public final class ParserUtils
extends java.lang.Object
Constructor and Description |
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ParserUtils() |
Modifier and Type | Method and Description |
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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) |
public static final PhylogenyParser createParserDependingFileContents(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnFileType(java.io.File file, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final PhylogenyParser createParserDependingOnSuffix(java.lang.String filename, boolean phyloxml_validate_against_xsd)
filename
- public static final PhylogenyParser createParserDependingOnUrlContents(java.net.URL url, boolean phyloxml_validate_against_xsd) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static java.io.BufferedReader createReader(java.lang.Object source) throws java.io.IOException, java.io.FileNotFoundException
java.io.IOException
java.io.FileNotFoundException
public static java.lang.String extractTaxonomyCodeFromNodeName(java.lang.String name, PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction)
name
- public static final Phylogeny[] readPhylogenies(java.io.File file) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final Phylogeny[] readPhylogenies(java.lang.String file_name) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException