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

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

public class NexusParser
extends java.lang.Object

Field Summary

static java.util.regex.Pattern	BLOCK_BEGIN_PATTERN
static java.util.regex.Pattern	BLOCK_END_PATTERN
static java.util.regex.Pattern	COMMAND_PATTERN
static char	COMMAND_SEPARATOR
static char	COMMENT_END
static char	COMMENT_START
static java.util.regex.Pattern	EMPTY_PATTERN
static java.util.regex.Pattern	ENCLOSED_NAME_PATTERN
static java.lang.String	NAME_BLOCK_BEGIN
static java.lang.String	NAME_BLOCK_END
static char	NAME_DELIMITER
static java.lang.String	NAME_NEXUS
static java.util.regex.Pattern	NAME_SEPARATOR_PATTERN
static java.lang.String	NAME_TRANSL_TABLE
static java.lang.String	NAME_TREES
static java.lang.String	ROOTED_COMMAND
static java.util.regex.Pattern	TRANSL_TABLE_PATTERN
static java.util.regex.Pattern	TRANSL_TABLE_SEPARATOR_PATTERN
static java.lang.String	TREE_COMMAND
static java.util.regex.Pattern	TREE_COMMAND_PATTERN
static char	TREE_NAME_SEPERATOR
static java.util.regex.Pattern	TREES_PATTERN
static java.lang.String	UNROOTED_COMMAND
static java.util.regex.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, java.util.regex.Pattern namePattern, java.util.regex.Pattern tokenPattern) Searches for the first occurence of the given command.
static int	nextPosOutsideComment(java.lang.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(java.lang.String content)
private static java.lang.String	parseName(java.lang.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(java.lang.String tokens, NexusDocument document) Reads a tree from the passed nexus command tokens and adds it to the passed document.
static java.lang.String	removeComments(java.lang.String content) Returns the specified string without any comments (seperated by "[" and "]").
private static NexusCommand[]	scan(java.lang.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 java.lang.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 java.util.regex.Pattern NAME_SEPARATOR_PATTERN

ENCLOSED_NAME_PATTERN

public static final java.util.regex.Pattern ENCLOSED_NAME_PATTERN

COMMAND_SEPARATOR

public static final char COMMAND_SEPARATOR

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Constant Field Values

COMMAND_PATTERN

public static final java.util.regex.Pattern COMMAND_PATTERN

ROOTED_COMMAND

public static final java.lang.String ROOTED_COMMAND

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Constant Field Values

UNROOTED_COMMAND

public static final java.lang.String UNROOTED_COMMAND

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Constant Field Values

NAME_BLOCK_BEGIN

public static final java.lang.String NAME_BLOCK_BEGIN

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Constant Field Values

BLOCK_BEGIN_PATTERN

public static final java.util.regex.Pattern BLOCK_BEGIN_PATTERN

NAME_BLOCK_END

public static final java.lang.String NAME_BLOCK_END

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Constant Field Values

BLOCK_END_PATTERN

public static final java.util.regex.Pattern BLOCK_END_PATTERN

NAME_TREES

public static final java.lang.String NAME_TREES

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Constant Field Values

TREES_PATTERN

public static final java.util.regex.Pattern TREES_PATTERN

NAME_TRANSL_TABLE

public static final java.lang.String NAME_TRANSL_TABLE

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Constant Field Values

TRANSL_TABLE_PATTERN

public static final java.util.regex.Pattern TRANSL_TABLE_PATTERN

TRANSL_TABLE_SEPARATOR_PATTERN

public static final java.util.regex.Pattern TRANSL_TABLE_SEPARATOR_PATTERN

TREE_COMMAND

public static final java.lang.String TREE_COMMAND

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Constant Field Values

TREE_COMMAND_PATTERN

public static final java.util.regex.Pattern TREE_COMMAND_PATTERN

WHITESPACE_PATTERN

public static final java.util.regex.Pattern WHITESPACE_PATTERN

EMPTY_PATTERN

public static final java.util.regex.Pattern EMPTY_PATTERN

TREE_NAME_SEPERATOR

public static final char TREE_NAME_SEPERATOR

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Constant Field Values

Constructor Detail

NexusParser

public NexusParser()

Method Detail

scan

private static NexusCommand[] scan(java.lang.String content)

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

Parameters:

content -

Returns:

nextPosOutsideComment

public static int nextPosOutsideComment(java.lang.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 java.lang.String removeComments(java.lang.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,
                               java.util.regex.Pattern namePattern,
                               java.util.regex.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 java.lang.String parseName(java.lang.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(java.lang.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(java.lang.String content)
                           throws NexusException

Throws:

NexusException