Index (GBIF Common 1.0-SNAPSHOT API)

A B C D E F G H I J L M N O P Q R S T U W Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

add(T) - Method in class org.gbif.utils.collection.CompactHashSet: Adds the specified element to this set if it is not already present.
AnnotationUtils - Class in org.gbif.utils: Utility method to work with annotations.
arrayMerge(byte[]...) - Static method in class org.gbif.utils.collection.ArrayUtils
arrayMerge(T[]...) - Static method in class org.gbif.utils.collection.ArrayUtils
ArrayUtils - Class in org.gbif.utils.collection
authorityUrl(String) - Static method in class org.gbif.utils.rs.RsGbifOrg

B

BigDecimalUtils - Class in org.gbif.utils.number: Utility class to work with BigDecimal.
BomSafeInputStreamWrapper - Class in org.gbif.utils.file: Deprecated.
use org.apache.commons.io.input.BOMInputStream instead
BomSafeInputStreamWrapper(InputStream) - Constructor for class org.gbif.utils.file.BomSafeInputStreamWrapper: Deprecated.
build(File) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Assumes 1 header row
build(File, Integer) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Build a CSVReader and try to detect the encoding, delimiter and quotes.
build(File, String, boolean) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Build a CSVReader with specific delimiter and presence or not of a header line.
build(File, String, String, Character, Integer) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Build a CSVReader with specific encoding, delimiter, quotes character and number of header row(s).
build(File, String, String, Integer) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Build a CSVReader with specific encoding, delimiter and number of header row(s) but default quote character (quotation marks)
build(InputStream, String, String, Character, Integer) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Build a CSVReader with specific encoding, delimiter quotes and number of header row(s)
buildTabReader(InputStream, String, Integer) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory
buildUtf8TabReader(InputStream) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory
byteArrayToInt(byte[]) - Static method in class org.gbif.utils.collection.ArrayUtils
bytes(long) - Static method in class org.gbif.utils.HumanSize

C

CharsetDetection - Class in org.gbif.utils.file: Utility class to guess the encoding of a given file or byte array.
checkArgument(boolean) - Static method in class org.gbif.utils.PreconditionUtils: Ensures the truth of an expression involving one or more parameters to the calling method.
checkArgument(boolean, Object) - Static method in class org.gbif.utils.PreconditionUtils: Ensures the truth of an expression involving one or more parameters to the calling method.
checkState(boolean) - Static method in class org.gbif.utils.PreconditionUtils: Ensures the truth of an expression involving the state of the calling instance, but not involving any parameters to the calling method.
checkState(boolean, Object) - Static method in class org.gbif.utils.PreconditionUtils: Ensures the truth of an expression involving the state of the calling instance, but not involving any parameters to the calling method.
classpath2Filepath(String) - Static method in class org.gbif.utils.file.FileUtils
classpathStream(String) - Static method in class org.gbif.utils.file.FileUtils
classpathStream(String) - Method in class org.gbif.utils.file.InputStreamUtils
clear() - Method in class org.gbif.utils.collection.CompactHashSet: Removes all of the elements from this set.
ClosableIterator<T> - Interface in org.gbif.utils.file: An iterator that needs to be explicitly closed when it is not used anymore.
ClosableReportingIterator<T> - Interface in org.gbif.utils.file: Interface that extends the ClosableIterator providing a means to check if there is an error, log what it is, store the actual Exception, and skip over it to continue reading.
close() - Method in class org.gbif.utils.file.csv.CSVReader
coalesce(Iterable<T>) - Static method in class org.gbif.utils.ObjectUtils
coalesce(T...) - Static method in class org.gbif.utils.ObjectUtils: Returns the first of the given parameters that is not null.
columnsToSet(InputStream, int...) - Static method in class org.gbif.utils.file.FileUtils
columnsToSet(InputStream, Set<String>, int...) - Static method in class org.gbif.utils.file.FileUtils: Reads a file and returns a unique set of multiple columns from lines which are no comments (starting with #) and trims whitespace.
CompactHashSet<T> - Class in org.gbif.utils.collection: A HashSet implementation taken from Ontopia which is both faster and more compact than java.util.HashSet
CompactHashSet() - Constructor for class org.gbif.utils.collection.CompactHashSet: Constructs a new, empty set.
CompactHashSet(int) - Constructor for class org.gbif.utils.collection.CompactHashSet: Constructs a new, empty set.
CompactHashSet(Collection) - Constructor for class org.gbif.utils.collection.CompactHashSet: Constructs a new set containing the elements in the specified collection.
compare(String, String) - Method in class org.gbif.utils.text.LineComparator
compare(String, String) - Method in class org.gbif.utils.text.StringComparator
compare(String, String) - Method in class org.gbif.utils.text.StringLengthComparator
CompressionUtil - Class in org.gbif.utils.file
CompressionUtil.UnsupportedCompressionType - Exception in org.gbif.utils.file
contains(Object) - Method in class org.gbif.utils.collection.CompactHashSet: Returns true if this set contains the specified element.
copy(File, String, boolean, String...) - Static method in class org.gbif.utils.file.ResourcesUtil: Copies classpath resources to real files.
copyStreams(InputStream, OutputStream) - Static method in class org.gbif.utils.file.FileUtils
copyStreamToFile(InputStream, File) - Static method in class org.gbif.utils.file.FileUtils
createParentDirs(File) - Static method in class org.gbif.utils.file.FileUtils: Creates any necessary but nonexistent parent directories of the specified file.
createTempDir() - Static method in class org.gbif.utils.file.FileUtils
createTempDir(String, String) - Static method in class org.gbif.utils.file.FileUtils
CSVMetadata() - Constructor for class org.gbif.utils.file.csv.CSVReaderFactory.CSVMetadata
CSVReader - Class in org.gbif.utils.file.csv
CSVReader(File, String, String, Character, Integer) - Constructor for class org.gbif.utils.file.csv.CSVReader
CSVReader(InputStream, String, String, Character, Integer) - Constructor for class org.gbif.utils.file.csv.CSVReader
CSVReader(InputStream, String, String, Character, Integer, int) - Constructor for class org.gbif.utils.file.csv.CSVReader
CSVReaderFactory - Class in org.gbif.utils.file.csv
CSVReaderFactory() - Constructor for class org.gbif.utils.file.csv.CSVReaderFactory
CSVReaderFactory.CSVMetadata - Class in org.gbif.utils.file.csv: Data about the CSV file
currLineNumber() - Method in class org.gbif.utils.file.csv.CSVReader

D

decodeUtf8Garbage(String) - Static method in class org.gbif.utils.text.StringUtils: Tries to decode a UTF8 string only if common UTF8 character combinations are found which are unlikely to be correctly encoded text.
decompressFile(File) - Static method in class org.gbif.utils.file.CompressionUtil: Tries to decompress a file into a newly created temporary directory, trying gzip or zip regardless of the filename or its suffix.
decompressFile(File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Defaults keeping subDirectories to false.
decompressFile(File, File, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Defaults keeping subDirectories to false and unzipped file name to null.
decompressFile(File, File, String) - Static method in class org.gbif.utils.file.CompressionUtil: Defaults keeping subDirectories to false, but provides unzipped file name.
decompressFile(File, File, String, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Tries to decompress a file using TAR+gzip, gzip, TAR or Zip regardless of the filename or its suffix.
deleteDirectoryRecursively(File) - Static method in class org.gbif.utils.file.FileUtils: Delete directory recursively, including all its files, sub-folders, and sub-folder's files.
deleteWhitespace(String) - Static method in class org.gbif.utils.text.StringUtils: Removes all whitespace characters from the String.
delimiter - Variable in class org.gbif.utils.file.csv.CSVReader
detectEncoding() - Method in class org.gbif.utils.file.CharsetDetection: Guess the encoding of the provided buffer.
detectEncoding(File) - Static method in class org.gbif.utils.file.CharsetDetection
detectEncoding(File, int) - Static method in class org.gbif.utils.file.CharsetDetection
dictionaryUrl(String) - Static method in class org.gbif.utils.rs.RsGbifOrg
DirectExecutor - Class in org.gbif.utils.concurrent: Executor that runs tasks syncroneously and immediately.
DirectExecutor() - Constructor for class org.gbif.utils.concurrent.DirectExecutor
DOMAIN - Static variable in class org.gbif.utils.rs.RsGbifOrg
dump() - Method in class org.gbif.utils.collection.CompactHashSet: INTERNAL: Used for debugging only.

E

email - Variable in class org.gbif.utils.text.EmailUtils.EmailWithName
EmailUtils - Class in org.gbif.utils.text
EmailUtils.EmailWithName - Class in org.gbif.utils.text
EmailWithName() - Constructor for class org.gbif.utils.text.EmailUtils.EmailWithName
emptyLowerCase(String) - Static method in class org.gbif.utils.text.StringUtils: Returns an empty string or the trimmed lower case version of any input, but never NULL.
encoding - Variable in class org.gbif.utils.file.csv.CSVReader
escapeFilename(String) - Static method in class org.gbif.utils.file.FileUtils: Escapes a filename so it is a valid filename on all systems, replacing /.
execute(Runnable) - Method in class org.gbif.utils.concurrent.DirectExecutor
ExecutorUtils - Class in org.gbif.utils.concurrent
ExecutorUtils() - Constructor for class org.gbif.utils.concurrent.ExecutorUtils
extractCsvMetadata(File, String) - Static method in class org.gbif.utils.file.csv.CSVReaderFactory: Replaced by TabularFileMetadataExtractor Extract metadata from a CSV file.
extractTabularFileMetadata(Path) - Static method in class org.gbif.utils.file.tabular.TabularFileMetadataExtractor: Extract metadata from a tabular file using a sample (defined by TabularFileMetadataExtractor.MAX_SAMPLE_SIZE) of the file.

F

FILENAME_AUTHORS - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_BLACKLIST - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_EPITHETA - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_EPITHETA_AMIGOUS - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_GENERA - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_GENERA_AMIGOUS - Static variable in class org.gbif.utils.rs.RsGbifOrg
FILENAME_SUPRAGENERIC - Static variable in class org.gbif.utils.rs.RsGbifOrg
FileSplitter - Class in org.gbif.utils.file: A utility to split files into chucks.
FileUtils - Class in org.gbif.utils.file: Collection of file utils.
FileUtils() - Constructor for class org.gbif.utils.file.FileUtils
filterProperties(Properties, String) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Filters and translates Properties with a prefix.
foldToAscii(String) - Static method in class org.gbif.utils.text.StringUtils: Removes accents & diacretics and converts ligatures into several chars
fromDouble(Double, boolean) - Static method in class org.gbif.utils.number.BigDecimalUtils: Convert a double to a BigDecimal.

G

getClasspathFile(String) - Static method in class org.gbif.utils.file.FileUtils
getColumnComparator() - Method in class org.gbif.utils.text.LineComparator
getDefaultSystemCharset() - Static method in class org.gbif.utils.file.CharsetDetection: Retrieve the default charset of the system.
getDelimiter() - Method in class org.gbif.utils.file.csv.CSVReaderFactory.CSVMetadata
getDelimiter() - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
getDelimiterChar(List<String>) - Static method in class org.gbif.utils.file.tabular.TabularFileMetadataExtractor: Given a sample of line, this method tries to determine the delimiter char used.
getEmptyLines() - Method in class org.gbif.utils.file.csv.CSVReader
getEncoding() - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
getErrorMessage() - Method in interface org.gbif.utils.file.ClosableReportingIterator: Return an informative message about the error encountered while iterating over row.
getErrorMessage() - Method in class org.gbif.utils.file.csv.CSVReader
getException() - Method in interface org.gbif.utils.file.ClosableReportingIterator: Return the Exception encountered while iterating over row.
getException() - Method in class org.gbif.utils.file.csv.CSVReader
getFileExtension(String) - Static method in class org.gbif.utils.file.FileUtils: Returns the file extension for the given file name, or the empty string if the file has no extension.
getHeader() - Method in class org.gbif.utils.file.csv.CSVReader: Get the header, or null if none
getHeaderLine() - Method in interface org.gbif.utils.file.tabular.TabularDataFileReader: Get the header line of the tabular data file (if possible).
getInputStream(File) - Static method in class org.gbif.utils.file.FileUtils
getInputStreamReader(InputStream) - Static method in class org.gbif.utils.file.FileUtils
getInputStreamReader(InputStream, String) - Static method in class org.gbif.utils.file.FileUtils
getLastRecordLineNumber() - Method in interface org.gbif.utils.file.tabular.TabularDataFileReader: The line number of where the last record returned by TabularDataFileReader.read() starts.
getLastRecordNumber() - Method in interface org.gbif.utils.file.tabular.TabularDataFileReader: Represents the number of record returned by the TabularDataFileReader.read() method.
getLineIterator(InputStream) - Static method in class org.gbif.utils.file.FileUtils
getLineIterator(InputStream, String) - Static method in class org.gbif.utils.file.FileUtils
getLinesPerMemorySort() - Method in class org.gbif.utils.file.FileUtils
getOrDefault(Map<K, V>, K, V) - Static method in class org.gbif.utils.collection.MapUtils: Returns a maps value or a given default if not present.
getQuotedBy() - Method in class org.gbif.utils.file.csv.CSVReaderFactory.CSVMetadata
getQuotedBy() - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
getReadRows() - Method in class org.gbif.utils.file.csv.CSVReader
getResource(String) - Static method in class org.gbif.utils.file.ResourcesUtil: Returns a URL pointing to resourceName if the resource is found using the context class loader.
getStackTrace(Throwable) - Static method in class org.gbif.utils.text.StringUtils: Reads a stack trace from an exception and returns it as a String.
getUtf8Reader(File) - Static method in class org.gbif.utils.file.FileUtils

H

hasNext() - Method in class org.gbif.utils.file.csv.CSVReader
hasRowError() - Method in interface org.gbif.utils.file.ClosableReportingIterator: Return true if an error was encountered while iterating over row.
hasRowError() - Method in class org.gbif.utils.file.csv.CSVReader
header - Variable in class org.gbif.utils.file.csv.CSVReader
headerRows - Variable in class org.gbif.utils.file.csv.CSVReader
humanReadableByteCount(long, boolean) - Static method in class org.gbif.utils.file.FileUtils: Converts the byte size into human-readable format.
HumanSize - Class in org.gbif.utils
HumanSize() - Constructor for class org.gbif.utils.HumanSize

I

increase(String) - Static method in class org.gbif.utils.text.StringUtils: Increase a given string by 1, i.e.
InputStreamUtils - Class in org.gbif.utils.file
InputStreamUtils() - Constructor for class org.gbif.utils.file.InputStreamUtils
intToByteArray(int) - Static method in class org.gbif.utils.collection.ArrayUtils
isCompressedFile(File) - Static method in class org.gbif.utils.file.FileUtils
isEmpty() - Method in class org.gbif.utils.collection.CompactHashSet: Returns true if this set contains no elements.
isFieldDeprecated(Class<?>, String) - Static method in class org.gbif.utils.AnnotationUtils: Check if a field is annotated with @Deprecated in the provided class.
isGzipFormat(File) - Static method in class org.gbif.utils.file.CompressionUtil: Check the file's first two bytes, to see if they are the gzip magic number.
isTarFormat(File) - Static method in class org.gbif.utils.file.CompressionUtil: Check the file is a Tape ARchive (TAR).
iterable(Iterator<T>) - Static method in class org.gbif.utils.collection.IterableUtils: Converts an interator into an Iterable for one time use only.
IterableUtils - Class in org.gbif.utils.collection
IterableUtils() - Constructor for class org.gbif.utils.collection.IterableUtils
iterator() - Method in class org.gbif.utils.collection.CompactHashSet: Returns an iterator over the elements in this set.

J

joinIfNotNull(String, Object...) - Static method in class org.gbif.utils.text.StringUtils: Joins a list of objects into a string, skipping null values and calling toString on each object.

