org.forester.util

Class ForesterUtil

java.lang.Object

org.forester.util.ForesterUtil

public final class ForesterUtil
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	FILE_SEPARATOR
static NumberFormat	FORMATTER_06
static NumberFormat	FORMATTER_3
static NumberFormat	FORMATTER_6
static NumberFormat	FORMATTER_9
static String	JAVA_VENDOR
static String	JAVA_VERSION
static String	LINE_SEPARATOR
static String	NCBI_GI
static String	NCBI_NUCCORE
static String	NCBI_PROTEIN
static BigDecimal	NULL_BD
static String	OS_ARCH
static String	OS_NAME
static String	OS_VERSION
static String	PDB
static String	UNIPROT_KB
static double	ZERO_DIFF

Method Summary

Modifier and Type	Method and Description
static void	appendSeparatorIfNotEmpty(StringBuffer sb, char separator)
static Color	calcColor(double value, double min, double max, Color minColor, Color maxColor) This calculates a color.
static Color	calcColor(double value, double min, double max, double mean, Color minColor, Color maxColor, Color meanColor) This calculates a color.
static int	calculateOverlap(Domain domain, List<Boolean> covered_positions)
static String	collapseWhiteSpace(String s)
static void	collection2file(File file, Collection<?> data, String separator)
static void	collection2writer(Writer writer, Collection<?> data, String separator)
static String	colorToHex(Color color)
static void	copyFile(File in, File out)
static int	countChars(String str, char c)
static BufferedWriter	createBufferedWriter(File file)
static BufferedWriter	createBufferedWriter(String name)
static EasyWriter	createEasyWriter(File file)
static BufferedWriter	createEasyWriter(String name)
static File	createFileForWriting(String name)
static void	ensurePresenceOfDate(PhylogenyNode node)
static void	ensurePresenceOfDistribution(PhylogenyNode node)
static void	ensurePresenceOfSequence(PhylogenyNode node)
static void	ensurePresenceOfTaxonomy(PhylogenyNode node)
static void	fatalError(String message)
static void	fatalError(String prg_name, String message)
static void	fatalErrorIfFileNotReadable(File file)
static void	fatalErrorIfFileNotReadable(String prg_name, File file)
static String[][]	file22dArray(File file)
static String[]	file2array(File file)
static List<String>	file2list(File file)
static SortedSet<String>	file2set(File file)
static String	getCurrentDateTime()
static String	getFileSeparator()
static String	getFirstLine(Object source)
static String	getForesterLibraryInformation()
static String	getLineSeparator()
static MolecularSequence.TYPE	guessMolecularSequenceType(String mol_seq)
static void	increaseCountingMap(Map<String,Integer> counting_map, String item_name)
static boolean	isEmpty(List<?> l)
static boolean	isEmpty(Set<?> s)
static boolean	isEmpty(String s)
static boolean	isEngulfed(Domain domain, List<Boolean> covered_positions) Returns true is Domain domain falls in an uninterrupted stretch of covered positions.
static boolean	isEqual(double a, double b)
static boolean	isEven(int n)
static boolean	isIntersecting(String[] a, String[] b) This determines whether String[] a and String[] b have at least one String in common (intersect).
static double	isLargerOrEqualToZero(double d)
static boolean	isMac()
static boolean	isNull(BigDecimal s)
static String	isReadableFile(File f)
static String	isReadableFile(String s)
static boolean	isWindows()
static String	isWritableFile(File f)
static int	limitRangeForColor(int i) Helper for method "stringToColor".
static SortedMap<Object,Integer>	listToSortedCountsMap(List<?> list)
static void	map2file(File file, Map<?,?> data, String entry_separator, String data_separator)
static void	map2writer(Writer writer, Map<?,?> data, String entry_separator, String data_separator)
static StringBuffer	mapToStringBuffer(Map<Object,Object> map, String key_value_separator)
static String	normalizeString(String s, int length, boolean left_pad, char pad_char)
static Color	obtainColorDependingOnTaxonomyGroup(String tax_group)
static String	obtainNormalizedTaxonomyGroup(String tax)
static BufferedReader	obtainReader(Object source)
static void	outOfMemoryError(OutOfMemoryError e)
static StringBuffer	pad(double number, int size, char pad, boolean left_pad)
static StringBuffer	pad(StringBuffer string, int size, char pad, boolean left_pad)
static StringBuffer	pad(String string, int size, char pad, boolean left_pad)
static double	parseDouble(String str)
static int	parseInt(String str)
static void	printArray(Object[] a)
static void	printCountingMap(Map<String,Integer> counting_map)
static void	printErrorMessage(String prg_name, String message)
static void	printProgramInformation(String prg_name, String prg_version, String date)
static void	printProgramInformation(String prg_name, String prg_version, String date, String email, String www)
static void	printProgramInformation(String prg_name, String desc, String prg_version, String date, String email, String www, String based_on)
static void	printWarningMessage(String prg_name, String message)
static void	programMessage(String prg_name, String message)
static List<String>	readUrl(String url_str)
static Protein	removeOverlappingDomains(int max_allowed_overlap, boolean remove_engulfed_domains, Protein protein) Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignored
static String	removeSuffix(String file_name)
static String	removeWhiteSpace(String s) Removes all white space from String s.
static String	replaceIllegalNhxCharacters(String nhx)
static double	round(double value, int decimal_place)
static int	roundToInt(double d) Rounds d to an int.
static int	roundToInt(float f)
static short	roundToShort(double d)
static String	sanitizeString(String s)
static StringBuilder	santitizeStringForNH(String data)
static boolean	seqIsLikelyToBeAa(String s)
static String	stringArrayToString(String[] a)
static String	stringArrayToString(String[] a, String separator)
static String[]	stringListToArray(List<String> list)
static String	stringListToString(List<String> l, String separator)
static String[]	stringSetToArray(Set<String> strings)
static void	unexpectedFatalError(Error e)
static void	unexpectedFatalError(Exception e)
static void	unexpectedFatalError(String message)
static void	unexpectedFatalError(String prg_name, Exception e)
static void	unexpectedFatalError(String prg_name, String message)
static void	unexpectedFatalError(String prg_name, String message, Exception e)
static void	updateProgress(double progress_percentage)
static void	updateProgress(int i, DecimalFormat f)
static String	wordWrap(String str, int width)

Methods inherited from class java.lang.Object

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

Field Detail

FILE_SEPARATOR

public static final String FILE_SEPARATOR

FORMATTER_06

public static final NumberFormat FORMATTER_06

FORMATTER_3

public static final NumberFormat FORMATTER_3

FORMATTER_6

public static final NumberFormat FORMATTER_6

FORMATTER_9

public static final NumberFormat FORMATTER_9

JAVA_VENDOR

public static final String JAVA_VENDOR

JAVA_VERSION

public static final String JAVA_VERSION

LINE_SEPARATOR

public static final String LINE_SEPARATOR

NCBI_GI

public static final String NCBI_GI

See Also:

Constant Field Values

NCBI_NUCCORE

public static final String NCBI_NUCCORE

See Also:

Constant Field Values

NCBI_PROTEIN

public static final String NCBI_PROTEIN

See Also:

Constant Field Values

NULL_BD

public static final BigDecimal NULL_BD

OS_ARCH

public static final String OS_ARCH

OS_NAME

public static final String OS_NAME

OS_VERSION

public static final String OS_VERSION

PDB

public static final String PDB

See Also:

Constant Field Values

UNIPROT_KB

public static final String UNIPROT_KB

See Also:

Constant Field Values

ZERO_DIFF

public static final double ZERO_DIFF

See Also:

Constant Field Values

Method Detail

appendSeparatorIfNotEmpty

public static final void appendSeparatorIfNotEmpty(StringBuffer sb,
                                                   char separator)

calcColor

public static final Color calcColor(double value,
                                    double min,
                                    double max,
                                    Color minColor,
                                    Color maxColor)

This calculates a color. If value is equal to min the returned color is minColor, if value is equal to max the returned color is maxColor, otherwise a color 'proportional' to value is returned.

Parameters:

value - the value

min - the smallest value

max - the largest value

minColor - the color for min

maxColor - the color for max

Returns:

a Color

calcColor

public static final Color calcColor(double value,
                                    double min,
                                    double max,
                                    double mean,
                                    Color minColor,
                                    Color maxColor,
                                    Color meanColor)

This calculates a color. If value is equal to min the returned color is minColor, if value is equal to max the returned color is maxColor, if value is equal to mean the returned color is meanColor, otherwise a color 'proportional' to value is returned -- either between min-mean or mean-max

Parameters:

value - the value

min - the smallest value

max - the largest value

mean - the mean/median value

minColor - the color for min

maxColor - the color for max

meanColor - the color for mean

Returns:

a Color

calculateOverlap

public static int calculateOverlap(Domain domain,
                                   List<Boolean> covered_positions)

collapseWhiteSpace

public static final String collapseWhiteSpace(String s)

collection2file

public static final void collection2file(File file,
                                         Collection<?> data,
                                         String separator)
                                  throws IOException

