public final class ForesterUtil
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
ForesterUtil.PhylogenyNodeField |
Modifier and Type | Field and 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.math.BigDecimal |
NULL_BD |
static java.lang.String |
OS_ARCH |
static java.lang.String |
OS_NAME |
static java.lang.String |
OS_VERSION |
static double |
ZERO_DIFF |
Modifier and Type | Method and Description |
---|---|
static void |
appendSeparatorIfNotEmpty(java.lang.StringBuffer sb,
char separator) |
static java.awt.Color |
calcColor(double value,
double min,
double max,
java.awt.Color minColor,
java.awt.Color maxColor)
This calculates a color.
|
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.lang.String |
collapseWhiteSpace(java.lang.String s) |
static java.lang.String |
colorToHex(java.awt.Color color) |
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 java.io.File |
createFileForWriting(java.lang.String name) |
static PhylogenyParser |
createParserDependingFileContents(java.io.File file,
boolean phyloxml_validate_against_xsd) |
static PhylogenyParser |
createParserDependingOnFileType(java.io.File file,
boolean phyloxml_validate_against_xsd) |
static PhylogenyParser |
createParserDependingOnSuffix(java.lang.String filename,
boolean phyloxml_validate_against_xsd)
Return null if it can not guess the parser to use based on name suffix.
|
static PhylogenyParser |
createParserDependingOnUrlContents(java.net.URL url,
boolean phyloxml_validate_against_xsd) |
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 prg_name,
java.lang.String message) |
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 |
getLineSeparator() |
static java.util.Hashtable<java.lang.String,java.lang.Boolean> |
getPropertyRefs(Phylogeny phylogeny)
Returns all custom data tag names of this Phylogeny as Hashtable.
|
static void |
increaseCountingMap(java.util.Map<java.lang.String,java.lang.Integer> counting_map,
java.lang.String item_name) |
static boolean |
isAllNonEmptyInternalLabelsArePositiveNumbers(Phylogeny phy) |
static boolean |
isEmpty(java.lang.String s) |
static boolean |
isEqual(double a,
double b) |
static boolean |
isEven(int n) |
static boolean |
isHasAtLeastNodeWithEvent(Phylogeny phy) |
static boolean |
isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)
Returns true if at least one branch has a length larger than zero.
|
static boolean |
isHasAtLeastOneBranchWithSupportValues(Phylogeny phy) |
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 |
isNull(java.math.BigDecimal s) |
static java.lang.String |
isReadableFile(java.io.File f) |
static java.lang.String |
isReadableFile(java.lang.String s) |
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 java.lang.StringBuffer |
mapToStringBuffer(java.util.Map 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.io.BufferedReader |
obtainReader(java.lang.Object source) |
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 |
postOrderRelabelInternalNodes(Phylogeny phylogeny,
int starting_number) |
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 |
printWarningMessage(java.lang.String prg_name,
java.lang.String message) |
static void |
programMessage(java.lang.String prg_name,
java.lang.String message) |
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 |
replaceIllegalNhCharacters(java.lang.String nh) |
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 java.lang.String |
sanitizeString(java.lang.String s) |
static java.lang.String |
stringArrayToString(java.lang.String[] a) |
static void |
transferInternalNamesToBootstrapSupport(Phylogeny phy) |
static void |
transferInternalNodeNamesToConfidence(Phylogeny phy) |
static void |
transferNodeNameToField(Phylogeny phy,
ForesterUtil.PhylogenyNodeField field) |
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 java.lang.String |
wordWrap(java.lang.String str,
int width) |
public static final java.lang.String FILE_SEPARATOR
public static final java.lang.String LINE_SEPARATOR
public static final java.lang.String JAVA_VENDOR
public static final java.lang.String JAVA_VERSION
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 double ZERO_DIFF
public static final java.math.BigDecimal NULL_BD
public static final java.text.NumberFormat FORMATTER_9
public static final java.text.NumberFormat FORMATTER_6
public static final java.text.NumberFormat FORMATTER_06
public static final java.text.NumberFormat FORMATTER_3
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 final java.lang.String collapseWhiteSpace(java.lang.String s)
public static final java.lang.String colorToHex(java.awt.Color color)
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 java.io.File createFileForWriting(java.lang.String name) throws java.io.IOException
java.io.IOException
public static final PhylogenyParser createParserDependingFileContents(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnFileType(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnSuffix(java.lang.String filename, boolean phyloxml_validate_against_xsd)
filename
- public static final PhylogenyParser createParserDependingOnUrlContents(java.net.URL url, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
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 prg_name, java.lang.String message)
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 getLineSeparator()
public static final java.util.Hashtable<java.lang.String,java.lang.Boolean> getPropertyRefs(Phylogeny phylogeny)
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 isAllNonEmptyInternalLabelsArePositiveNumbers(Phylogeny phy)
public static final boolean isEmpty(java.lang.String s)
public static final boolean isEqual(double a, double b)
public static final boolean isEven(int n)
public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)
public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)
phy
- public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
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 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 java.lang.String isWritableFile(java.io.File f)
public static final java.lang.String wordWrap(java.lang.String str, int width)
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 java.lang.StringBuffer mapToStringBuffer(java.util.Map 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.io.BufferedReader obtainReader(java.lang.Object source) throws java.io.IOException, java.io.FileNotFoundException
java.io.IOException
java.io.FileNotFoundException
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 postOrderRelabelInternalNodes(Phylogeny phylogeny, int starting_number)
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 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 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 replaceIllegalNhCharacters(java.lang.String nh)
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 java.lang.String sanitizeString(java.lang.String s)
public static final java.lang.String stringArrayToString(java.lang.String[] a)
public static final void transferInternalNamesToBootstrapSupport(Phylogeny phy)
public static final void transferInternalNodeNamesToConfidence(Phylogeny phy)
public static final void transferNodeNameToField(Phylogeny phy, ForesterUtil.PhylogenyNodeField field)
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)