Package org.forester.util

Class ForesterUtil

  • public final class ForesterUtil
extends java.lang.Object

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void appendSeparatorIfNotEmpty​(java.lang.StringBuffer sb, char separator)  
      static java.awt.Color calcColor​(double value, double min, double max, double mean, java.awt.Color minColor, java.awt.Color maxColor, java.awt.Color meanColor)
      This calculates a color.
      static java.awt.Color calcColor​(double value, double min, double max, java.awt.Color minColor, java.awt.Color maxColor)
      This calculates a color.
      static int calculateOverlap​(Domain domain, java.util.List<java.lang.Boolean> covered_positions)  
      static java.lang.String collapseWhiteSpace​(java.lang.String s)  
      static void collection2file​(java.io.File file, java.util.Collection<?> data, java.lang.String separator)  
      static void collection2writer​(java.io.Writer writer, java.util.Collection<?> data, java.lang.String separator)  
      static java.lang.String colorToHex​(java.awt.Color color)  
      static void copyFile​(java.io.File in, java.io.File out)  
      static int countChars​(java.lang.String str, char c)  
      static java.io.BufferedWriter createBufferedWriter​(java.io.File file)  
      static java.io.BufferedWriter createBufferedWriter​(java.lang.String name)  
      static EasyWriter createEasyWriter​(java.io.File file)  
      static java.io.BufferedWriter createEasyWriter​(java.lang.String name)  
      static java.io.File createFileForWriting​(java.lang.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​(java.lang.String message)  
      static void fatalError​(java.lang.String prg_name, java.lang.String message)  
      static void fatalErrorIfFileNotReadable​(java.io.File file)  
      static void fatalErrorIfFileNotReadable​(java.lang.String prg_name, java.io.File file)  
      static java.lang.String[][] file22dArray​(java.io.File file)  
      static java.lang.String[] file2array​(java.io.File file)  
      static java.util.List<java.lang.String> file2list​(java.io.File file)  
      static java.util.SortedSet<java.lang.String> file2set​(java.io.File file)  
      static java.lang.String getCurrentDateTime()  
      static java.lang.String getFileSeparator()  
      static java.lang.String getFirstLine​(java.lang.Object source)  
      static java.lang.String getForesterLibraryInformation()  
      static java.lang.String getLineSeparator()  
      static MolecularSequence.TYPE guessMolecularSequenceType​(java.lang.String mol_seq)  
      static void increaseCountingMap​(java.util.Map<java.lang.String,​java.lang.Integer> counting_map, java.lang.String item_name)  
      static boolean isEmpty​(java.lang.String s)  
      static boolean isEmpty​(java.util.List<?> l)  
      static boolean isEmpty​(java.util.Set<?> s)  
      static boolean isEngulfed​(Domain domain, java.util.List<java.lang.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​(java.lang.String[] a, java.lang.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​(java.math.BigDecimal s)  
      static java.lang.String isReadableFile​(java.io.File f)  
      static java.lang.String isReadableFile​(java.lang.String s)  
      static boolean isWindows()  
      static java.lang.String isWritableFile​(java.io.File f)  
      static int limitRangeForColor​(int i)
      Helper for method "stringToColor".
      static java.util.SortedMap<java.lang.Object,​java.lang.Integer> listToSortedCountsMap​(java.util.List<?> list)  
      static void map2file​(java.io.File file, java.util.Map<?,​?> data, java.lang.String entry_separator, java.lang.String data_separator)  
      static void map2writer​(java.io.Writer writer, java.util.Map<?,​?> data, java.lang.String entry_separator, java.lang.String data_separator)  
      static java.lang.StringBuffer mapToStringBuffer​(java.util.Map<java.lang.Object,​java.lang.Object> map, java.lang.String key_value_separator)  
      static java.lang.String normalizeString​(java.lang.String s, int length, boolean left_pad, char pad_char)  
      static java.awt.Color obtainColorDependingOnTaxonomyGroup​(java.lang.String tax_group)  
      static java.lang.String obtainNormalizedTaxonomyGroup​(java.lang.String tax)  
      static java.io.BufferedReader obtainReader​(java.lang.Object source)  
      static void outOfMemoryError​(java.lang.OutOfMemoryError e)  
      static java.lang.StringBuffer pad​(double number, int size, char pad, boolean left_pad)  
      static java.lang.StringBuffer pad​(java.lang.StringBuffer string, int size, char pad, boolean left_pad)  
      static java.lang.StringBuffer pad​(java.lang.String string, int size, char pad, boolean left_pad)  
      static double parseDouble​(java.lang.String str)  
      static int parseInt​(java.lang.String str)  
      static void printArray​(java.lang.Object[] a)  
      static void printCountingMap​(java.util.Map<java.lang.String,​java.lang.Integer> counting_map)  
      static void printErrorMessage​(java.lang.String prg_name, java.lang.String message)  
      static void printProgramInformation​(java.lang.String prg_name, java.lang.String prg_version, java.lang.String date)  
      static void printProgramInformation​(java.lang.String prg_name, java.lang.String prg_version, java.lang.String date, java.lang.String email, java.lang.String www)  
      static void printProgramInformation​(java.lang.String prg_name, java.lang.String desc, java.lang.String prg_version, java.lang.String date, java.lang.String email, java.lang.String www, java.lang.String based_on)  
      static void printWarningMessage​(java.lang.String prg_name, java.lang.String message)  
      static void programMessage​(java.lang.String prg_name, java.lang.String message)  
      static java.util.List<java.lang.String> readUrl​(java.lang.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 java.lang.String removeSuffix​(java.lang.String file_name)  
      static java.lang.String removeWhiteSpace​(java.lang.String s)
      Removes all white space from String s.
      static java.lang.String replaceIllegalNhxCharacters​(java.lang.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 java.lang.String sanitizeString​(java.lang.String s)  
      static java.lang.StringBuilder santitizeStringForNH​(java.lang.String data)  
      static boolean seqIsLikelyToBeAa​(java.lang.String s)  
      static java.lang.String stringArrayToString​(java.lang.String[] a)  
      static java.lang.String stringArrayToString​(java.lang.String[] a, java.lang.String separator)  
      static java.lang.String[] stringListToArray​(java.util.List<java.lang.String> list)  
      static java.lang.String stringListToString​(java.util.List<java.lang.String> l, java.lang.String separator)  
      static java.lang.String[] stringSetToArray​(java.util.Set<java.lang.String> strings)  
      static void unexpectedFatalError​(java.lang.Error e)  
      static void unexpectedFatalError​(java.lang.Exception e)  
      static void unexpectedFatalError​(java.lang.String message)  
      static void unexpectedFatalError​(java.lang.String prg_name, java.lang.Exception e)  
      static void unexpectedFatalError​(java.lang.String prg_name, java.lang.String message)  
      static void unexpectedFatalError​(java.lang.String prg_name, java.lang.String message, java.lang.Exception e)  
      static void updateProgress​(double progress_percentage)  
      static void updateProgress​(int i, java.text.DecimalFormat f)  
      static java.lang.String wordWrap​(java.lang.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 java.lang.String FILE_SEPARATOR

      • FORMATTER_06

        public static final java.text.NumberFormat FORMATTER_06

      • FORMATTER_3

        public static final java.text.NumberFormat FORMATTER_3

      • FORMATTER_6

        public static final java.text.NumberFormat FORMATTER_6

      • FORMATTER_9

        public static final java.text.NumberFormat FORMATTER_9

      • JAVA_VENDOR

        public static final java.lang.String JAVA_VENDOR

      • JAVA_VERSION

        public static final java.lang.String JAVA_VERSION

      • LINE_SEPARATOR

        public static final java.lang.String LINE_SEPARATOR

      • NULL_BD

        public static final java.math.BigDecimal NULL_BD

      • OS_ARCH

        public static final java.lang.String OS_ARCH

      • OS_NAME

        public static final java.lang.String OS_NAME

      • OS_VERSION

        public static final java.lang.String OS_VERSION

    • Method Detail

      • appendSeparatorIfNotEmpty

        public static final void appendSeparatorIfNotEmpty​(java.lang.StringBuffer sb,
                                                   char separator)

      • calcColor

        public static final java.awt.Color calcColor​(double value,
                                             double min,
                                             double max,
                                             java.awt.Color minColor,
                                             java.awt.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 java.awt.Color calcColor​(double value,
                                             double min,
                                             double max,
                                             double mean,
                                             java.awt.Color minColor,
                                             java.awt.Color maxColor,
                                             java.awt.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,
                                   java.util.List<java.lang.Boolean> covered_positions)

      • collapseWhiteSpace

        public static final java.lang.String collapseWhiteSpace​(java.lang.String s)

      • collection2file

        public static final void collection2file​(java.io.File file,
                                         java.util.Collection<?> data,
                                         java.lang.String separator)
                                  throws java.io.IOException
        Throws:
        java.io.IOException

      • collection2writer

        public static final void collection2writer​(java.io.Writer writer,
                                           java.util.Collection<?> data,
                                           java.lang.String separator)
                                    throws java.io.IOException
        Throws:
        java.io.IOException

      • colorToHex

        public static final java.lang.String colorToHex​(java.awt.Color color)

      • copyFile

        public static void copyFile​(java.io.File in,
                            java.io.File out)
                     throws java.io.IOException
        Throws:
        java.io.IOException

      • countChars

        public static final int countChars​(java.lang.String str,
                                   char c)

      • createBufferedWriter

        public static final java.io.BufferedWriter createBufferedWriter​(java.io.File file)
                                                         throws java.io.IOException
        Throws:
        java.io.IOException

      • createBufferedWriter

        public static final java.io.BufferedWriter createBufferedWriter​(java.lang.String name)
                                                         throws java.io.IOException
        Throws:
        java.io.IOException

      • createEasyWriter

        public static final EasyWriter createEasyWriter​(java.io.File file)
                                         throws java.io.IOException
        Throws:
        java.io.IOException

      • createEasyWriter

        public static final java.io.BufferedWriter createEasyWriter​(java.lang.String name)
                                                     throws java.io.IOException
        Throws:
        java.io.IOException

      • createFileForWriting

        public static final java.io.File createFileForWriting​(java.lang.String name)
                                               throws java.io.IOException
        Throws:
        java.io.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​(java.lang.String message)

      • fatalError

        public static void fatalError​(java.lang.String prg_name,
                              java.lang.String message)

      • fatalErrorIfFileNotReadable

        public static void fatalErrorIfFileNotReadable​(java.io.File file)

      • fatalErrorIfFileNotReadable

        public static void fatalErrorIfFileNotReadable​(java.lang.String prg_name,
                                               java.io.File file)

      • file22dArray

        public static java.lang.String[][] file22dArray​(java.io.File file)
                                         throws java.io.IOException
        Throws:
        java.io.IOException

      • file2array

        public static java.lang.String[] file2array​(java.io.File file)
                                     throws java.io.IOException
        Throws:
        java.io.IOException

      • file2list

        public static final java.util.List<java.lang.String> file2list​(java.io.File file)
                                                        throws java.io.IOException
        Throws:
        java.io.IOException

      • file2set

        public static final java.util.SortedSet<java.lang.String> file2set​(java.io.File file)
                                                            throws java.io.IOException
        Throws:
        java.io.IOException

      • getCurrentDateTime

        public static final java.lang.String getCurrentDateTime()

      • getFileSeparator

        public static final java.lang.String getFileSeparator()

      • getFirstLine

        public static final java.lang.String getFirstLine​(java.lang.Object source)
                                           throws java.io.FileNotFoundException,
                                                  java.io.IOException
        Throws:
        java.io.FileNotFoundException
        java.io.IOException

      • getForesterLibraryInformation

        public static final java.lang.String getForesterLibraryInformation()

      • getLineSeparator

        public static final java.lang.String getLineSeparator()

      • guessMolecularSequenceType

        public static final MolecularSequence.TYPE guessMolecularSequenceType​(java.lang.String mol_seq)

      • increaseCountingMap

        public static final void increaseCountingMap​(java.util.Map<java.lang.String,​java.lang.Integer> counting_map,
                                             java.lang.String item_name)

      • isEmpty

        public static final boolean isEmpty​(java.util.List<?> l)

      • isEmpty

        public static final boolean isEmpty​(java.util.Set<?> s)

      • isEmpty

        public static final boolean isEmpty​(java.lang.String s)

      • isEngulfed

        public static boolean isEngulfed​(Domain domain,
                                 java.util.List<java.lang.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​(java.lang.String[] a,
                                           java.lang.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​(java.math.BigDecimal s)

      • isReadableFile

        public static final java.lang.String isReadableFile​(java.io.File f)

      • isReadableFile

        public static final java.lang.String isReadableFile​(java.lang.String s)

      • isWindows

        public static final boolean isWindows()

      • isWritableFile

        public static final java.lang.String isWritableFile​(java.io.File f)

      • limitRangeForColor

        public static final int limitRangeForColor​(int i)
        Helper for method "stringToColor".

        (Last modified: 12/20/03)

      • listToSortedCountsMap

        public static final java.util.SortedMap<java.lang.Object,​java.lang.Integer> listToSortedCountsMap​(java.util.List<?> list)

      • map2file

        public static final void map2file​(java.io.File file,
                                  java.util.Map<?,​?> data,
                                  java.lang.String entry_separator,
                                  java.lang.String data_separator)
                           throws java.io.IOException
        Throws:
        java.io.IOException

      • map2writer

        public static final void map2writer​(java.io.Writer writer,
                                    java.util.Map<?,​?> data,
                                    java.lang.String entry_separator,
                                    java.lang.String data_separator)
                             throws java.io.IOException
        Throws:
        java.io.IOException

      • mapToStringBuffer

        public static final java.lang.StringBuffer mapToStringBuffer​(java.util.Map<java.lang.Object,​java.lang.Object> map,
                                                             java.lang.String key_value_separator)

      • normalizeString

        public static final java.lang.String normalizeString​(java.lang.String s,
                                                     int length,
                                                     boolean left_pad,
                                                     char pad_char)

      • obtainColorDependingOnTaxonomyGroup

        public static final java.awt.Color obtainColorDependingOnTaxonomyGroup​(java.lang.String tax_group)

      • obtainNormalizedTaxonomyGroup

        public static final java.lang.String obtainNormalizedTaxonomyGroup​(java.lang.String tax)

      • obtainReader

        public static final java.io.BufferedReader obtainReader​(java.lang.Object source)
                                                 throws java.io.IOException,
                                                        java.io.FileNotFoundException
        Throws:
        java.io.IOException
        java.io.FileNotFoundException

      • outOfMemoryError

        public static final void outOfMemoryError​(java.lang.OutOfMemoryError e)

      • pad

        public static final java.lang.StringBuffer pad​(double number,
                                               int size,
                                               char pad,
                                               boolean left_pad)

      • pad

        public static final java.lang.StringBuffer pad​(java.lang.String string,
                                               int size,
                                               char pad,
                                               boolean left_pad)

      • pad

        public static final java.lang.StringBuffer pad​(java.lang.StringBuffer string,
                                               int size,
                                               char pad,
                                               boolean left_pad)

      • parseDouble

        public static final double parseDouble​(java.lang.String str)
                                throws java.text.ParseException
        Throws:
        java.text.ParseException

      • parseInt

        public static final int parseInt​(java.lang.String str)
                          throws java.text.ParseException
        Throws:
        java.text.ParseException

      • printArray

        public static final void printArray​(java.lang.Object[] a)

      • printCountingMap

        public static final void printCountingMap​(java.util.Map<java.lang.String,​java.lang.Integer> counting_map)

      • printErrorMessage

        public static final void printErrorMessage​(java.lang.String prg_name,
                                           java.lang.String message)

      • printProgramInformation

        public static final void printProgramInformation​(java.lang.String prg_name,
                                                 java.lang.String prg_version,
                                                 java.lang.String date)

      • printProgramInformation

        public static final void printProgramInformation​(java.lang.String prg_name,
                                                 java.lang.String prg_version,
                                                 java.lang.String date,
                                                 java.lang.String email,
                                                 java.lang.String www)

      • printProgramInformation

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

      • printWarningMessage

        public static final void printWarningMessage​(java.lang.String prg_name,
                                             java.lang.String message)

      • programMessage

        public static final void programMessage​(java.lang.String prg_name,
                                        java.lang.String message)

      • readUrl

        public static java.util.List<java.lang.String> readUrl​(java.lang.String url_str)
                                                throws java.io.IOException
        Throws:
        java.io.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 java.lang.String removeSuffix​(java.lang.String file_name)

      • removeWhiteSpace

        public static final java.lang.String removeWhiteSpace​(java.lang.String s)
        Removes all white space from String s.
        Returns:
        String s with white space removed

      • replaceIllegalNhxCharacters

        public static final java.lang.String replaceIllegalNhxCharacters​(java.lang.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 java.lang.String sanitizeString​(java.lang.String s)

      • santitizeStringForNH

        public static final java.lang.StringBuilder santitizeStringForNH​(java.lang.String data)

      • seqIsLikelyToBeAa

        public static boolean seqIsLikelyToBeAa​(java.lang.String s)

      • stringArrayToString

        public static final java.lang.String stringArrayToString​(java.lang.String[] a)

      • stringArrayToString

        public static final java.lang.String stringArrayToString​(java.lang.String[] a,
                                                         java.lang.String separator)

      • stringListToArray

        public static final java.lang.String[] stringListToArray​(java.util.List<java.lang.String> list)

      • stringListToString

        public static final java.lang.String stringListToString​(java.util.List<java.lang.String> l,
                                                        java.lang.String separator)

      • stringSetToArray

        public static final java.lang.String[] stringSetToArray​(java.util.Set<java.lang.String> strings)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.Error e)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.Exception e)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.String message)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.String prg_name,
                                              java.lang.Exception e)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.String prg_name,
                                              java.lang.String message)

      • unexpectedFatalError

        public static final void unexpectedFatalError​(java.lang.String prg_name,
                                              java.lang.String message,
                                              java.lang.Exception e)

      • updateProgress

        public static final void updateProgress​(double progress_percentage)

      • updateProgress

        public static final void updateProgress​(int i,
                                        java.text.DecimalFormat f)

      • wordWrap

        public static final java.lang.String wordWrap​(java.lang.String str,
                                              int width)