edu.upenn.crimson.io
Class NexusFile

java.lang.Object
  edu.upenn.crimson.io.NexusFile

public class NexusFile
extends java.lang.Object

Functions related to loading NEXUS files.

Version:

$Id: NexusFile.java,v 1.54 2007/06/14 19:48:42 fisher Exp $

Notes:

Should see if can optimize db access by maintaining one Statement that is created every time a database connection is made.

Field Summary

private static java.util.regex.Pattern	needsQuotesPattern From Mark Holder
private static java.lang.String	regexPat
private static java.util.regex.Pattern	shortStrNeedsQuotePattern From Mark Holder

Constructor Summary

NexusFile()

Method Summary

static Tree	append(java.lang.String filename, java.lang.String treeID, java.lang.String partitionID) Appends a Nexus file into the current database.
static java.lang.String	doQuote(java.lang.String text) From Mark Holder
private static int	findLabelEnd(java.lang.String newick, int start) Keep incrementing until we find the end of the number or label.
static Tree	load(java.lang.String filename, java.lang.String treeID, java.lang.String partitionID) Loads a Nexus file.
static Tree	loadNewick(java.lang.String filename) Loads a tree structure from a Nexus file into memory.
private static boolean	multiCharStringNeedsQuotes(java.lang.String text) From Mark Holder
static Tree	parseNewick(Tree tree) This might be faster if we use char[] instead of String for "newick".
static Tree	parseNewick(Tree tree, java.lang.String newick) This might be faster if we use char[] instead of String for "newick".
static java.lang.String	quote(java.lang.String text) From Mark Holder This will properly quote a word that is to be included in a NEXUS file.
static java.lang.String[]	quote(java.lang.String[] text) From Mark Holder This will properly quote a word that is to be included in a NEXUS file.
private static boolean	shortStringNeedsQuotes(java.lang.String text) From Mark Holder handles strings of len 1 or 0 only.

Methods inherited from class java.lang.Object

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

Field Detail

regexPat

private static final java.lang.String regexPat

See Also:

Constant Field Values

needsQuotesPattern

private static final java.util.regex.Pattern needsQuotesPattern

From Mark Holder

shortStrNeedsQuotePattern

private static final java.util.regex.Pattern shortStrNeedsQuotePattern

From Mark Holder

Constructor Detail

NexusFile

public NexusFile()

Method Detail

loadNewick

public static Tree loadNewick(java.lang.String filename)

Loads a tree structure from a Nexus file into memory. This is meant to be used for debugging.

findLabelEnd

private static int findLabelEnd(java.lang.String newick,
                                int start)

Keep incrementing until we find the end of the number or label.

parseNewick

public static Tree parseNewick(Tree tree)

This might be faster if we use char[] instead of String for "newick". This will break if there are blank spaces (' ') in the tree structure.

parseNewick

public static Tree parseNewick(Tree tree,
                               java.lang.String newick)

This might be faster if we use char[] instead of String for "newick". This will break if there are blank spaces (' ') in the tree structure.

load

public static Tree load(java.lang.String filename,
                        java.lang.String treeID,
                        java.lang.String partitionID)

Loads a Nexus file. This will not load the tree if the tree already exist in the database.

append

public static Tree append(java.lang.String filename,
                          java.lang.String treeID,
                          java.lang.String partitionID)

Appends a Nexus file into the current database. This will not append the tree if the tree don't exist or any of the data files are missing.

doQuote

public static java.lang.String doQuote(java.lang.String text)

From Mark Holder

quote

public static java.lang.String quote(java.lang.String text)

From Mark Holder This will properly quote a word that is to be included in a NEXUS file.

quote

public static java.lang.String[] quote(java.lang.String[] text)

From Mark Holder This will properly quote a word that is to be included in a NEXUS file.

multiCharStringNeedsQuotes

private static boolean multiCharStringNeedsQuotes(java.lang.String text)

From Mark Holder

shortStringNeedsQuotes

private static boolean shortStringNeedsQuotes(java.lang.String text)

From Mark Holder handles strings of len 1 or 0 only. The only single punctuation characters that need quoting are []'_ Note that an empty string and whitespac. must be quoted too.

Parameters:

text -

Returns:

true for "", "[", "