htsjdk.tribble.util

Class ParsingUtils

java.lang.Object

htsjdk.tribble.util.ParsingUtils

public class ParsingUtils
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Map<java.lang.Object,java.awt.Color>	colorCache

Constructor Summary

Constructors

Constructor and Description
ParsingUtils()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	appendToPath(java.lang.String filepath, java.lang.String indexExtension) Add the indexExtension to the filepath, preserving query string elements if present.
static URLHelper	getURLHelper(java.net.URL url) Return a URLHelper from the current URLHelperFactory
static URLHelperFactory	getURLHelperFactory()
static <T extends java.lang.Comparable<? super T>> boolean	isSorted(java.lang.Iterable<T> iterable)
static <T> java.lang.String	join(java.lang.String separator, java.util.Collection<T> objects)
static java.lang.String	join(java.lang.String separator, java.lang.String[] strings) join an array of strings given a seperator
static java.lang.String	join(java.lang.String separator, java.lang.String[] strings, int start, int end) join a set of strings, using the separator provided, from index start to index stop
static java.io.InputStream	openInputStream(java.lang.String path)
static java.io.InputStream	openInputStream(java.lang.String uri, java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper) open an input stream from the given path and wrap the raw byte stream with a wrapper if given the wrapper will only be applied to paths that are not http, https, ftp, or file, i.e.
static java.awt.Color	parseColor(java.lang.String string) Convert an rgb string, hex, or symbol to a color.
static boolean	resourceExists(java.lang.String resource)
static void	setURLHelperFactory(URLHelperFactory factory) Set the factory object for providing URLHelpers.
static <T extends java.lang.Comparable<T>,V> java.lang.String	sortedString(java.util.Map<T,V> c)
static <T extends java.lang.Comparable> java.util.List<T>	sortList(java.util.Collection<T> list) a small utility function for sorting a list
static java.util.List<java.lang.String>	split(java.lang.String input, char delim) Split the string into tokens separated by the given delimiter.
static int	split(java.lang.String aString, java.lang.String[] tokens, char delim) Split the string into tokesn separated by the given delimiter.
static int	split(java.lang.String aString, java.lang.String[] tokens, char delim, boolean condenseTrailingTokens) Split the string into tokens separated by the given delimiter.
static int	splitWhitespace(java.lang.String aString, java.lang.String[] tokens) Split the string into tokens separated by tab or space(s).
static java.lang.String	trim(java.lang.String str, char ch)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

colorCache

public static final java.util.Map<java.lang.Object,java.awt.Color> colorCache

Constructor Detail

ParsingUtils

public ParsingUtils()

Method Detail

openInputStream

public static java.io.InputStream openInputStream(java.lang.String path)
                                           throws java.io.IOException

Returns:

an input stream from the given path

Throws:

java.io.IOException

openInputStream

public static java.io.InputStream openInputStream(java.lang.String uri,
                                                  java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> wrapper)
                                           throws java.io.IOException

open an input stream from the given path and wrap the raw byte stream with a wrapper if given the wrapper will only be applied to paths that are not http, https, ftp, or file, i.e. any Path using a custom filesystem plugin

Parameters:

uri - a uri like string

wrapper - to wrap the input stream in, may be used to implement caching or prefetching, etc

Returns:

An inputStream appropriately created from uri and conditionally wrapped with wrapper (only in certain cases)

Throws:

java.io.IOException - when stream cannot be opened against uri

join

public static <T> java.lang.String join(java.lang.String separator,
                                        java.util.Collection<T> objects)

sortList

public static <T extends java.lang.Comparable> java.util.List<T> sortList(java.util.Collection<T> list)

a small utility function for sorting a list

Type Parameters:

T -

Parameters:

list -

Returns:

sortedString

public static <T extends java.lang.Comparable<T>,V> java.lang.String sortedString(java.util.Map<T,V> c)

join

public static java.lang.String join(java.lang.String separator,
                                    java.lang.String[] strings)

join an array of strings given a seperator

Parameters:

separator - the string to insert between each array element

strings - the array of strings

Returns:

a string, which is the joining of all array values with the separator

join

public static java.lang.String join(java.lang.String separator,
                                    java.lang.String[] strings,
                                    int start,
                                    int end)

join a set of strings, using the separator provided, from index start to index stop

Parameters:

separator - the separator to use

strings - the list of strings

start - the start position (index in the list)0

end - the end position (index in the list)

Returns:

a joined string, or "" if end - start == 0

split

public static java.util.List<java.lang.String> split(java.lang.String input,
                                                     char delim)

Split the string into tokens separated by the given delimiter. This looks suspiciously like what String.split should do. It is here because String.split has particularly poor performance for this use case in some versions of the Java SE API because of use of java.util.regex APIs (see bug report at http://bugs.java.com/view_bug.do?bug_id=6840246 for information).

Parameters:

input - the string to split

delim - the character that delimits tokens

Returns:

a list of the tokens

split

public static int split(java.lang.String aString,
                        java.lang.String[] tokens,
                        char delim)

Split the string into tokesn separated by the given delimiter. Profiling has revealed that the standard string.split() method typically takes > 1/2 the total time when used for parsing ascii files.

Parameters:

aString - the string to split

tokens - an array to hold the parsed tokens

delim - character that delimits tokens

Returns:

the number of tokens parsed

split

public static int split(java.lang.String aString,
                        java.lang.String[] tokens,
                        char delim,
                        boolean condenseTrailingTokens)

Split the string into tokens separated by the given delimiter. Profiling has revealed that the standard string.split() method typically takes > 1/2 the total time when used for parsing ascii files.

Parameters:

aString - the string to split

tokens - an array to hold the parsed tokens

delim - character that delimits tokens

condenseTrailingTokens - if true and there are more tokens than will fit in the tokens array, condense all trailing tokens into the last token

Returns:

the number of tokens parsed

trim

public static java.lang.String trim(java.lang.String str,
                                    char ch)

splitWhitespace

public static int splitWhitespace(java.lang.String aString,
                                  java.lang.String[] tokens)

Split the string into tokens separated by tab or space(s). This method was added so support wig and bed files, which apparently accept space delimiters.

Note: TODO REGEX expressions are not used for speed. This should be re-evaluated with JDK 1.5 or later

Parameters:

aString - the string to split

tokens - an array to hold the parsed tokens

Returns:

the number of tokens parsed

isSorted

public static <T extends java.lang.Comparable<? super T>> boolean isSorted(java.lang.Iterable<T> iterable)

parseColor

public static java.awt.Color parseColor(java.lang.String string)

Convert an rgb string, hex, or symbol to a color.

Parameters:

string -

Returns:

resourceExists

public static boolean resourceExists(java.lang.String resource)
                              throws java.io.IOException

Throws:

java.io.IOException

getURLHelper

public static URLHelper getURLHelper(java.net.URL url)

Return a URLHelper from the current URLHelperFactory

Parameters:

url -

Returns:

See Also:

setURLHelperFactory(URLHelperFactory)

setURLHelperFactory

public static void setURLHelperFactory(URLHelperFactory factory)

Set the factory object for providing URLHelpers. URLHelperFactory.

Parameters:

factory -

getURLHelperFactory

public static URLHelperFactory getURLHelperFactory()

appendToPath

public static java.lang.String appendToPath(java.lang.String filepath,
                                            java.lang.String indexExtension)

Add the indexExtension to the filepath, preserving query string elements if present. Intended for use where filepath is a URL. Will behave correctly on regular file paths (just add the extension to the end)

Parameters:

filepath -

indexExtension -

Returns: