org.forester.io.parsers.util
Class ParserUtils

java.lang.Object
  org.forester.io.parsers.util.ParserUtils

public final class ParserUtils
extends java.lang.Object

Constructor Summary

ParserUtils()

Method Summary

static PhylogenyParser	createParserDependingFileContents(java.io.File file, boolean phyloxml_validate_against_xsd)
static PhylogenyParser	createParserDependingOnFileType(java.io.File file, boolean phyloxml_validate_against_xsd)
static PhylogenyParser	createParserDependingOnSuffix(java.lang.String filename, boolean phyloxml_validate_against_xsd) Return null if it can not guess the parser to use based on name suffix.
static PhylogenyParser	createParserDependingOnUrlContents(java.net.URL url, boolean phyloxml_validate_against_xsd)
static java.io.BufferedReader	createReader(java.lang.Object source)
static java.lang.String	extractTaxonomyCodeFromNodeName(java.lang.String name, PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction) Extracts a code if and only if: one and only one _, shorter than 25, no |, no ., if / present it has to be after the _, if PFAM_STYLE_ONLY: / must be present, tax code can only contain uppercase letters and numbers, and must contain at least one uppercase letter.
static Phylogeny[]	readPhylogenies(java.io.File file)
static Phylogeny[]	readPhylogenies(java.lang.String file_name)

Methods inherited from class java.lang.Object

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

Constructor Detail

ParserUtils

public ParserUtils()

Method Detail

createParserDependingFileContents

public static final PhylogenyParser createParserDependingFileContents(java.io.File file,
                                                                      boolean phyloxml_validate_against_xsd)
                                                               throws java.io.FileNotFoundException,
                                                                      java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

createParserDependingOnFileType

public static final PhylogenyParser createParserDependingOnFileType(java.io.File file,
                                                                    boolean phyloxml_validate_against_xsd)
                                                             throws java.io.FileNotFoundException,
                                                                    java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

createParserDependingOnSuffix

public static final PhylogenyParser createParserDependingOnSuffix(java.lang.String filename,
                                                                  boolean phyloxml_validate_against_xsd)

Return null if it can not guess the parser to use based on name suffix.

Parameters:

filename -

Returns:

createParserDependingOnUrlContents

public static final PhylogenyParser createParserDependingOnUrlContents(java.net.URL url,
                                                                       boolean phyloxml_validate_against_xsd)
                                                                throws java.io.FileNotFoundException,
                                                                       java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

createReader

public static java.io.BufferedReader createReader(java.lang.Object source)
                                           throws java.io.IOException,
                                                  java.io.FileNotFoundException

Throws:

java.io.IOException

java.io.FileNotFoundException

extractTaxonomyCodeFromNodeName

public static java.lang.String extractTaxonomyCodeFromNodeName(java.lang.String name,
                                                               PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction)

Extracts a code if and only if: one and only one _, shorter than 25, no |, no ., if / present it has to be after the _, if PFAM_STYLE_ONLY: / must be present, tax code can only contain uppercase letters and numbers, and must contain at least one uppercase letter. Return null if no code extractable.

Parameters:

name -

Returns:

readPhylogenies

public static final Phylogeny[] readPhylogenies(java.io.File file)
                                         throws java.io.FileNotFoundException,
                                                java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

readPhylogenies

public static final Phylogeny[] readPhylogenies(java.lang.String file_name)
                                         throws java.io.FileNotFoundException,
                                                java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException