Home / Development / Documentation / 2.0.44 / NexusParser

Download

System requirements

How to install

License

Help

Alphabetical index

Tutorials

Categories

Random page

Development

Subversion repository

Recent changes

Source download

Documentation

Latest Javadoc

XTG format

Libraries and tools

Publications

Version 1

Subversion repository

About

info.bioinfweb.treegraph.document.io.nexus
Class NexusParser

java.lang.Object
  info.bioinfweb.treegraph.document.io.nexus.NexusParser

public class NexusParser
extends Object

Field Summary

static Pattern	BLOCK_BEGIN_PATTERN
static Pattern	BLOCK_END_PATTERN
static Pattern	COMMAND_PATTERN
static char	COMMAND_SEPARATOR
static char	COMMENT_END
static char	COMMENT_START
static Pattern	EMPTY_PATTERN
static Pattern	ENCLOSED_NAME_PATTERN
static String	NAME_BLOCK_BEGIN
static String	NAME_BLOCK_END
static char	NAME_DELIMITER
static String	NAME_NEXUS
static Pattern	NAME_SEPARATOR_PATTERN
static String	NAME_TRANSL_TABLE
static String	NAME_TREES
static String	ROOTED_COMMAND
static Pattern	TRANSL_TABLE_PATTERN
static Pattern	TRANSL_TABLE_SEPARATOR_PATTERN
static String	TREE_COMMAND
static Pattern	TREE_COMMAND_PATTERN
static char	TREE_NAME_SEPERATOR
static Pattern	TREES_PATTERN
static String	UNROOTED_COMMAND
static Pattern	WHITESPACE_PATTERN

Constructor Summary

NexusParser()

Method Summary

private static int	findBlockEnd(NexusCommand[] commands, int start, int end)
private static int	findCommand(NexusCommand[] commands, int start, int end, Pattern namePattern, Pattern tokenPattern) Searches for the first occurence of the given command.
static int	nextPosOutsideComment(String text, int start, char character) Returns the index of the next occurence of character after start which is not located inside a comment.
static NexusDocument	parse(String content)
private static String	parseName(String name)
private static void	readTranslTable(NexusCommand command, TranslTable translTable) Reads the content of the passed translation table from the passed command.
private static boolean	readTree(String tokens, NexusDocument document) Reads a tree from the passed nexus command tokens and adds it to the passed document.
static String	removeComments(String content) Returns the specified string without any comments (seperated by "[" and "]").
private static NexusCommand[]	scan(String content) Splite the passed text into Nexus commands.

Methods inherited from class java.lang.Object

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

Field Detail

NAME_NEXUS

public static final String NAME_NEXUS

See Also:

Constant Field Values

COMMENT_START

public static final char COMMENT_START

See Also:

Constant Field Values

COMMENT_END

public static final char COMMENT_END

See Also:

Constant Field Values

NAME_DELIMITER

public static final char NAME_DELIMITER

See Also:

Constant Field Values

NAME_SEPARATOR_PATTERN

public static final Pattern NAME_SEPARATOR_PATTERN

ENCLOSED_NAME_PATTERN

public static final Pattern ENCLOSED_NAME_PATTERN

COMMAND_SEPARATOR

public static final char COMMAND_SEPARATOR

See Also:

Constant Field Values

COMMAND_PATTERN

public static final Pattern COMMAND_PATTERN

ROOTED_COMMAND

public static final String ROOTED_COMMAND

See Also:

Constant Field Values

UNROOTED_COMMAND

public static final String UNROOTED_COMMAND

See Also:

Constant Field Values

NAME_BLOCK_BEGIN

public static final String NAME_BLOCK_BEGIN

See Also:

Constant Field Values

BLOCK_BEGIN_PATTERN

public static final Pattern BLOCK_BEGIN_PATTERN

NAME_BLOCK_END

public static final String NAME_BLOCK_END

See Also:

Constant Field Values

BLOCK_END_PATTERN

public static final Pattern BLOCK_END_PATTERN

NAME_TREES

public static final String NAME_TREES

See Also:

Constant Field Values

TREES_PATTERN

public static final Pattern TREES_PATTERN

NAME_TRANSL_TABLE

public static final String NAME_TRANSL_TABLE

See Also:

Constant Field Values

TRANSL_TABLE_PATTERN

public static final Pattern TRANSL_TABLE_PATTERN

TRANSL_TABLE_SEPARATOR_PATTERN

public static final Pattern TRANSL_TABLE_SEPARATOR_PATTERN

TREE_COMMAND

public static final String TREE_COMMAND

See Also:

Constant Field Values

TREE_COMMAND_PATTERN

public static final Pattern TREE_COMMAND_PATTERN

WHITESPACE_PATTERN

public static final Pattern WHITESPACE_PATTERN

EMPTY_PATTERN

public static final Pattern EMPTY_PATTERN

TREE_NAME_SEPERATOR

public static final char TREE_NAME_SEPERATOR

See Also:

Constant Field Values

Constructor Detail

NexusParser

public NexusParser()

Method Detail

scan

private static NexusCommand[] scan(String content)

Splite the passed text into Nexus commands. Comments are not removed.

Parameters:

content -

Returns:

nextPosOutsideComment

public static int nextPosOutsideComment(String text,
                                        int start,
                                        char character)

Returns the index of the next occurence of character after start which is not located inside a comment.

Parameters:

text - the text to be searched

start - the position to start searching

character - the sought-after character

Returns:

the position or -1 if the character was not found

removeComments

public static String removeComments(String content)

Returns the specified string without any comments (seperated by "[" and "]").

Parameters:

content -

Returns:

findCommand

private static int findCommand(NexusCommand[] commands,
                               int start,
                               int end,
                               Pattern namePattern,
                               Pattern tokenPattern)

Searches for the first occurence of the given command.

Parameters:

commands - the list if all commands

start - the command index to start the search

end - the command index to stop the search

namePattern - the name of the command (The pattern should describe all possible names. Patterns are not matched case sensitive)

tokenPattern - describes how the token of the command should look like (Patterns are not matched case sensitive)

Returns:

the index of the first match in the given array of command or -1 if none was found

findBlockEnd

private static int findBlockEnd(NexusCommand[] commands,
                                int start,
                                int end)

parseName

private static String parseName(String name)

readTranslTable

private static void readTranslTable(NexusCommand command,
                                    TranslTable translTable)

Reads the content of the passed translation table from the passed command. The command tokens-string may contain comments.

Parameters:

command -

translTable -

readTree

private static boolean readTree(String tokens,
                                NexusDocument document)

Reads a tree from the passed nexus command tokens and adds it to the passed document. Comments are left inside both the name and the tree string.

Parameters:

tokens -

document -

parse

public static NexusDocument parse(String content)
                           throws NexusException

Throws:

NexusException