ParserUtils

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

public final class ParserUtils
extends java.lang.Object

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`TAX_CODE`
`static java.lang.String`	`TAX_CODE_LO`
`static java.util.regex.Pattern`	`TAXOMONY_CODE_PATTERN_A`
`static java.util.regex.Pattern`	`TAXOMONY_CODE_PATTERN_A_LO`
`static java.util.regex.Pattern`	`TAXOMONY_CODE_PATTERN_BRACKETED`
`static java.util.regex.Pattern`	`TAXOMONY_CODE_PATTERN_PFR`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_GENUS`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_SN`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_SNS`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_SNS2`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_SP`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_STRAIN_1`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_STRAIN_2`
`static java.util.regex.Pattern`	`TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN`

Constructor Summary

Constructors
Constructor and Description

ParserUtils()

Constructors
Constructor and Description
`ParserUtils()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`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`	`createParserDependingOnUrlContents(java.net.URL url, boolean phyloxml_validate_against_xsd)`
`static java.io.BufferedReader`	`createReader(java.lang.Object source)`
`static java.lang.String`	`extractScientificNameFromNodeName(java.lang.String name)`
`static java.lang.String`	`extractTaxonomyCodeFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)`
`static java.lang.String`	`extractTaxonomyDataFromNodeName(PhylogenyNode node, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)`
`static java.lang.String`	`extractUniprotTaxonomyIdFromNodeName(java.lang.String name, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)`
`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

Field Detail

TAX_CODE

public static final java.lang.String TAX_CODE

See Also:: Constant Field Values

TAX_CODE_LO

public static final java.lang.String TAX_CODE_LO

See Also:: Constant Field Values

TAXOMONY_CODE_PATTERN_A

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A

TAXOMONY_CODE_PATTERN_A_LO

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_A_LO

TAXOMONY_CODE_PATTERN_BRACKETED

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_BRACKETED

TAXOMONY_CODE_PATTERN_PFR

public static final java.util.regex.Pattern TAXOMONY_CODE_PATTERN_PFR

TAXOMONY_SN_PATTERN_GENUS

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_GENUS

TAXOMONY_SN_PATTERN_SN

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SN

TAXOMONY_SN_PATTERN_SNS

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS

TAXOMONY_SN_PATTERN_SNS2

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SNS2

TAXOMONY_SN_PATTERN_SP

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_SP

TAXOMONY_SN_PATTERN_STRAIN_1

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_1

TAXOMONY_SN_PATTERN_STRAIN_2

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_2

TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

public static final java.util.regex.Pattern TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

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

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

extractScientificNameFromNodeName

public static final java.lang.String extractScientificNameFromNodeName(java.lang.String name)

extractTaxonomyCodeFromNodeName

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

extractTaxonomyDataFromNodeName

public static final java.lang.String extractTaxonomyDataFromNodeName(PhylogenyNode node,
                                                                     NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)
                                                              throws PhyloXmlDataFormatException

Throws:: PhyloXmlDataFormatException

extractUniprotTaxonomyIdFromNodeName

public static final java.lang.String extractUniprotTaxonomyIdFromNodeName(java.lang.String name,
                                                                          NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)

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

Class ParserUtils

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TAX_CODE

TAX_CODE_LO

TAXOMONY_CODE_PATTERN_A

TAXOMONY_CODE_PATTERN_A_LO

TAXOMONY_CODE_PATTERN_BRACKETED

TAXOMONY_CODE_PATTERN_PFR

TAXOMONY_SN_PATTERN_GENUS

TAXOMONY_SN_PATTERN_SN

TAXOMONY_SN_PATTERN_SNS

TAXOMONY_SN_PATTERN_SNS2

TAXOMONY_SN_PATTERN_SP

TAXOMONY_SN_PATTERN_STRAIN_1

TAXOMONY_SN_PATTERN_STRAIN_2

TAXOMONY_SN_PATTERN_STRAIN_SUBSTRAIN

Constructor Detail

ParserUtils

Method Detail

createParserDependingFileContents

createParserDependingOnFileType

createParserDependingOnUrlContents

createReader

extractScientificNameFromNodeName

extractTaxonomyCodeFromNodeName

extractTaxonomyDataFromNodeName

extractUniprotTaxonomyIdFromNodeName

readPhylogenies

readPhylogenies