Throws:

IOException

collection2writer

public static final void collection2writer(Writer writer,
                                           Collection<?> data,
                                           String separator)
                                    throws IOException

Throws:

IOException

colorToHex

public static final String colorToHex(Color color)

copyFile

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

Throws:

IOException

countChars

public static final int countChars(String str,
                                   char c)

createBufferedWriter

public static final BufferedWriter createBufferedWriter(File file)
                                                 throws IOException

Throws:

IOException

createBufferedWriter

public static final BufferedWriter createBufferedWriter(String name)
                                                 throws IOException

Throws:

IOException

createEasyWriter

public static final EasyWriter createEasyWriter(File file)
                                         throws IOException

Throws:

IOException

createEasyWriter

public static final BufferedWriter createEasyWriter(String name)
                                             throws IOException

Throws:

IOException

createFileForWriting

public static final File createFileForWriting(String name)
                                       throws IOException

Throws:

IOException

ensurePresenceOfDate

public static final void ensurePresenceOfDate(PhylogenyNode node)

ensurePresenceOfDistribution

public static final void ensurePresenceOfDistribution(PhylogenyNode node)

ensurePresenceOfSequence

public static void ensurePresenceOfSequence(PhylogenyNode node)

ensurePresenceOfTaxonomy

public static void ensurePresenceOfTaxonomy(PhylogenyNode node)

fatalError

public static void fatalError(String message)

fatalError

public static void fatalError(String prg_name,
                              String message)

fatalErrorIfFileNotReadable

public static void fatalErrorIfFileNotReadable(File file)

fatalErrorIfFileNotReadable

public static void fatalErrorIfFileNotReadable(String prg_name,
                                               File file)

file22dArray

public static String[][] file22dArray(File file)
                               throws IOException

Throws:

IOException

file2array

public static String[] file2array(File file)
                           throws IOException

Throws:

IOException

file2list

public static final List<String> file2list(File file)
                                    throws IOException

Throws:

IOException

file2set

public static final SortedSet<String> file2set(File file)
                                        throws IOException

Throws:

IOException

getCurrentDateTime

public static final String getCurrentDateTime()

getFileSeparator

public static final String getFileSeparator()

getFirstLine

public static final String getFirstLine(Object source)
                                 throws FileNotFoundException,
                                        IOException

Throws:

FileNotFoundException

IOException

getForesterLibraryInformation

public static final String getForesterLibraryInformation()

getLineSeparator

public static final String getLineSeparator()

guessMolecularSequenceType

public static final MolecularSequence.TYPE guessMolecularSequenceType(String mol_seq)

increaseCountingMap

public static final void increaseCountingMap(Map<String,Integer> counting_map,
                                             String item_name)

isEmpty

public static final boolean isEmpty(List<?> l)

isEmpty

public static final boolean isEmpty(Set<?> s)

isEmpty

public static final boolean isEmpty(String s)

isEngulfed

public static boolean isEngulfed(Domain domain,
                                 List<Boolean> covered_positions)

Returns true is Domain domain falls in an uninterrupted stretch of covered positions.

Parameters:

domain -

covered_positions -

Returns:

isEqual

public static final boolean isEqual(double a,
                                    double b)

isEven

public static final boolean isEven(int n)

isIntersecting

public static final boolean isIntersecting(String[] a,
                                           String[] b)

This determines whether String[] a and String[] b have at least one String in common (intersect). Returns false if at least one String[] is null or empty.

Parameters:

a - a String[] b a String[]

Returns:

true if both a and b or not empty or null and contain at least one element in common false otherwise

isLargerOrEqualToZero

public static final double isLargerOrEqualToZero(double d)

isMac

public static final boolean isMac()

isNull

public static final boolean isNull(BigDecimal s)

isReadableFile

public static final String isReadableFile(File f)

isReadableFile

public static final String isReadableFile(String s)

isWindows

public static final boolean isWindows()

isWritableFile

public static final String isWritableFile(File f)

limitRangeForColor

public static final int limitRangeForColor(int i)

Helper for method "stringToColor".

(Last modified: 12/20/03)

listToSortedCountsMap

public static final SortedMap<Object,Integer> listToSortedCountsMap(List<?> list)

map2file

public static final void map2file(File file,
                                  Map<?,?> data,
                                  String entry_separator,
                                  String data_separator)
                           throws IOException

Throws:

IOException

map2writer

public static final void map2writer(Writer writer,
                                    Map<?,?> data,
                                    String entry_separator,
                                    String data_separator)
                             throws IOException

Throws:

IOException

mapToStringBuffer

public static final StringBuffer mapToStringBuffer(Map<Object,Object> map,
                                                   String key_value_separator)

normalizeString

public static final String normalizeString(String s,
                                           int length,
                                           boolean left_pad,
                                           char pad_char)

obtainColorDependingOnTaxonomyGroup

public static final Color obtainColorDependingOnTaxonomyGroup(String tax_group)

obtainNormalizedTaxonomyGroup

public static final String obtainNormalizedTaxonomyGroup(String tax)

obtainReader

public static final BufferedReader obtainReader(Object source)
                                         throws IOException,
                                                FileNotFoundException

Throws:

IOException

FileNotFoundException

outOfMemoryError

public static final void outOfMemoryError(OutOfMemoryError e)

pad

public static final StringBuffer pad(double number,
                                     int size,
                                     char pad,
                                     boolean left_pad)

pad

public static final StringBuffer pad(String string,
                                     int size,
                                     char pad,
                                     boolean left_pad)

pad

public static final StringBuffer pad(StringBuffer string,
                                     int size,
                                     char pad,
                                     boolean left_pad)

parseDouble

public static final double parseDouble(String str)
                                throws ParseException

Throws:

ParseException

parseInt

public static final int parseInt(String str)
                          throws ParseException

Throws:

ParseException

printArray

public static final void printArray(Object[] a)

printCountingMap

public static final void printCountingMap(Map<String,Integer> counting_map)

printErrorMessage

public static final void printErrorMessage(String prg_name,
                                           String message)

printProgramInformation

public static final void printProgramInformation(String prg_name,
                                                 String prg_version,
                                                 String date)

printProgramInformation

public static final void printProgramInformation(String prg_name,
                                                 String prg_version,
                                                 String date,
                                                 String email,
                                                 String www)

printProgramInformation

public static final void printProgramInformation(String prg_name,
                                                 String desc,
                                                 String prg_version,
                                                 String date,
                                                 String email,
                                                 String www,
                                                 String based_on)

printWarningMessage

public static final void printWarningMessage(String prg_name,
                                             String message)

programMessage

public static final void programMessage(String prg_name,
                                        String message)

readUrl

public static List<String> readUrl(String url_str)
                            throws IOException

Throws:

IOException

removeOverlappingDomains

public static Protein removeOverlappingDomains(int max_allowed_overlap,
                                               boolean remove_engulfed_domains,
                                               Protein protein)

Example regarding engulfment: ------------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_ ignored

Parameters:

max_allowed_overlap - maximal allowed overlap (inclusive) to be still considered not overlapping (zero or negative value to allow any overlap)

remove_engulfed_domains - to remove domains which are completely engulfed by coverage of domains with better support

protein -

Returns:

removeSuffix

public static final String removeSuffix(String file_name)

removeWhiteSpace

public static final String removeWhiteSpace(String s)

Removes all white space from String s.

Returns:

String s with white space removed

replaceIllegalNhxCharacters

public static final String replaceIllegalNhxCharacters(String nhx)

round

public static final double round(double value,
                                 int decimal_place)

roundToInt

public static final int roundToInt(double d)

Rounds d to an int.

roundToInt

public static final int roundToInt(float f)

roundToShort

public static final short roundToShort(double d)

sanitizeString

public static final String sanitizeString(String s)

santitizeStringForNH

public static final StringBuilder santitizeStringForNH(String data)

seqIsLikelyToBeAa

public static boolean seqIsLikelyToBeAa(String s)

stringArrayToString

public static final String stringArrayToString(String[] a)

stringArrayToString

public static final String stringArrayToString(String[] a,
                                               String separator)

stringListToArray

public static final String[] stringListToArray(List<String> list)

stringListToString

public static final String stringListToString(List<String> l,
                                              String separator)

stringSetToArray

public static final String[] stringSetToArray(Set<String> strings)

unexpectedFatalError

public static final void unexpectedFatalError(Error e)

unexpectedFatalError

public static final void unexpectedFatalError(Exception e)

unexpectedFatalError

public static final void unexpectedFatalError(String message)

unexpectedFatalError

public static final void unexpectedFatalError(String prg_name,
                                              Exception e)

unexpectedFatalError

public static final void unexpectedFatalError(String prg_name,
                                              String message)

unexpectedFatalError

public static final void unexpectedFatalError(String prg_name,
                                              String message,
                                              Exception e)

updateProgress

public static final void updateProgress(double progress_percentage)

updateProgress

public static final void updateProgress(int i,
                                        DecimalFormat f)

wordWrap

public static final String wordWrap(String str,
                                    int width)