L

LineComparator - Class in org.gbif.utils.text: A comparator for delimited lines that compares the content of a given column number for all rows.
LineComparator(int, String) - Constructor for class org.gbif.utils.text.LineComparator
LineComparator(int, String, Character) - Constructor for class org.gbif.utils.text.LineComparator
LineComparator(int, String, Character, Comparator<String>) - Constructor for class org.gbif.utils.text.LineComparator
LineComparator(int, String, Comparator<String>) - Constructor for class org.gbif.utils.text.LineComparator
LINNEAN_YEAR - Static variable in class org.gbif.utils.text.StringUtils
list(Class, String) - Static method in class org.gbif.utils.file.ResourcesUtil: List directory contents for a resource folder.
loadProperties(String) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Loads a properties file.

M

MapUtils - Class in org.gbif.utils.collection
mergeSortedFiles(List<File>, Writer, Comparator<String>) - Method in class org.gbif.utils.file.FileUtils: Merges a list of intermediary sort chunk files into a single sorted file.

N

name - Variable in class org.gbif.utils.text.EmailUtils.EmailWithName
NamedThreadFactory - Class in org.gbif.utils.concurrent: Modified Executors DefaultThreadFactory to allow custom named thread pools.
NamedThreadFactory(String) - Constructor for class org.gbif.utils.concurrent.NamedThreadFactory: Creates a new named user thread factory using a normal priority.
NamedThreadFactory(String, int, boolean) - Constructor for class org.gbif.utils.concurrent.NamedThreadFactory: Creates a new named thread factory using explicit priority and daemon settings.
newTabularFileReader(Reader, char, boolean) - Static method in class org.gbif.utils.file.tabular.TabularFiles: Get a new TabularDataFileReader using default quote char (") and default endOfLineSymbols (\n).
newTabularFileReader(Reader, char, String, Character, boolean) - Static method in class org.gbif.utils.file.tabular.TabularFiles: Get a new TabularDataFileReader.
newTabularFileReader(Reader, char, String, Character, boolean, Integer) - Static method in class org.gbif.utils.file.tabular.TabularFiles: Get a new TabularDataFileReader.
newThread(Runnable) - Method in class org.gbif.utils.concurrent.NamedThreadFactory
next() - Method in class org.gbif.utils.file.csv.CSVReader
NORMALIZED_END_OF_LINE - Static variable in class org.gbif.utils.file.tabular.TabularFileNormalizer
normalizeFile(Path, Path, Charset, char, String, Character) - Static method in class org.gbif.utils.file.tabular.TabularFileNormalizer: Normalizes the provided tabular "file" (provided as Reader to let the caller deal with charset).

O

ObjectUtils - Class in org.gbif.utils
org.gbif.utils - package org.gbif.utils
org.gbif.utils.collection - package org.gbif.utils.collection
org.gbif.utils.concurrent - package org.gbif.utils.concurrent
org.gbif.utils.file - package org.gbif.utils.file
org.gbif.utils.file.csv - package org.gbif.utils.file.csv
org.gbif.utils.file.properties - package org.gbif.utils.file.properties
org.gbif.utils.file.tabular - package org.gbif.utils.file.tabular
org.gbif.utils.number - package org.gbif.utils.number
org.gbif.utils.rs - package org.gbif.utils.rs
org.gbif.utils.text - package org.gbif.utils.text

P

parseBoolean(String) - Static method in class org.gbif.utils.text.StringUtils: Simple boolean parsing method that understands yes,y,true,t or 1 as true and respective values for false.
parseEmail(String) - Static method in class org.gbif.utils.text.EmailUtils
parseInteger(String) - Static method in class org.gbif.utils.text.StringUtils: Simple integer parsing method that does not throw any exception but returns null instead.
PreconditionUtils - Class in org.gbif.utils
PropertiesUtil - Class in org.gbif.utils.file.properties: Utility class for handling properties files.
propertyAsBool(Properties, String, boolean) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads and casts the named property as a boolean.
propertyAsDouble(Properties, String, boolean, Double) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads and casts the named property as an Double.
propertyAsFloat(Properties, String, boolean, Float) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads and casts the named property as an Float.
propertyAsInt(Properties, String, boolean, Integer) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads and casts the named property as an Integer.
propertyAsUTF8Bytes(Properties, String, boolean, byte[]) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads and converts the named property as UTF8 bytes.

