public final class ForesterUtil
extends java.lang.Object
Modifier and Type | Field | Description |
---|---|---|
static java.lang.String |
FILE_SEPARATOR |
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static java.text.NumberFormat |
FORMATTER_06 |
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static java.text.NumberFormat |
FORMATTER_3 |
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static java.text.NumberFormat |
FORMATTER_6 |
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static java.text.NumberFormat |
FORMATTER_9 |
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static java.lang.String |
JAVA_VENDOR |
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static java.lang.String |
JAVA_VERSION |
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static java.lang.String |
LINE_SEPARATOR |
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static java.lang.String |
NCBI_GI |
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static java.lang.String |
NCBI_NUCCORE |
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static java.lang.String |
NCBI_PROTEIN |
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static java.math.BigDecimal |
NULL_BD |
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static java.lang.String |
OS_ARCH |
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static java.lang.String |
OS_NAME |
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static java.lang.String |
OS_VERSION |
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static java.lang.String |
PDB |
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static java.lang.String |
UNIPROT_KB |
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static double |
ZERO_DIFF |
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) |
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static java.lang.String |
collapseWhiteSpace(java.lang.String s) |
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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) |
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static void |
copyFile(java.io.File in,
java.io.File out) |
|
static int |
countChars(java.lang.String str,
char c) |
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static java.io.BufferedWriter |
createBufferedWriter(java.io.File file) |
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static java.io.BufferedWriter |
createBufferedWriter(java.lang.String name) |
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static EasyWriter |
createEasyWriter(java.io.File file) |
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static java.io.BufferedWriter |
createEasyWriter(java.lang.String name) |
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static java.io.File |
createFileForWriting(java.lang.String name) |
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static void |
ensurePresenceOfDate(PhylogenyNode node) |
|
static void |
ensurePresenceOfDistribution(PhylogenyNode node) |
|
static void |
ensurePresenceOfSequence(PhylogenyNode node) |
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static void |
ensurePresenceOfTaxonomy(PhylogenyNode node) |
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static void |
fatalError(java.lang.String message) |
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static void |
fatalError(java.lang.String prg_name,
java.lang.String message) |
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static void |
fatalErrorIfFileNotReadable(java.io.File file) |
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static void |
fatalErrorIfFileNotReadable(java.lang.String prg_name,
java.io.File file) |
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static java.lang.String[][] |
file22dArray(java.io.File file) |
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static java.lang.String[] |
file2array(java.io.File file) |
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static java.util.List<java.lang.String> |
file2list(java.io.File file) |
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static java.util.SortedSet<java.lang.String> |
file2set(java.io.File file) |
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static java.lang.String |
getCurrentDateTime() |
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static java.lang.String |
getFileSeparator() |
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static java.lang.String |
getFirstLine(java.lang.Object source) |
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static java.lang.String |
getForesterLibraryInformation() |
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static java.lang.String |
getLineSeparator() |
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static MolecularSequence.TYPE |
guessMolecularSequenceType(java.lang.String mol_seq) |
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static void |
increaseCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map,
java.lang.String item_name) |
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static boolean |
isEmpty(java.lang.String s) |
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static boolean |
isEmpty(java.util.List<?> l) |
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static boolean |
isEmpty(java.util.Set<?> s) |
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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.
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static boolean |
isEqual(double a,
double b) |
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static boolean |
isEven(int n) |
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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).
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static double |
isLargerOrEqualToZero(double d) |
|
static boolean |
isMac() |
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static boolean |
isNull(java.math.BigDecimal s) |
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static java.lang.String |
isReadableFile(java.io.File f) |
|
static java.lang.String |
isReadableFile(java.lang.String s) |
|
static boolean |
isWindows() |
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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) |
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static java.lang.String |
normalizeString(java.lang.String s,
int length,
boolean left_pad,
char pad_char) |
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static java.awt.Color |
obtainColorDependingOnTaxonomyGroup(java.lang.String tax_group) |
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static java.lang.String |
obtainNormalizedTaxonomyGroup(java.lang.String tax) |
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static java.io.BufferedReader |
obtainReader(java.lang.Object source) |
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static void |
outOfMemoryError(java.lang.OutOfMemoryError e) |
|
static java.lang.StringBuffer |
pad(double number,
int size,
char pad,
boolean left_pad) |
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static java.lang.StringBuffer |
pad(java.lang.StringBuffer string,
int size,
char pad,
boolean left_pad) |
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static java.lang.StringBuffer |
pad(java.lang.String string,
int size,
char pad,
boolean left_pad) |
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static double |
parseDouble(java.lang.String str) |
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static int |
parseInt(java.lang.String str) |
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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) |
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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) |
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static java.lang.String |
sanitizeString(java.lang.String s) |
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static java.lang.StringBuilder |
santitizeStringForNH(java.lang.String data) |
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static boolean |
seqIsLikelyToBeAa(java.lang.String s) |
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static java.lang.String |
stringArrayToString(java.lang.String[] a) |
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static java.lang.String |
stringArrayToString(java.lang.String[] a,
java.lang.String separator) |
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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) |
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static java.lang.String[] |
stringSetToArray(java.util.Set<java.lang.String> strings) |
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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) |
public static final java.lang.String FILE_SEPARATOR
public static final java.text.NumberFormat FORMATTER_06
public static final java.text.NumberFormat FORMATTER_3
public static final java.text.NumberFormat FORMATTER_6
public static final java.text.NumberFormat FORMATTER_9
public static final java.lang.String JAVA_VENDOR
public static final java.lang.String JAVA_VERSION
public static final java.lang.String LINE_SEPARATOR
public static final java.lang.String NCBI_GI
public static final java.lang.String NCBI_NUCCORE
public static final java.lang.String NCBI_PROTEIN
public static final java.math.BigDecimal NULL_BD
public static final java.lang.String OS_ARCH
public static final java.lang.String OS_NAME
public static final java.lang.String OS_VERSION
public static final java.lang.String PDB
public static final java.lang.String UNIPROT_KB
public static final double ZERO_DIFF
public static final void appendSeparatorIfNotEmpty(java.lang.StringBuffer sb, char separator)
public static final java.awt.Color calcColor(double value, double min, double max, java.awt.Color minColor, java.awt.Color maxColor)
value
- the valuemin
- the smallest valuemax
- the largest valueminColor
- the color for minmaxColor
- the color for maxpublic 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)
value
- the valuemin
- the smallest valuemax
- the largest valuemean
- the mean/median valueminColor
- the color for minmaxColor
- the color for maxmeanColor
- the color for meanpublic static int calculateOverlap(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
public static final java.lang.String collapseWhiteSpace(java.lang.String s)
public static final void collection2file(java.io.File file, java.util.Collection<?> data, java.lang.String separator) throws java.io.IOException
java.io.IOException
public static final void collection2writer(java.io.Writer writer, java.util.Collection<?> data, java.lang.String separator) throws java.io.IOException
java.io.IOException
public static final java.lang.String colorToHex(java.awt.Color color)
public static void copyFile(java.io.File in, java.io.File out) throws java.io.IOException
java.io.IOException
public static final int countChars(java.lang.String str, char c)
public static final java.io.BufferedWriter createBufferedWriter(java.io.File file) throws java.io.IOException
java.io.IOException
public static final java.io.BufferedWriter createBufferedWriter(java.lang.String name) throws java.io.IOException
java.io.IOException
public static final EasyWriter createEasyWriter(java.io.File file) throws java.io.IOException
java.io.IOException
public static final java.io.BufferedWriter createEasyWriter(java.lang.String name) throws java.io.IOException
java.io.IOException
public static final java.io.File createFileForWriting(java.lang.String name) throws java.io.IOException
java.io.IOException
public static final void ensurePresenceOfDate(PhylogenyNode node)
public static final void ensurePresenceOfDistribution(PhylogenyNode node)
public static void ensurePresenceOfSequence(PhylogenyNode node)
public static void ensurePresenceOfTaxonomy(PhylogenyNode node)
public static void fatalError(java.lang.String message)
public static void fatalError(java.lang.String prg_name, java.lang.String message)
public static void fatalErrorIfFileNotReadable(java.io.File file)
public static void fatalErrorIfFileNotReadable(java.lang.String prg_name, java.io.File file)
public static java.lang.String[][] file22dArray(java.io.File file) throws java.io.IOException
java.io.IOException
public static java.lang.String[] file2array(java.io.File file) throws java.io.IOException
java.io.IOException
public static final java.util.List<java.lang.String> file2list(java.io.File file) throws java.io.IOException
java.io.IOException
public static final java.util.SortedSet<java.lang.String> file2set(java.io.File file) throws java.io.IOException
java.io.IOException
public static final java.lang.String getCurrentDateTime()
public static final java.lang.String getFileSeparator()
public static final java.lang.String getFirstLine(java.lang.Object source) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final java.lang.String getForesterLibraryInformation()
public static final java.lang.String getLineSeparator()
public static final MolecularSequence.TYPE guessMolecularSequenceType(java.lang.String mol_seq)
public static final void increaseCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map, java.lang.String item_name)
public static final boolean isEmpty(java.util.List<?> l)
public static final boolean isEmpty(java.util.Set<?> s)
public static final boolean isEmpty(java.lang.String s)
public static boolean isEngulfed(Domain domain, java.util.List<java.lang.Boolean> covered_positions)
domain
- covered_positions
- public static final boolean isEqual(double a, double b)
public static final boolean isEven(int n)
public static final boolean isIntersecting(java.lang.String[] a, java.lang.String[] b)
a
- a String[] b a String[]public static final double isLargerOrEqualToZero(double d)
public static final boolean isMac()
public static final boolean isNull(java.math.BigDecimal s)
public static final java.lang.String isReadableFile(java.io.File f)
public static final java.lang.String isReadableFile(java.lang.String s)
public static final boolean isWindows()
public static final java.lang.String isWritableFile(java.io.File f)
public static final int limitRangeForColor(int i)
(Last modified: 12/20/03)
public static final java.util.SortedMap<java.lang.Object,java.lang.Integer> listToSortedCountsMap(java.util.List<?> list)
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
java.io.IOException
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
java.io.IOException
public static final java.lang.StringBuffer mapToStringBuffer(java.util.Map<java.lang.Object,java.lang.Object> map, java.lang.String key_value_separator)
public static final java.lang.String normalizeString(java.lang.String s, int length, boolean left_pad, char pad_char)
public static final java.awt.Color obtainColorDependingOnTaxonomyGroup(java.lang.String tax_group)
public static final java.lang.String obtainNormalizedTaxonomyGroup(java.lang.String tax)
public static final java.io.BufferedReader obtainReader(java.lang.Object source) throws java.io.IOException, java.io.FileNotFoundException
java.io.IOException
java.io.FileNotFoundException
public static final void outOfMemoryError(java.lang.OutOfMemoryError e)
public static final java.lang.StringBuffer pad(double number, int size, char pad, boolean left_pad)
public static final java.lang.StringBuffer pad(java.lang.String string, int size, char pad, boolean left_pad)
public static final java.lang.StringBuffer pad(java.lang.StringBuffer string, int size, char pad, boolean left_pad)
public static final double parseDouble(java.lang.String str) throws java.text.ParseException
java.text.ParseException
public static final int parseInt(java.lang.String str) throws java.text.ParseException
java.text.ParseException
public static final void printArray(java.lang.Object[] a)
public static final void printCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map)
public static final void printErrorMessage(java.lang.String prg_name, java.lang.String message)
public static final void printProgramInformation(java.lang.String prg_name, java.lang.String prg_version, java.lang.String date)
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)
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)
public static final void printWarningMessage(java.lang.String prg_name, java.lang.String message)
public static final void programMessage(java.lang.String prg_name, java.lang.String message)
public static java.util.List<java.lang.String> readUrl(java.lang.String url_str) throws java.io.IOException
java.io.IOException
public static Protein removeOverlappingDomains(int max_allowed_overlap, boolean remove_engulfed_domains, Protein protein)
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
- public static final java.lang.String removeSuffix(java.lang.String file_name)
public static final java.lang.String removeWhiteSpace(java.lang.String s)
public static final java.lang.String replaceIllegalNhxCharacters(java.lang.String nhx)
public static final double round(double value, int decimal_place)
public static final int roundToInt(double d)
public static final int roundToInt(float f)
public static final short roundToShort(double d)
public static final java.lang.String sanitizeString(java.lang.String s)
public static final java.lang.StringBuilder santitizeStringForNH(java.lang.String data)
public static boolean seqIsLikelyToBeAa(java.lang.String s)
public static final java.lang.String stringArrayToString(java.lang.String[] a)
public static final java.lang.String stringArrayToString(java.lang.String[] a, java.lang.String separator)
public static final java.lang.String[] stringListToArray(java.util.List<java.lang.String> list)
public static final java.lang.String stringListToString(java.util.List<java.lang.String> l, java.lang.String separator)
public static final java.lang.String[] stringSetToArray(java.util.Set<java.lang.String> strings)
public static final void unexpectedFatalError(java.lang.Error e)
public static final void unexpectedFatalError(java.lang.Exception e)
public static final void unexpectedFatalError(java.lang.String message)
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.Exception e)
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.String message)
public static final void unexpectedFatalError(java.lang.String prg_name, java.lang.String message, java.lang.Exception e)
public static final void updateProgress(double progress_percentage)
public static final void updateProgress(int i, java.text.DecimalFormat f)
public static final java.lang.String wordWrap(java.lang.String str, int width)