com.compomics.util

Class Util

java.lang.Object

com.compomics.util.Util

public class Util
extends Object

Includes general help methods that are used by the other classes.

Author:

Harald Barsnes, Marc Vaudel

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	forbiddenCharacters Forbidden characters in file names.
static String	separator Separator which can be used to separate things.

Constructor Summary

Constructors

Constructor and Description
Util()

Method Summary

Modifier and Type	Method and Description
static void	append(File in, File out) Appends the content of a file to another.
static String	appendSuffix(String fileName, String suffix) Appends a suffix to a file name before the file extension.
static boolean	checkIfURLExists(String targetUrlAsString, String userName, String password) Check if a given URL exists.
static String	color2Hex(Color color) Converts a color to hex format for use in HTML tags.
static boolean	containsForbiddenCharacter(String string) Indicates whether a string contains characters forbidden in file names.
static Integer	convertBooleanToInteger(Boolean booleanToConvert) Converts a boolean value to the corresponding integer value, 0 for false and 1 for true.
static void	copyFile(File in, File out) Copy the content of a file to another.
static void	copyFile(File in, File out, boolean overwrite) Copy the content of one file to another.
static boolean	deleteDir(File dir) Deletes all files and subdirectories under dir and dir itself.
static boolean	emptyDir(File dir) Deletes all files and subdirectories under dir.
static double	floorDouble(double d, int places) Floors a double value to the wanted number of decimal places.
static String	getExtension(File file) Returns the extensions of a file.
static String	getFileName(File file) An OS independent getName alternative.
static String	getFileName(String filePath) An OS independent getName alternative.
static int	getFileSize(URL url) Returns the size of the file located at the given URL.
static ArrayList<Integer>	getIndexes(String bigString, String smallString) Returns at which indexes a small string can be found in a big string.
static int	getNumberOfLines(File file) Returns the number of lines in the given file.
static int	getOccurrence(String input, char character) Returns the occurrence of a character in a string.
static double	getPpmError(double theoreticalMzValue, double massError) Returns the ppm value of the given mass error relative to its theoretical m/z value.
static FileAndFileFilter	getUserSelectedFile(Component parent, String[] fileEndings, String[] fileFormatDescriptions, String aDialogTitle, String lastSelectedFolder, String aSuggestedFileName, boolean openDialog, boolean formatSelectedByUser, boolean showAllFilesOption, int defaultFilterIndex) Returns the file selected by the user, or null if no file was selected.
static File	getUserSelectedFile(Component parent, String aFileEnding, String aFileFormatDescription, String aDialogTitle, String lastSelectedFolder, String aSuggestedFileName, boolean openDialog) Returns the file selected by the user, or null if no file was selected.
static File	getUserSelectedFolder(Component parent, String aDialogTitle, String lastSelectedFolder, String aFolderDescription, String approveButtonText, boolean openDialog) Returns the folder selected by the user, or null if no folder was selected.
static double	readDoubleAsString(String doubleAsString) Method for reading a double value as a string which uses either "," or "." as the decimal symbol.
static String	removeExtension(String fileName) Removes the extension from a file name or path.
static String	removeForbiddenCharacters(String string) Removes the forbidden characters from a string.
static double	roundDouble(double d, int places) Rounds a double value to the wanted number of decimal places.
static boolean	sameLists(ArrayList list1, ArrayList list2) Convenience methods indicating whether the content of two lists have the same content.
static boolean	sameListsFirstListSorted(ArrayList list1, ArrayList list2) Convenience methods indicating whether the content of two lists have the same content.
static boolean	sameSets(HashSet set1, HashSet set2) Convenience methods indicating whether the content of two sets have the same content.
static File	saveUrl(File saveFile, String targetUrlAsString, int fileSizeInBytes, String userName, String password, WaitingHandler waitingHandler) Save a file from a URL.
static void	tableToFile(JTable table, String separator, ProgressDialogX progressDialog, boolean removeHtml, BufferedWriter writer) Writes the table to a file as separated text.
static String	tableToText(JTable table, String separator, ProgressDialogX progressDialog, boolean removeHtml) Returns the table as a separated text file.

Methods inherited from class java.lang.Object

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

Field Detail

forbiddenCharacters

public static final String[] forbiddenCharacters

Forbidden characters in file names.

separator

public static final String separator

Separator which can be used to separate things.

See Also:

Constant Field Values

Constructor Detail

Util

public Util()

Method Detail

removeForbiddenCharacters

public static String removeForbiddenCharacters(String string)

Removes the forbidden characters from a string.

Parameters:

string - the string of interest

Returns:

a version without forbidden characters

containsForbiddenCharacter

public static boolean containsForbiddenCharacter(String string)

Indicates whether a string contains characters forbidden in file names.

Parameters:

string - the string of interest

Returns:

a boolean indicating whether a string contains characters forbidden in file names

roundDouble

public static double roundDouble(double d,
                                 int places)

Rounds a double value to the wanted number of decimal places.

Parameters:

d - the double to round of

places - number of decimal places wanted

Returns:

double - the new double

floorDouble

public static double floorDouble(double d,
                                 int places)

Floors a double value to the wanted number of decimal places.

Parameters:

d - the double to floor of

places - number of decimal places wanted

Returns:

double - the new double

emptyDir

public static boolean emptyDir(File dir)

Deletes all files and subdirectories under dir. Returns true if all deletions were successful. If a deletion fails, the method stops attempting to delete and returns false.

Parameters:

dir - the directory to delete

Returns:

rue if all deletions were successful

deleteDir

public static boolean deleteDir(File dir)

Deletes all files and subdirectories under dir and dir itself. Returns true if all deletions were successful. If a deletion fails, the method stops attempting to delete and returns false.

Parameters:

dir - the directory to delete

Returns:

rue if all deletions were successful

getPpmError

public static double getPpmError(double theoreticalMzValue,
                                 double massError)

Returns the ppm value of the given mass error relative to its theoretical m/z value.

Parameters:

theoreticalMzValue - the theoretical mass

massError - the mass error

Returns:

the mass error as a ppm value relative to the theoretical mass

color2Hex

public static String color2Hex(Color color)

Converts a color to hex format for use in HTML tags.

Parameters:

color - the color to convert

Returns:

the color in hex format

getFileName

public static String getFileName(String filePath)

An OS independent getName alternative. Useful if the path is provided as a hardcoded string and opened in a different OS.

Parameters:

filePath - the file path as a string

Returns:

the file name, or the complete path of no file name is detected

getFileName

public static String getFileName(File file)

An OS independent getName alternative. Useful if the path is provided as a hardcoded string and opened in a different OS.

Parameters:

file - the file

Returns:

the file name, or the complete path of no file name is detected

getExtension

public static String getExtension(File file)

Returns the extensions of a file.

Parameters:

file - the file

Returns:

the extension of a file

appendSuffix

public static String appendSuffix(String fileName,
                                  String suffix)

Appends a suffix to a file name before the file extension.

Parameters:

fileName - the file name

suffix - the suffix to add

Returns:

the file name with suffix

removeExtension

public static String removeExtension(String fileName)

Removes the extension from a file name or path.

Parameters:

fileName - the file name

Returns:

the file name without extension

getUserSelectedFile

public static File getUserSelectedFile(Component parent,
                                       String aFileEnding,
                                       String aFileFormatDescription,
                                       String aDialogTitle,
                                       String lastSelectedFolder,
                                       String aSuggestedFileName,
                                       boolean openDialog)

Returns the file selected by the user, or null if no file was selected. Note that the last selected folder value is not updated during this method, and the code calling this method therefore has to take care of this if wanted.

Parameters:

parent - the parent dialog or frame

aFileEnding - the file type, e.g., .txt

aFileFormatDescription - the file format description, e.g., (Mascot Generic Format) *.mgf

aDialogTitle - the title for the dialog

lastSelectedFolder - the last selected folder

aSuggestedFileName - the suggested file name, can be null

openDialog - if true an open dialog is shown, false results in a save dialog

Returns:

the file selected by the user, or null if no file was selected

getUserSelectedFile

public static FileAndFileFilter getUserSelectedFile(Component parent,
                                                    String[] fileEndings,
                                                    String[] fileFormatDescriptions,
                                                    String aDialogTitle,
                                                    String lastSelectedFolder,
                                                    String aSuggestedFileName,
                                                    boolean openDialog,
                                                    boolean formatSelectedByUser,
                                                    boolean showAllFilesOption,
                                                    int defaultFilterIndex)

Returns the file selected by the user, or null if no file was selected. Note that the last selected folder value is not updated during this method, and the code calling this method therefore has to take care of this if wanted.

Parameters:

parent - the parent dialog or frame

fileEndings - the file types, e.g., .txt

fileFormatDescriptions - the file format description, e.g., (Mascot Generic Format) *.mgf

aDialogTitle - the title for the dialog

lastSelectedFolder - the last selected folder

aSuggestedFileName - the suggested file name, can be null

openDialog - if true an open dialog is shown, false results in a save dialog

formatSelectedByUser - if true the user will have to select the format by himself, otherwise all formats will be available

showAllFilesOption - if true, the 'All files' filter option will be included

defaultFilterIndex - the index of the filter selected by default

Returns:

the file selected and the file filter used, null if the selection was canceled.

getUserSelectedFolder

public static File getUserSelectedFolder(Component parent,
                                         String aDialogTitle,
                                         String lastSelectedFolder,
                                         String aFolderDescription,
                                         String approveButtonText,
                                         boolean openDialog)

Returns the folder selected by the user, or null if no folder was selected. Note that the last selected folder value is not updated during this method, and the code calling this method therefore has to take care of this if wanted.

Parameters:

parent - the parent dialog or frame

aDialogTitle - the title for the dialog

lastSelectedFolder - the last selected folder

aFolderDescription - the folder description, e.g., CPS Folder

approveButtonText - the text on the approve button

openDialog - if true the folder has to exist, if false the user will be asked if he/she wants to create the folder is missing

Returns:

the file selected by the user, or null if no file was selected

tableToText

public static String tableToText(JTable table,
                                 String separator,
                                 ProgressDialogX progressDialog,
                                 boolean removeHtml)

Returns the table as a separated text file.

Parameters:

table - the table to turn in to text

separator - the text separator

progressDialog - the progress dialog

removeHtml - if true, HTML is converted to text

Returns:

the table as a separated text file

tableToFile

public static void tableToFile(JTable table,
                               String separator,
                               ProgressDialogX progressDialog,
                               boolean removeHtml,
                               BufferedWriter writer)
                        throws IOException

Writes the table to a file as separated text.

Parameters:

table - the table to write to file

separator - the text separator

progressDialog - the progress dialog

removeHtml - if true, HTML is converted to text

writer - the writer where the file is to be written

Throws:

IOException - if a problem occurs when writing to the file

copyFile

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

Copy the content of a file to another.

Parameters:

in - the file to copy from

out - the file to copy to

Throws:

IOException - if a problem occurs when writing to the file

append

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

Appends the content of a file to another.

Parameters:

in - the file to copy from

out - the file to copy to

Throws:

IOException - if a problem occurs when writing to the file

copyFile

public static void copyFile(File in,
                            File out,
                            boolean overwrite)
                     throws IOException

Copy the content of one file to another.

Parameters:

in - the file to copy from

out - the file to copy to

overwrite - boolean indicating whether out should be overwritten

Throws:

IOException - if a problem occurs when writing to the file

getNumberOfLines

public static int getNumberOfLines(File file)
                            throws IOException

Returns the number of lines in the given file.

Parameters:

file - the file to find the number of lines in

Returns:

the number of lines in the given file

Throws:

IOException - if a problem occurs when writing to the file

sameLists

public static boolean sameLists(ArrayList list1,
                                ArrayList list2)

Convenience methods indicating whether the content of two lists have the same content. Equality is based on the hash of the objects.

Parameters:

list1 - the first list

list2 - the second list

Returns:

a boolean indicating whether list1 has the same content as list2

sameSets

public static boolean sameSets(HashSet set1,
                               HashSet set2)

Convenience methods indicating whether the content of two sets have the same content. Equality is based on the hash of the objects.

Parameters:

set1 - the first set

set2 - the second set

Returns:

a boolean indicating whether list1 has the same content as list2

sameListsFirstListSorted

public static boolean sameListsFirstListSorted(ArrayList list1,
                                               ArrayList list2)

Convenience methods indicating whether the content of two lists have the same content. Assumes that the first list is already sorted.

Parameters:

list1 - the first list

list2 - the second list

Returns:

a boolean indicating whether list1 has the same content as list2

getOccurrence

public static int getOccurrence(String input,
                                char character)

Returns the occurrence of a character in a string.

Parameters:

input - the string of interest

character - the character to look for

Returns:

the occurrence of a character in a string

getIndexes

public static ArrayList<Integer> getIndexes(String bigString,
                                            String smallString)

Returns at which indexes a small string can be found in a big string.

Parameters:

bigString - the big string

smallString - the small string

Returns:

a list of the indexes where the small string can be found in the big string

readDoubleAsString

public static double readDoubleAsString(String doubleAsString)
                                 throws NumberFormatException

Method for reading a double value as a string which uses either "," or "." as the decimal symbol.

Parameters:

doubleAsString - the double value as a string

Returns:

the double value

Throws:

NumberFormatException - thrown if the double cannot be read as a double

saveUrl

public static File saveUrl(File saveFile,
                           String targetUrlAsString,
                           int fileSizeInBytes,
                           String userName,
                           String password,
                           WaitingHandler waitingHandler)
                    throws MalformedURLException,
                           IOException,
                           FileNotFoundException

Save a file from a URL.

Parameters:

saveFile - the file to save to

targetUrlAsString - the target URL as a string

fileSizeInBytes - the file size in bytes

userName - the user name

password - the password

waitingHandler - the waiting handler

Returns:

the saved file

Throws:

MalformedURLException - thrown if an MalformedURLException occurs

IOException - thrown if an IOException occurs

FileNotFoundException - thrown if a FileNotFoundException occurs

checkIfURLExists

public static boolean checkIfURLExists(String targetUrlAsString,
                                       String userName,
                                       String password)

Check if a given URL exists.

Parameters:

targetUrlAsString - the URL to check

userName - the user name

password - the password

Returns:

true of it exists

getFileSize

public static int getFileSize(URL url)

Returns the size of the file located at the given URL.

Parameters:

url - the url of the file

Returns:

the size of the file

convertBooleanToInteger

public static Integer convertBooleanToInteger(Boolean booleanToConvert)

Converts a boolean value to the corresponding integer value, 0 for false and 1 for true.

Parameters:

booleanToConvert - the boolean value to convert

Returns:

0 for false and 1 for true