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
static java.lang.Class	urlHelperClass

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 the registered URLHelper, constructed with the provided URL
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.awt.Color	parseColor(java.lang.String string) Convert an rgb string, hex, or symbol to a color.
static void	registerHelperClass(java.lang.Class helperClass) Register a URLHelper class to be used for URL operations.
static boolean	resourceExists(java.lang.String resource)
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 java.util.Map<java.lang.Object,java.awt.Color> colorCache

urlHelperClass

public static java.lang.Class urlHelperClass

Constructor Detail

ParsingUtils

public ParsingUtils()

Method Detail

openInputStream

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

Throws:

java.io.IOException

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 the registered URLHelper, constructed with the provided URL

Parameters:

url -

Returns:

See Also:

registerHelperClass(Class)

registerHelperClass

public static void registerHelperClass(java.lang.Class helperClass)

Register a URLHelper class to be used for URL operations. The helper may be used for both FTP and HTTP operations, so if any FTP URLs are used the URLHelper must support it. The default helper class is RemoteURLHelper, which delegates to FTP/HTTP helpers as appropriate.

Parameters:

helperClass - Class which implements URLHelper, and have a constructor which takes a URL as it's only argument.

See Also:

URLHelper

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: