Package org.snpeff.nextProt

Class NextProtParserV2

java.lang.Object

org.snpeff.nextProt.NextProtParser

org.snpeff.nextProt.NextProtParserV2

public class NextProtParserV2
extends NextProtParser

Parse NetxProt XML file (version 2) http://www.nextprot.org/

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
protected java.lang.String	ATTR_NAME_POSITION
protected java.lang.String	NODE_NAME_ANNOTATION_CATEGORY

Fields inherited from class org.snpeff.nextProt.NextProtParser

ATTR_NAME_ACCESSION, ATTR_NAME_ANNOTATION_LIST, ATTR_NAME_CATAGORY, ATTR_NAME_DATABASE, ATTR_NAME_FIRST, ATTR_NAME_ISOFORM_REF, ATTR_NAME_LAST, ATTR_NAME_PROPERTY_NAME, ATTR_NAME_UNIQUE_NAME, ATTR_NAME_VALUE, ATTR_VALUE_ENSEMBL, ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID, ATTR_VALUE_REFSEQ, CATAGORY_BLACK_LIST_STR, HIGHLY_CONSERVED_AA_COUNT, HIGHLY_CONSERVED_AA_PERCENT, NODE_NAME_ANNOTATION, NODE_NAME_ANNOTATION_LIST, NODE_NAME_CVNAME, NODE_NAME_DESCRIPTION, NODE_NAME_GENE, NODE_NAME_POSITION, NODE_NAME_PROPERTY, NODE_NAME_PROTEIN, NODE_NAME_SEQUENCE, NODE_NAME_TRANSCRIPT, NODE_NAME_XREF

Constructor Summary

Constructors

Constructor	Description
NextProtParserV2(Config config)

Method Summary

Modifier and Type	Method	Description
protected void	defineNextProtXmlTerms()
protected int	getAaEnd(org.w3c.dom.Node posNode)	Get AA end position from position node
protected int	getAaStart(org.w3c.dom.Node posNode)	Get AA start position from position node
protected java.lang.String	getIsoformRefFromPos(org.w3c.dom.Node posNode)

Methods inherited from class org.snpeff.nextProt.NextProtParser

fatalError, getMarkers, parse, setDebug, setTrIdFile, setVerbose

Methods inherited from class java.lang.Object

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

Field Detail

NODE_NAME_ANNOTATION_CATEGORY

protected java.lang.String NODE_NAME_ANNOTATION_CATEGORY

ATTR_NAME_POSITION

protected java.lang.String ATTR_NAME_POSITION

Constructor Detail

NextProtParserV2

public NextProtParserV2(Config config)

Method Detail

defineNextProtXmlTerms

protected void defineNextProtXmlTerms()

Overrides:

defineNextProtXmlTerms in class NextProtParser

getAaEnd

protected int getAaEnd(org.w3c.dom.Node posNode)

Get AA end position from position node

Overrides:

getAaEnd in class NextProtParser

getAaStart

protected int getAaStart(org.w3c.dom.Node posNode)

Get AA start position from position node

Overrides:

getAaStart in class NextProtParser

getIsoformRefFromPos

protected java.lang.String getIsoformRefFromPos(org.w3c.dom.Node posNode)

Overrides:

getIsoformRefFromPos in class NextProtParser