Package org.snpeff.nextProt
Class NextProtParserV2
- java.lang.Object
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- org.snpeff.nextProt.NextProtParser
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- org.snpeff.nextProt.NextProtParserV2
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public class NextProtParserV2 extends NextProtParser
Parse NetxProt XML file (version 2) http://www.nextprot.org/- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
ATTR_NAME_POSITION
protected java.lang.String
NODE_NAME_ANNOTATION_CATEGORY
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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
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Constructor Summary
Constructors Constructor Description NextProtParserV2(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
defineNextProtXmlTerms()
protected int
getAaEnd(org.w3c.dom.Node posNode)
Get AA end position from position nodeprotected int
getAaStart(org.w3c.dom.Node posNode)
Get AA start position from position nodeprotected java.lang.String
getIsoformRefFromPos(org.w3c.dom.Node posNode)
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Methods inherited from class org.snpeff.nextProt.NextProtParser
fatalError, getMarkers, parse, setDebug, setTrIdFile, setVerbose
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Constructor Detail
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NextProtParserV2
public NextProtParserV2(Config config)
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Method Detail
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defineNextProtXmlTerms
protected void defineNextProtXmlTerms()
- Overrides:
defineNextProtXmlTerms
in classNextProtParser
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getAaEnd
protected int getAaEnd(org.w3c.dom.Node posNode)
Get AA end position from position node- Overrides:
getAaEnd
in classNextProtParser
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getAaStart
protected int getAaStart(org.w3c.dom.Node posNode)
Get AA start position from position node- Overrides:
getAaStart
in classNextProtParser
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getIsoformRefFromPos
protected java.lang.String getIsoformRefFromPos(org.w3c.dom.Node posNode)
- Overrides:
getIsoformRefFromPos
in classNextProtParser
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