Package org.forester.util
Class ForesterUtil
- java.lang.Object
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- org.forester.util.ForesterUtil
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public final class ForesterUtil extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
FILE_SEPARATOR
static java.text.NumberFormat
FORMATTER_06
static java.text.NumberFormat
FORMATTER_3
static java.text.NumberFormat
FORMATTER_6
static java.text.NumberFormat
FORMATTER_9
static java.lang.String
JAVA_VENDOR
static java.lang.String
JAVA_VERSION
static java.lang.String
LINE_SEPARATOR
static java.lang.String
NCBI_GI
static java.lang.String
NCBI_NUCCORE
static java.lang.String
NCBI_PROTEIN
static java.math.BigDecimal
NULL_BD
static java.lang.String
OS_ARCH
static java.lang.String
OS_NAME
static java.lang.String
OS_VERSION
static java.lang.String
PDB
static java.lang.String
UNIPROT_KB
static double
ZERO_DIFF
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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_ ignoredstatic 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)
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Field Detail
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FILE_SEPARATOR
public static final java.lang.String FILE_SEPARATOR
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FORMATTER_06
public static final java.text.NumberFormat FORMATTER_06
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FORMATTER_3
public static final java.text.NumberFormat FORMATTER_3
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FORMATTER_6
public static final java.text.NumberFormat FORMATTER_6
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FORMATTER_9
public static final java.text.NumberFormat FORMATTER_9
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JAVA_VENDOR
public static final java.lang.String JAVA_VENDOR
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JAVA_VERSION
public static final java.lang.String JAVA_VERSION
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LINE_SEPARATOR
public static final java.lang.String LINE_SEPARATOR
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NCBI_GI
public static final java.lang.String NCBI_GI
- See Also:
- Constant Field Values
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NCBI_NUCCORE
public static final java.lang.String NCBI_NUCCORE
- See Also:
- Constant Field Values
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NCBI_PROTEIN
public static final java.lang.String NCBI_PROTEIN
- See Also:
- Constant Field Values
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NULL_BD
public static final java.math.BigDecimal NULL_BD
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OS_ARCH
public static final java.lang.String OS_ARCH
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OS_NAME
public static final java.lang.String OS_NAME
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OS_VERSION
public static final java.lang.String OS_VERSION
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PDB
public static final java.lang.String PDB
- See Also:
- Constant Field Values
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UNIPROT_KB
public static final java.lang.String UNIPROT_KB
- See Also:
- Constant Field Values
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ZERO_DIFF
public static final double ZERO_DIFF
- See Also:
- Constant Field Values
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Method Detail
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appendSeparatorIfNotEmpty
public static final void appendSeparatorIfNotEmpty(java.lang.StringBuffer sb, char separator)
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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 valuemin
- the smallest valuemax
- the largest valueminColor
- the color for minmaxColor
- the color for max- Returns:
- a Color
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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 valuemin
- the smallest valuemax
- the largest valuemean
- the mean/median valueminColor
- the color for minmaxColor
- the color for maxmeanColor
- the color for mean- Returns:
- a Color
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calculateOverlap
public static int calculateOverlap(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
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collapseWhiteSpace
public static final java.lang.String collapseWhiteSpace(java.lang.String s)
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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
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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
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colorToHex
public static final java.lang.String colorToHex(java.awt.Color color)
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copyFile
public static void copyFile(java.io.File in, java.io.File out) throws java.io.IOException
- Throws:
java.io.IOException
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countChars
public static final int countChars(java.lang.String str, char c)
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createBufferedWriter
public static final java.io.BufferedWriter createBufferedWriter(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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createBufferedWriter
public static final java.io.BufferedWriter createBufferedWriter(java.lang.String name) throws java.io.IOException
- Throws:
java.io.IOException
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createEasyWriter
public static final EasyWriter createEasyWriter(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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createEasyWriter
public static final java.io.BufferedWriter createEasyWriter(java.lang.String name) throws java.io.IOException
- Throws:
java.io.IOException
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createFileForWriting
public static final java.io.File createFileForWriting(java.lang.String name) throws java.io.IOException
- Throws:
java.io.IOException
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ensurePresenceOfDate
public static final void ensurePresenceOfDate(PhylogenyNode node)
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ensurePresenceOfDistribution
public static final void ensurePresenceOfDistribution(PhylogenyNode node)
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ensurePresenceOfSequence
public static void ensurePresenceOfSequence(PhylogenyNode node)
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ensurePresenceOfTaxonomy
public static void ensurePresenceOfTaxonomy(PhylogenyNode node)
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fatalError
public static void fatalError(java.lang.String message)
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fatalError
public static void fatalError(java.lang.String prg_name, java.lang.String message)
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fatalErrorIfFileNotReadable
public static void fatalErrorIfFileNotReadable(java.io.File file)
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fatalErrorIfFileNotReadable
public static void fatalErrorIfFileNotReadable(java.lang.String prg_name, java.io.File file)
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file22dArray
public static java.lang.String[][] file22dArray(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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file2array
public static java.lang.String[] file2array(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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file2list
public static final java.util.List<java.lang.String> file2list(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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file2set
public static final java.util.SortedSet<java.lang.String> file2set(java.io.File file) throws java.io.IOException
- Throws:
java.io.IOException
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getCurrentDateTime
public static final java.lang.String getCurrentDateTime()
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getFileSeparator
public static final java.lang.String getFileSeparator()
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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
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getForesterLibraryInformation
public static final java.lang.String getForesterLibraryInformation()
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getLineSeparator
public static final java.lang.String getLineSeparator()
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guessMolecularSequenceType
public static final MolecularSequence.TYPE guessMolecularSequenceType(java.lang.String mol_seq)
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increaseCountingMap
public static final void increaseCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map, java.lang.String item_name)
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isEmpty
public static final boolean isEmpty(java.util.List<?> l)
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isEmpty
public static final boolean isEmpty(java.util.Set<?> s)
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isEmpty
public static final boolean isEmpty(java.lang.String s)
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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:
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isEqual
public static final boolean isEqual(double a, double b)
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isEven
public static final boolean isEven(int n)
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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
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isLargerOrEqualToZero
public static final double isLargerOrEqualToZero(double d)
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isMac
public static final boolean isMac()
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isNull
public static final boolean isNull(java.math.BigDecimal s)
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isReadableFile
public static final java.lang.String isReadableFile(java.io.File f)
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isReadableFile
public static final java.lang.String isReadableFile(java.lang.String s)
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isWindows
public static final boolean isWindows()
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isWritableFile
public static final java.lang.String isWritableFile(java.io.File f)
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limitRangeForColor
public static final int limitRangeForColor(int i)
Helper for method "stringToColor".(Last modified: 12/20/03)
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listToSortedCountsMap
public static final java.util.SortedMap<java.lang.Object,java.lang.Integer> listToSortedCountsMap(java.util.List<?> list)
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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
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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
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mapToStringBuffer
public static final java.lang.StringBuffer mapToStringBuffer(java.util.Map<java.lang.Object,java.lang.Object> map, java.lang.String key_value_separator)
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normalizeString
public static final java.lang.String normalizeString(java.lang.String s, int length, boolean left_pad, char pad_char)
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obtainColorDependingOnTaxonomyGroup
public static final java.awt.Color obtainColorDependingOnTaxonomyGroup(java.lang.String tax_group)
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obtainNormalizedTaxonomyGroup
public static final java.lang.String obtainNormalizedTaxonomyGroup(java.lang.String tax)
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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
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outOfMemoryError
public static final void outOfMemoryError(java.lang.OutOfMemoryError e)
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pad
public static final java.lang.StringBuffer pad(double number, int size, char pad, boolean left_pad)
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pad
public static final java.lang.StringBuffer pad(java.lang.String string, int size, char pad, boolean left_pad)
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pad
public static final java.lang.StringBuffer pad(java.lang.StringBuffer string, int size, char pad, boolean left_pad)
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parseDouble
public static final double parseDouble(java.lang.String str) throws java.text.ParseException
- Throws:
java.text.ParseException
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parseInt
public static final int parseInt(java.lang.String str) throws java.text.ParseException
- Throws:
java.text.ParseException
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printArray
public static final void printArray(java.lang.Object[] a)
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printCountingMap
public static final void printCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map)
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printErrorMessage
public static final void printErrorMessage(java.lang.String prg_name, java.lang.String message)
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printProgramInformation
public static final void printProgramInformation(java.lang.String prg_name, java.lang.String prg_version, java.lang.String date)
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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)
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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)
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printWarningMessage
public static final void printWarningMessage(java.lang.String prg_name, java.lang.String message)
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programMessage
public static final void programMessage(java.lang.String prg_name, java.lang.String message)
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readUrl
public static java.util.List<java.lang.String> readUrl(java.lang.String url_str) throws java.io.IOException
- Throws:
java.io.IOException
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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 supportprotein
-- Returns:
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removeSuffix
public static final java.lang.String removeSuffix(java.lang.String file_name)
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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
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replaceIllegalNhxCharacters
public static final java.lang.String replaceIllegalNhxCharacters(java.lang.String nhx)
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round
public static final double round(double value, int decimal_place)
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roundToInt
public static final int roundToInt(double d)
Rounds d to an int.
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roundToInt
public static final int roundToInt(float f)
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roundToShort
public static final short roundToShort(double d)
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sanitizeString
public static final java.lang.String sanitizeString(java.lang.String s)
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santitizeStringForNH
public static final java.lang.StringBuilder santitizeStringForNH(java.lang.String data)
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seqIsLikelyToBeAa
public static boolean seqIsLikelyToBeAa(java.lang.String s)
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stringArrayToString
public static final java.lang.String stringArrayToString(java.lang.String[] a)
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stringArrayToString
public static final java.lang.String stringArrayToString(java.lang.String[] a, java.lang.String separator)
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stringListToArray
public static final java.lang.String[] stringListToArray(java.util.List<java.lang.String> list)
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stringListToString
public static final java.lang.String stringListToString(java.util.List<java.lang.String> l, java.lang.String separator)
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stringSetToArray
public static final java.lang.String[] stringSetToArray(java.util.Set<java.lang.String> strings)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.Error e)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.Exception e)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.String message)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.Exception e)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.String message)
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unexpectedFatalError
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.String message, java.lang.Exception e)
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updateProgress
public static final void updateProgress(double progress_percentage)
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updateProgress
public static final void updateProgress(int i, java.text.DecimalFormat f)
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wordWrap
public static final java.lang.String wordWrap(java.lang.String str, int width)
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