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 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 thr first occurence of the given command.
static NexusDocument	parse(String content)
private static String	parseName(String name)
private static void	readTranslTable(NexusCommand command, TranslTable translTable)
private static NexusCommand[]	scan(String content)

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

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Constant Field Values

COMMENT_START

public static final char COMMENT_START

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Constant Field Values

COMMENT_END

public static final char COMMENT_END

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Constant Field Values

NAME_DELIMITER

public static final char NAME_DELIMITER

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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

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Constant Field Values

COMMAND_PATTERN

public static final Pattern COMMAND_PATTERN

ROOTED_COMMAND

public static final String ROOTED_COMMAND

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Constant Field Values

UNROOTED_COMMAND

public static final String UNROOTED_COMMAND

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Constant Field Values

NAME_BLOCK_BEGIN

public static final String NAME_BLOCK_BEGIN

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Constant Field Values

BLOCK_BEGIN_PATTERN

public static final Pattern BLOCK_BEGIN_PATTERN

NAME_BLOCK_END

public static final String NAME_BLOCK_END

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Constant Field Values

BLOCK_END_PATTERN

public static final Pattern BLOCK_END_PATTERN

NAME_TREES

public static final String NAME_TREES

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Constant Field Values

TREES_PATTERN

public static final Pattern TREES_PATTERN

NAME_TRANSL_TABLE

public static final String NAME_TRANSL_TABLE

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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

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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

Constructor Detail

NexusParser

public NexusParser()

Method Detail

scan

private static NexusCommand[] scan(String content)

findCommand

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

Searches for thr 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. Pattern are not matched case sensitive)

tokenPattern - - describes how the token of the command should look like (The pattern should describe all possible names. Pattern are not matched case sensitive)

Returns:

the index of the first match in the given array of command

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)

parse

public static NexusDocument parse(String content)
                           throws NexusException

Throws:

NexusException