileToUncompress) Use to read in xxx.bz2 files directly to a String[].
static void	checkFile(java.lang.String par) Check to see that a file exists and is not a directory.
static java.io.File[]	collapseFileArray(java.io.File[][] f) Merges all files in File[][] to a File[].
static java.lang.String	concatinateFileFullPathNames(java.io.File[] f, java.lang.String seperator) Concatinates the full path file names for the given File array.
static boolean	copy(java.io.File source, java.io.File dest) Fast & simple file copy.
static boolean	copyDirectoryRecursive(java.io.File sourceDir, java.io.File destDir, java.lang.String extension) Copies a given directory and it's contents to the destination directory.
static long	countNonBlankLines(java.io.File file) Counts the number of lines in a file skipping blanks.
static long	countNumberOfLines(java.io.File file) Counts the number of lines in a file
static int	countNumberThatExist(java.io.File[] f) Counts the number of File in the array that actually exist.
static boolean	deleteDirectory(java.io.File directory) Deletes a directories contents, and then the directory.
static boolean	deleteFile(java.io.File file) Attempts to delete a file.
static boolean	deleteFile(java.lang.String fullPathFileName) Attempts to delete a file.
static boolean	deleteFiles(java.io.File[] files) Attempts to delete the array of File.
static boolean	deleteFiles(java.io.File directory, java.lang.String extension) Deletes files in a given directory with a given extension.
static void	deleteFiles(java.io.File directory, java.lang.String prefix, int minutes) Deletes files in a given directory with a given prefix, that are older cutoff.
static void	deleteFiles(java.lang.String directory, java.lang.String endsWith) Looks in the given directory for files ending with given String and deletes them.
static void	deleteFilesNotEndingInExtension(java.io.File directory, java.lang.String extension) Deletes files in a given directory that don't end in a given extension.
static java.lang.String[]	executeCommandLine(java.lang.String[] command) Executes tokenized params on command line, use full paths.
static java.lang.String[]	executeCommandLine(java.lang.String[] command, java.io.File txtOutPutFile) Executes tokenized params on command line, use full paths.
static java.lang.String[]	executeCommandLine(java.lang.String[] command, java.io.File txtOutPutFile, java.lang.String[] env) Executes tokenized params on command line, use full paths.
static java.lang.String[]	executeCommandLineReturnAll(java.lang.String[] command) Executes tokenized params on command line, use full paths.
static java.lang.String[]	executeShellScript(java.lang.String shellScript, java.io.File tempDirectory) Executes a String of shell script commands via a temp file.
static java.io.File[]	extractFiles(java.io.File directory) Extracts the full path file names of all the files and directories in a given directory.
static java.io.File[]	extractFiles(java.io.File dirOrFile, java.lang.String extension) Extracts the full path file names of all the files in a given directory with a given extension (ie txt or .txt).
static java.io.File[]	extractFiles(java.lang.String commaSeparList) Extracts all files from a comma delimited string of files and directories.
static java.io.File[]	extractFiles(java.lang.String[] dirFiles, java.lang.String extension) Given full path file or directory names, extracts all files given an extension.
static java.io.File[]	extractFiles(java.lang.String commaSeparList, java.lang.String extension) Extracts all files with a given extension from a comma delimited string of files and directories.
static java.io.File[]	extractFilesReturnFiles(java.io.File directory, java.lang.String extension) Extracts the full path file names of all the files in a given directory with a given extension.
static java.lang.String[]	extractFilesStringNames(java.io.File directory, java.lang.String extension) Extracts the full path file names of all the files in a given directory with a given extension.
static java.io.File[]	extractOnlyFiles(java.io.File directory) Extracts the full path file names of all the files not directories in a given directory.
static java.util.ArrayList	fetchAllFilesRecursively(java.io.File directory) Fetches all files in a directory recursing through sub directories.
static java.util.ArrayList	fetchAllFilesRecursively(java.io.File directory, java.lang.String extension) Fetches all files with a given extension in a directory recursing through sub directories.
static java.util.ArrayList	fetchArrayList(java.io.File file) Fetches an ArrayList stored as a serialize object file.
static java.io.File[]	fetchFiles(java.lang.String[] baseNames, java.lang.String chromExtension) For each base name (ie /home/data/treat1 ), makes a File object using the chromExtenstion (ie /home/data/treat1.chromExtension ), if it actually exists, it is saved and a File[] returned.
static java.io.File[]	fetchFilesRecursively(java.io.File directory) Fetches all files in a directory recursing through sub directories.
static java.io.File[]	fetchFilesRecursively(java.io.File directory, java.lang.String extension) Fetches all files with a given extension in a directory recursing through sub directories.
static float[][][]	fetchFloatFloatArrays(java.io.File[] files) Loads float[][]s from disk.
static java.util.HashMap	fetchNamesAndDirectories(java.io.File directory) Given a directory, returns a HashMap of the containing directories' names and a File obj for the directory.
static java.lang.Object	fetchObject(java.io.File file) Fetches an Object stored as a serialized file.
static java.io.BufferedReader	fetchReaderOnZippedFile(java.io.File zippedFile) Returns a BufferedReader from which you can call readLine() directly from a zipped file without decompressing.
static java.lang.String	fireQSub(java.lang.String qsubParams, java.lang.String commands, java.io.File tempDir) Fires qsub with the commands.
static java.lang.String[]	fireQSub(java.lang.String queue, java.lang.String commands, java.lang.String fullPathToTempDir, boolean waitAndClean) Fires qsub with the commands, will wait and return results and delete x.sh and the output files if you like.
static java.lang.String	getFullPathName(java.io.File fileDirectory) Gets full path name using getCanonicalPath() on a File
static java.lang.String[]	getTruncatedNames(java.io.File[] files) Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.
static java.lang.String[][]	getTruncatedNames(java.io.File[][] files) Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.
static java.lang.String[]	loadFile(java.io.File file) Loads a file's lines into a String[], will save blank lines.
static java.util.HashMap	loadFileIntoHashMap(java.io.File file) Loads a file's lines into a hash first column is the key, second the value.
static java.util.HashSet	loadFileIntoHashSet(java.io.File file) Loads a file's lines into a hash set, keys only.
static java.util.HashSet	loadFileIntoHashSplitLines(java.io.File file) Loads a file's lines into a hash.
static java.lang.String[]	loadFileIntoStringArray(java.io.File file) Loads a file's lines into a String[] trimming blank lines
static java.util.LinkedHashMap	loadHash(java.io.File tabDelimited) Loads a tab delimited file into a LinkedHashMap where each line is broken into cells and loaded into a LinkedHashMap where the cells are the keys and the value is the line.
static java.util.LinkedHashMap	loadKeyValueFile(java.io.File file) Loads a key = value containing text file into a LinkedHashMap.
static java.util.LinkedHashMap	loadKeyValueSpaceTabDelimited(java.io.File file) Loads a key value containing text file into a LinkedHashMap.
static java.lang.String	makeFullPathName(java.lang.String resultsDirectory, java.lang.String fileName) Attempts to make a file and return it's canonical path name (full path name).
static int	numberFilesExist(java.io.File[] f) Returns the number of files that exist in the array.
static int	numberFilesExist(java.io.File directory, java.lang.String extension) Returns the number of files that end with the given extension.
static void	removeExtension(java.io.File directory, java.lang.String extension) Removes the extension from each File in the directory.
static void	renameFiles(java.io.File directory, java.lang.String toReplace, java.lang.String replaceWith) Renames files containing the toReplace with replaceWith using String.replaceAll(String, String)
static boolean	saveObject(java.io.File file, java.lang.Object ob)
static java.lang.String	winFileConvert(java.lang.String fileName, javax.servlet.http.HttpServletRequest request) Checks to see if the browser sending the request is from a windows machine.
static boolean	writeString(java.lang.String data, java.io.File file) Writes a String to disk.
static boolean	writeString(java.lang.String data, java.lang.String fullPathFileName) Writes a String to disk.
static boolean	writeStringAppend(java.lang.String data, java.io.File file) Writes a String onto the end of a file.
static boolean	zip(java.io.File[] filesToZip, java.io.File zipFile) Zip compresses an array of Files, be sure to name your zipFile with a .zip extension!
static boolean	zip(java.io.File fileToZip, java.io.File zipFile) Zip compress a single file.
static boolean	zipAndDelete(java.io.File f) Zip compresses the file and if sucessful, then deletes the original file.
static java.lang.String[]	zippedFile2StringArray(java.io.File zippedFile) Returns the contents of a zipped file.

Methods inherited from class java.lang.Object

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

Constructor Detail

IO

public IO()

Method Detail

loadHash

public static java.util.LinkedHashMap loadHash(java.io.File tabDelimited)

Loads a tab delimited file into a LinkedHashMap where each line is broken into cells and loaded into a LinkedHashMap where the cells are the keys and the value is the line.

numberFilesExist

public static int numberFilesExist(java.io.File directory,
                                   java.lang.String extension)

Returns the number of files that end with the given extension.

zipAndDelete

public static boolean zipAndDelete(java.io.File f)

Zip compresses the file and if sucessful, then deletes the original file.

zippedFile2StringArray

public static java.lang.String[] zippedFile2StringArray(java.io.File zippedFile)

Returns the contents of a zipped file. Returns null if there is a problem.

fetchReaderOnZippedFile

public static java.io.BufferedReader fetchReaderOnZippedFile(java.io.File zippedFile)

Returns a BufferedReader from which you can call readLine() directly from a zipped file without decompressing. Returns null if there is a problem.

concatinateFileFullPathNames

public static java.lang.String concatinateFileFullPathNames(java.io.File[] f,
                                                            java.lang.String seperator)

Concatinates the full path file names for the given File array.

winFileConvert

public static java.lang.String winFileConvert(java.lang.String fileName,
                                              javax.servlet.http.HttpServletRequest request)

Checks to see if the browser sending the request is from a windows machine. If so it converts the file name dividers to unix. In either case, replaces any spaces with underscores.

fetchFloatFloatArrays

public static float[][][] fetchFloatFloatArrays(java.io.File[] files)

Loads float[][]s from disk.

fetchFiles

public static java.io.File[] fetchFiles(java.lang.String[] baseNames,
                                        java.lang.String chromExtension)

For each base name (ie /home/data/treat1 ), makes a File object using the chromExtenstion (ie /home/data/treat1.chromExtension ), if it actually exists, it is saved and a File[] returned.

numberFilesExist

public static int numberFilesExist(java.io.File[] f)

Returns the number of files that exist in the array.

buildFileGroups

public static java.util.ArrayList buildFileGroups(java.lang.String map,
                                                  java.lang.String directoryFileExtensionFilter)

Converts a String of "grp1=/my/file1,grp1=/my/old/file2,grp2=/my/file2, grp2=/my/new/file3,grp3=/my/new/dir/,/my/default etc" to a File[][] where the files have been broken by grouping into different File[]. If no key is provided, the files are assigned to a common 'default' grouping. If a directory is provided all files within are grouped together. Mixing of keyed and unkeyed is permitted. Returns null if an error was thrown.

Parameters:

directoryFileExtensionFilter - - if directories are given in the map, you can filter which files to extract (ie 'cel'), case insensitive, set to "." for everything.

Returns:

- ArrayList containing String[] groupNames and a File[][] of grouped files, and a LinkedHashMap of the two.

fetchNamesAndDirectories

public static java.util.HashMap fetchNamesAndDirectories(java.io.File directory)

Given a directory, returns a HashMap of the containing directories' names and a File obj for the directory.

buildDirectoryFileGroups

public static java.util.LinkedHashMap buildDirectoryFileGroups(java.lang.String map)

Converts a String of "grp1=/my/Dir1,grp2=/my/Dir2, etc that contains directories into a LinkedHashMap. Returns null and prints an error message if an error was thrown, ie no directory, not a directory

renameFiles

public static void renameFiles(java.io.File directory,
                               java.lang.String toReplace,
                               java.lang.String replaceWith)

Renames files containing the toReplace with replaceWith using String.replaceAll(String, String)

zip

public static boolean zip(java.io.File fileToZip,
                          java.io.File zipFile)

Zip compress a single file.

zip

public static boolean zip(java.io.File[] filesToZip,
                          java.io.File zipFile)

Zip compresses an array of Files, be sure to name your zipFile with a .zip extension!

fetchFilesRecursively

public static java.io.File[] fetchFilesRecursively(java.io.File directory)

Fetches all files in a directory recursing through sub directories.

fetchAllFilesRecursively

public static java.util.ArrayList fetchAllFilesRecursively(java.io.File directory)

Fetches all files in a directory recursing through sub directories.

fetchFilesRecursively

public static java.io.File[] fetchFilesRecursively(java.io.File directory,
                                                   java.lang.String extension)

Fetches all files with a given extension in a directory recursing through sub directories. Will return a file if a file is given with the appropriate extension, or null.

fetchAllFilesRecursively

public static java.util.ArrayList fetchAllFilesRecursively(java.io.File directory,
                                                           java.lang.String extension)

Fetches all files with a given extension in a directory recursing through sub directories.

collapseFileArray

public static java.io.File[] collapseFileArray(java.io.File[][] f)

Merges all files in File[][] to a File[].

loadFileIntoHashSet

public static java.util.HashSet loadFileIntoHashSet(java.io.File file)

Loads a file's lines into a hash set, keys only.

loadFileIntoHashMap

public static java.util.HashMap loadFileIntoHashMap(java.io.File file)

Loads a file's lines into a hash first column is the key, second the value.

loadKeyValueFile

public static java.util.LinkedHashMap loadKeyValueFile(java.io.File file)

Loads a key = value containing text file into a LinkedHashMap. Strips all white space, ignores lines beginning with / or #. Ignores blank lines.

loadKeyValueSpaceTabDelimited

public static java.util.LinkedHashMap loadKeyValueSpaceTabDelimited(java.io.File file)

Loads a key value containing text file into a LinkedHashMap. Ignores lines beginning with / or #. Ignores blank lines. Splits on spaces/ tabs thus no spaces within key or value. Returns null if split keyValue number is != 2.

loadFileIntoHashSplitLines

public static java.util.HashSet loadFileIntoHashSplitLines(java.io.File file)

Loads a file's lines into a hash.

loadFileIntoStringArray

public static java.lang.String[] loadFileIntoStringArray(java.io.File file)

Loads a file's lines into a String[] trimming blank lines

loadFile

public static java.lang.String[] loadFile(java.io.File file)

Loads a file's lines into a String[], will save blank lines.

bunZip2

public static java.lang.String[] bunZip2(java.io.File bunZip2App,
                                         java.io.File bz2FileToUncompress)

Use to read in xxx.bz2 files directly to a String[]. Returns null if a problem encountered. Must have bunzip2 installed.

executeCommandLine

public static java.lang.String[] executeCommandLine(java.lang.String[] command)

Executes tokenized params on command line, use full paths. Put each param in its own String. Returns null if a problem is encountered.

executeCommandLineReturnAll

public static java.lang.String[] executeCommandLineReturnAll(java.lang.String[] command)

Executes tokenized params on command line, use full paths. Put each param in its own String. Returns null if a problem is encountered. Returns both error and data from execution.

executeShellScript

public static java.lang.String[] executeShellScript(java.lang.String shellScript,
                                                    java.io.File tempDirectory)

Executes a String of shell script commands via a temp file. Only good for Unix.

executeCommandLine

public static java.lang.String[] executeCommandLine(java.lang.String[] command,
                                                    java.io.File txtOutPutFile)

Executes tokenized params on command line, use full paths. Put each param in its own String. Writes lines to a file.

executeCommandLine

public static java.lang.String[] executeCommandLine(java.lang.String[] command,
                                                    java.io.File txtOutPutFile,
                                                    java.lang.String[] env)

Executes tokenized params on command line, use full paths. Put each param in its own String. Writes lines to a file.

copy

public static boolean copy(java.io.File source,
                           java.io.File dest)

Fast & simple file copy. From GForman http://www.experts-exchange.com/M_500026.html

copyDirectoryRecursive

public static boolean copyDirectoryRecursive(java.io.File sourceDir,
                                             java.io.File destDir,
                                             java.lang.String extension)

Copies a given directory and it's contents to the destination directory. Use a extension (e.g. "class$|properties$") to limit the files copied over or set to null for all.

deleteDirectory

public static boolean deleteDirectory(java.io.File directory)

Deletes a directories contents, and then the directory. Returns false if at any time a file cannot be deleted.

getFullPathName

public static java.lang.String getFullPathName(java.io.File fileDirectory)

Gets full path name using getCanonicalPath() on a File

countNumberOfLines

public static long countNumberOfLines(java.io.File file)

Counts the number of lines in a file

countNonBlankLines

public static long countNonBlankLines(java.io.File file)

Counts the number of lines in a file skipping blanks.

extractFiles

public static java.io.File[] extractFiles(java.lang.String commaSeparList,
                                          java.lang.String extension)

Extracts all files with a given extension from a comma delimited string of files and directories. No spaces.

extractFiles

public static java.io.File[] extractFiles(java.lang.String commaSeparList)

Extracts all files from a comma delimited string of files and directories. No spaces. Returns null if file.canRead() is false. Not recursive.

countNumberThatExist

public static int countNumberThatExist(java.io.File[] f)

Counts the number of File in the array that actually exist.

extractFiles

public static java.io.File[] extractFiles(java.io.File directory)

Extracts the full path file names of all the files and directories in a given directory. If a file is given it is returned as the File[0]. Skips files starting with a '.'

extractOnlyFiles

public static java.io.File[] extractOnlyFiles(java.io.File directory)

Extracts the full path file names of all the files not directories in a given directory. Skips files starting with a non word character (e.g. '.', '_', etc). Returns null if no files found.

extractFilesStringNames

public static java.lang.String[] extractFilesStringNames(java.io.File directory,
                                                         java.lang.String extension)

Extracts the full path file names of all the files in a given directory with a given extension.

extractFiles

public static java.io.File[] extractFiles(java.io.File dirOrFile,
                                          java.lang.String extension)

Extracts the full path file names of all the files in a given directory with a given extension (ie txt or .txt). If the dirFile is a file and ends with the extension then it returns a File[] with File[0] the given directory. Returns null if nothing found. Case insensitive.

extractFilesReturnFiles

public static java.io.File[] extractFilesReturnFiles(java.io.File directory,
                                                     java.lang.String extension)

Extracts the full path file names of all the files in a given directory with a given extension.

extractFiles

public static java.io.File[] extractFiles(java.lang.String[] dirFiles,
                                          java.lang.String extension)

Given full path file or directory names, extracts all files given an extension.

deleteFiles

public static boolean deleteFiles(java.io.File[] files)

Attempts to delete the array of File.

deleteFiles

public static boolean deleteFiles(java.io.File directory,
                                  java.lang.String extension)

Deletes files in a given directory with a given extension.

deleteFilesNotEndingInExtension

public static void deleteFilesNotEndingInExtension(java.io.File directory,
                                                   java.lang.String extension)

Deletes files in a given directory that don't end in a given extension.

removeExtension

public static void removeExtension(java.io.File directory,
                                   java.lang.String extension)

Removes the extension from each File in the directory.

deleteFiles

public static void deleteFiles(java.io.File directory,
                               java.lang.String prefix,
                               int minutes)

Deletes files in a given directory with a given prefix, that are older cutoff.

checkFile

public static void checkFile(java.lang.String par)

Check to see that a file exists and is not a directory.

deleteFiles

public static void deleteFiles(java.lang.String directory,
                               java.lang.String endsWith)

Looks in the given directory for files ending with given String and deletes them.

fireQSub

public static java.lang.String[] fireQSub(java.lang.String queue,
                                          java.lang.String commands,
                                          java.lang.String fullPathToTempDir,
                                          boolean waitAndClean)

Fires qsub with the commands, will wait and return results and delete x.sh and the output files if you like. Be sure to put an end of line '\n' after each command.

fireQSub

public static java.lang.String fireQSub(java.lang.String qsubParams,
                                        java.lang.String commands,
                                        java.io.File tempDir)

Fires qsub with the commands.

Parameters:

qsubParams - = '-q queue@loc -l nodes=1'

Returns:

String beginning with 'Error: ' if the error stream or java bombed. otherwise it returns a tab delimited list of the output and the qsub parameters. Will leave the shell file in the temp directory, renamed as the jobNumber.sh

makeFullPathName

public static java.lang.String makeFullPathName(java.lang.String resultsDirectory,
                                                java.lang.String fileName)

Attempts to make a file and return it's canonical path name (full path name).

writeString

public static boolean writeString(java.lang.String data,
                                  java.io.File file)

Writes a String to disk.

writeStringAppend

public static boolean writeStringAppend(java.lang.String data,
                                        java.io.File file)

Writes a String onto the end of a file. No need to add a \n onto the final end.

writeString

public static boolean writeString(java.lang.String data,
                                  java.lang.String fullPathFileName)

Writes a String to disk.

fetchArrayList

public static java.util.ArrayList fetchArrayList(java.io.File file)

Fetches an ArrayList stored as a serialize object file.

fetchObject

public static java.lang.Object fetchObject(java.io.File file)

Fetches an Object stored as a serialized file.

saveObject

public static boolean saveObject(java.io.File file,
                                 java.lang.Object ob)

deleteFile

public static boolean deleteFile(java.io.File file)

Attempts to delete a file.

deleteFile

public static boolean deleteFile(java.lang.String fullPathFileName)

Attempts to delete a file.

getTruncatedNames

public static java.lang.String[] getTruncatedNames(java.io.File[] files)

Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.

getTruncatedNames

public static java.lang.String[][] getTruncatedNames(java.io.File[][] files)

Fetches and truncates common chars, from file names, front and back, uses getName() so no path info is involved.