Q

quoteChar - Variable in class org.gbif.utils.file.csv.CSVReader

R

randomAuthor() - Static method in class org.gbif.utils.text.StringUtils
randomEpithet() - Static method in class org.gbif.utils.text.StringUtils
randomFamily() - Static method in class org.gbif.utils.text.StringUtils
randomGenus() - Static method in class org.gbif.utils.text.StringUtils
randomSpecies() - Static method in class org.gbif.utils.text.StringUtils: Creates a random species binomial with no meaning at all, but highly randomized.
randomSpeciesYear() - Static method in class org.gbif.utils.text.StringUtils
randomString(int) - Static method in class org.gbif.utils.text.StringUtils: Creates a random string in upper case of given length with purely latin characters only.
read() - Method in class org.gbif.utils.file.BomSafeInputStreamWrapper: Deprecated.
read() - Method in interface org.gbif.utils.file.tabular.TabularDataFileReader: Read a non-empty line of the tabular data file.
READ_AHEAD_BYTES - Static variable in class org.gbif.utils.file.FileSplitter
readByteBuffer(File) - Static method in class org.gbif.utils.file.FileUtils: Reads a complete file into a byte buffer.
readByteBuffer(File, int) - Static method in class org.gbif.utils.file.FileUtils: Reads the first bytes of a file into a byte buffer.
readEntireStream(InputStream) - Method in class org.gbif.utils.file.InputStreamUtils: Converts an entire InputStream to a single String with UTF8 as the character encoding.
readEntireStream(InputStream, String) - Method in class org.gbif.utils.file.InputStreamUtils: Converts an entire InputStream to a single String with explicitly provided character encoding.
readFromFile(String) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Reads a property file from an absolute filepath.
remove() - Method in class org.gbif.utils.file.csv.CSVReader
remove(Object) - Method in class org.gbif.utils.collection.CompactHashSet: Removes the specified element from the set.
removeProperties(Properties, String) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Remove properties from the original object and return the removed element(s) as new Properties object.
ResourcesUtil - Class in org.gbif.utils.file: Utils class dealing with classpath resources.
RsGbifOrg - Class in org.gbif.utils.rs: Utility class knowing the url layout of rs.gbif.org to access authority and dictionary files.
RsGbifOrg() - Constructor for class org.gbif.utils.rs.RsGbifOrg

S

scanToChunk(File, long) - Static method in class org.gbif.utils.file.FileSplitter
SEPARATOR - Static variable in class org.gbif.utils.file.FileSplitter
setDelimiter(Character) - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
setDelimiter(String) - Method in class org.gbif.utils.file.csv.CSVReaderFactory.CSVMetadata
setEncoding(Charset) - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
setLinesPerMemorySort(int) - Static method in class org.gbif.utils.file.FileUtils
setQuotedBy(Character) - Method in class org.gbif.utils.file.csv.CSVReaderFactory.CSVMetadata
setQuotedBy(Character) - Method in class org.gbif.utils.file.tabular.TabularFileMetadata
size() - Method in class org.gbif.utils.collection.CompactHashSet: Returns the number of elements in this set (its cardinality).
sort(File, File, String, int, String, Character, String, int) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied delimited line parameters.
sort(File, File, String, int, String, Character, String, int, Comparator<String>, boolean) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied delimited line parameters.
sort(List<File>, File, String, int, String, Character, String, int) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied delimited line parameters.
sort(List<File>, File, String, int, String, Character, String, int, Comparator<String>, boolean) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied delimited line parameters.
sortByValue(Map<K, V>) - Static method in class org.gbif.utils.collection.MapUtils: This orders a Map by its values and returns a new LinkedHashMap which maintains that order.
sortByValue(Map<K, V>, Comparator<V>) - Static method in class org.gbif.utils.collection.MapUtils: Order a Map by its values using the given value comparator and return a new LinkedHashMap which maintains that order.
sortInJava(File, File, String, Comparator<String>, int) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied lineComparator.
sortInJava(List<File>, File, String, Comparator<String>, int) - Method in class org.gbif.utils.file.FileUtils: Sorts the input file into the output file using the supplied lineComparator.
split(File, int, String) - Method in class org.gbif.utils.file.FileUtils: Splits the supplied file into files of set line size and with a suffix.
split(File, File, String, long) - Static method in class org.gbif.utils.file.FileSplitter: Splits a file "pumaConcolor.txt" into the target directory using the suffix ("part") like so: - pumaConcolor_part_0.txt - pumaConcolor_part_1.txt - pumaConcolor_part_2.txt Returns the files parts
startNewUtf8File(File) - Static method in class org.gbif.utils.file.FileUtils
startNewUtf8XmlFile(File) - Static method in class org.gbif.utils.file.FileUtils
stop(ExecutorService) - Static method in class org.gbif.utils.concurrent.ExecutorUtils: Shuts down an executor and waits up to 1 hour for the already submitted jobs to finish.
stop(ExecutorService, int, TimeUnit) - Static method in class org.gbif.utils.concurrent.ExecutorUtils: Shuts down an executor and waits for the job to finish until the given timeout is reached before forcing an immediate shutdown.
streamToList(InputStream) - Static method in class org.gbif.utils.file.FileUtils: Takes a utf8 encoded input stream and reads in every line/row into a list.
streamToList(InputStream, String) - Static method in class org.gbif.utils.file.FileUtils
streamToList(InputStream, List<String>) - Static method in class org.gbif.utils.file.FileUtils: Reads a file and returns a list of all lines which are no comments (starting with #) and trims whitespace.
streamToMap(InputStream) - Static method in class org.gbif.utils.file.FileUtils: Reads a utf8 encoded inut stream, splits
streamToMap(InputStream, int, int, boolean) - Static method in class org.gbif.utils.file.FileUtils
streamToMap(InputStream, Map<String, String>) - Static method in class org.gbif.utils.file.FileUtils: Read a hashmap from a tab delimited utf8 input stream using the row number as an integer value and the entire row as the value.
streamToMap(InputStream, Map<String, String>, int, int, boolean) - Static method in class org.gbif.utils.file.FileUtils: Read a hashmap from a tab delimited utf8 file, ignoring commented rows starting with #.
streamToSet(InputStream) - Static method in class org.gbif.utils.file.FileUtils
streamToSet(InputStream, Set<String>) - Static method in class org.gbif.utils.file.FileUtils: Reads a file and returns a unique set of all lines which are no comments (starting with #) and trims whitespace.
StringComparator - Class in org.gbif.utils.text: A comparator based around Javas String.compareTo().
StringComparator() - Constructor for class org.gbif.utils.text.StringComparator
StringLengthComparator - Class in org.gbif.utils.text
StringLengthComparator() - Constructor for class org.gbif.utils.text.StringLengthComparator
StringUtils - Class in org.gbif.utils.text: Utils class adding specific string methods to existing guava Strings and commons StringUtils.
subsetProperties(Properties, String) - Static method in class org.gbif.utils.file.properties.PropertiesUtil: Returns a new Properties object that contains only the elements where the key starts by the provided prefix.
synonymUrl(String) - Static method in class org.gbif.utils.rs.RsGbifOrg

T

TAB_DELIMITED - Static variable in class org.gbif.utils.file.FileUtils
TabularDataFileReader<T> - Interface in org.gbif.utils.file.tabular: Interface defining a reader for tabular data file (e.g.
TabularFileMetadata - Class in org.gbif.utils.file.tabular: Data about a tabular data file.
TabularFileMetadata() - Constructor for class org.gbif.utils.file.tabular.TabularFileMetadata
TabularFileMetadataExtractor - Class in org.gbif.utils.file.tabular: Utility class to extract metadata TabularFileMetadata from a tabular file.
TabularFileNormalizer - Class in org.gbif.utils.file.tabular: Utility class to rewrite a tabular file (e.g.
TabularFileNormalizer() - Constructor for class org.gbif.utils.file.tabular.TabularFileNormalizer
TabularFiles - Class in org.gbif.utils.file.tabular: Static utility methods related to TabularDataFileReader instances.
TabularFiles() - Constructor for class org.gbif.utils.file.tabular.TabularFiles
thenJoin(Function<String, String>, String...) - Static method in class org.gbif.utils.text.StringUtils: Apply a function then join the result using a space if not null.
toArray() - Method in class org.gbif.utils.collection.CompactHashSet
toArray(Object[]) - Method in class org.gbif.utils.collection.CompactHashSet
toFilePath(URL) - Static method in class org.gbif.utils.file.FileUtils
touch(File) - Static method in class org.gbif.utils.file.FileUtils: Creates an empty file or updates the last updated timestamp on the same as the unix command of the same name.
trim(String) - Static method in class org.gbif.utils.text.StringUtils: Strips a set of whitespace characters from the start and end of a String.

U

unescapeUnicodeChars(String) - Static method in class org.gbif.utils.text.StringUtils: Unescapes various unicode escapes if existing: java unicode escape, four hexadecimal digits \ uhhhh octal escape \nnn The octal value nnn, where nnn stands for 1 to 3 digits between ‘0’ and ‘7’.
ungzipFile(File, File, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Gunzip a file.
ungzipFile(File, File, String, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Gunzip a file.
UnknownCharsetException - Exception in org.gbif.utils.file
UnknownCharsetException(Exception) - Constructor for exception org.gbif.utils.file.UnknownCharsetException
UnknownCharsetException(String) - Constructor for exception org.gbif.utils.file.UnknownCharsetException
UnknownCharsetException(String, Exception) - Constructor for exception org.gbif.utils.file.UnknownCharsetException
UnknownDelimitersException - Exception in org.gbif.utils.file.csv
UnknownDelimitersException(Exception) - Constructor for exception org.gbif.utils.file.csv.UnknownDelimitersException
UnknownDelimitersException(String) - Constructor for exception org.gbif.utils.file.csv.UnknownDelimitersException
UnknownDelimitersException(String, Exception) - Constructor for exception org.gbif.utils.file.csv.UnknownDelimitersException
UnsupportedCompressionType() - Constructor for exception org.gbif.utils.file.CompressionUtil.UnsupportedCompressionType
UnsupportedCompressionType(String) - Constructor for exception org.gbif.utils.file.CompressionUtil.UnsupportedCompressionType
UnsupportedCompressionType(String, Throwable) - Constructor for exception org.gbif.utils.file.CompressionUtil.UnsupportedCompressionType
untarFile(File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Extracts a plain TAR file.
untgzFile(File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Extracts a gzipped TAR file.
unzipFile(File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Defaults keepSubdirectories to false.
unzipFile(File, File, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Extracts a zipped file into a target directory.
upper(Map<String, String>) - Static method in class org.gbif.utils.text.StringUtils: Uppercases all keys and values in a Map.
url(String...) - Static method in class org.gbif.utils.rs.RsGbifOrg
url2file(URL) - Static method in class org.gbif.utils.file.FileUtils
UTF8 - Static variable in class org.gbif.utils.file.FileUtils
UTF8_ENCODING - Static variable in class org.gbif.utils.file.properties.PropertiesUtil: When we encode strings, we always specify UTF8 encoding

W

WHITESPACES_LIST - Static variable in class org.gbif.utils.text.StringUtils: This includes some special whitespaces which not present in standard trim list: U+0085 Next Line (NEL) U+00A0 No-Break Space (NBSP) U+000C Form Feed (FF) U+2007 Figure Space

Z

zipDir(File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Zip a directory with all files but skipping included subdirectories.
zipDir(File, File, boolean) - Static method in class org.gbif.utils.file.CompressionUtil: Zip a directory with all files.
zipFile(File, File) - Static method in class org.gbif.utils.file.CompressionUtil
zipFiles(Collection<File>, File, File) - Static method in class org.gbif.utils.file.CompressionUtil: Creates a zip archive from a given collection of files.

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