Package org.snpeff.nextProt
Class NextProtParser
- java.lang.Object
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- org.snpeff.nextProt.NextProtParser
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- Direct Known Subclasses:
NextProtParserV2
public class NextProtParser extends java.lang.Object
Parse NetxProt XML file and build a database http://www.nextprot.org/- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
ATTR_NAME_ACCESSION
protected java.lang.String
ATTR_NAME_ANNOTATION_LIST
protected java.lang.String
ATTR_NAME_CATAGORY
protected java.lang.String
ATTR_NAME_DATABASE
protected java.lang.String
ATTR_NAME_FIRST
protected java.lang.String
ATTR_NAME_ISOFORM_REF
protected java.lang.String
ATTR_NAME_LAST
protected java.lang.String
ATTR_NAME_PROPERTY_NAME
protected java.lang.String
ATTR_NAME_UNIQUE_NAME
protected java.lang.String
ATTR_NAME_VALUE
protected java.lang.String
ATTR_VALUE_ENSEMBL
protected java.lang.String
ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID
protected java.lang.String
ATTR_VALUE_REFSEQ
static java.lang.String[]
CATAGORY_BLACK_LIST_STR
static int
HIGHLY_CONSERVED_AA_COUNT
static double
HIGHLY_CONSERVED_AA_PERCENT
protected java.lang.String
NODE_NAME_ANNOTATION
protected java.lang.String
NODE_NAME_ANNOTATION_LIST
protected java.lang.String
NODE_NAME_CVNAME
protected java.lang.String
NODE_NAME_DESCRIPTION
protected java.lang.String
NODE_NAME_GENE
protected java.lang.String
NODE_NAME_POSITION
protected java.lang.String
NODE_NAME_PROPERTY
protected java.lang.String
NODE_NAME_PROTEIN
protected java.lang.String
NODE_NAME_SEQUENCE
protected java.lang.String
NODE_NAME_TRANSCRIPT
protected java.lang.String
NODE_NAME_XREF
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Constructor Summary
Constructors Constructor Description NextProtParser(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
defineNextProtXmlTerms()
protected void
fatalError(java.lang.String message)
Show an error message and exitprotected 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)
Markers
getMarkers()
void
parse(org.w3c.dom.Node doc)
Parse XML documentvoid
setDebug(boolean debug)
void
setTrIdFile(java.lang.String trIdFile)
void
setVerbose(boolean verbose)
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Field Detail
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HIGHLY_CONSERVED_AA_PERCENT
public static final double HIGHLY_CONSERVED_AA_PERCENT
- See Also:
- Constant Field Values
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HIGHLY_CONSERVED_AA_COUNT
public static final int HIGHLY_CONSERVED_AA_COUNT
- See Also:
- Constant Field Values
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CATAGORY_BLACK_LIST_STR
public static final java.lang.String[] CATAGORY_BLACK_LIST_STR
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NODE_NAME_PROTEIN
protected java.lang.String NODE_NAME_PROTEIN
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NODE_NAME_GENE
protected java.lang.String NODE_NAME_GENE
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NODE_NAME_TRANSCRIPT
protected java.lang.String NODE_NAME_TRANSCRIPT
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NODE_NAME_ANNOTATION
protected java.lang.String NODE_NAME_ANNOTATION
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NODE_NAME_ANNOTATION_LIST
protected java.lang.String NODE_NAME_ANNOTATION_LIST
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NODE_NAME_POSITION
protected java.lang.String NODE_NAME_POSITION
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NODE_NAME_PROPERTY
protected java.lang.String NODE_NAME_PROPERTY
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NODE_NAME_DESCRIPTION
protected java.lang.String NODE_NAME_DESCRIPTION
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NODE_NAME_CVNAME
protected java.lang.String NODE_NAME_CVNAME
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NODE_NAME_SEQUENCE
protected java.lang.String NODE_NAME_SEQUENCE
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NODE_NAME_XREF
protected java.lang.String NODE_NAME_XREF
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ATTR_NAME_UNIQUE_NAME
protected java.lang.String ATTR_NAME_UNIQUE_NAME
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ATTR_NAME_DATABASE
protected java.lang.String ATTR_NAME_DATABASE
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ATTR_NAME_ACCESSION
protected java.lang.String ATTR_NAME_ACCESSION
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ATTR_NAME_ANNOTATION_LIST
protected java.lang.String ATTR_NAME_ANNOTATION_LIST
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ATTR_NAME_CATAGORY
protected java.lang.String ATTR_NAME_CATAGORY
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ATTR_NAME_FIRST
protected java.lang.String ATTR_NAME_FIRST
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ATTR_NAME_LAST
protected java.lang.String ATTR_NAME_LAST
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ATTR_NAME_ISOFORM_REF
protected java.lang.String ATTR_NAME_ISOFORM_REF
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ATTR_NAME_PROPERTY_NAME
protected java.lang.String ATTR_NAME_PROPERTY_NAME
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ATTR_NAME_VALUE
protected java.lang.String ATTR_NAME_VALUE
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ATTR_VALUE_ENSEMBL
protected java.lang.String ATTR_VALUE_ENSEMBL
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ATTR_VALUE_REFSEQ
protected java.lang.String ATTR_VALUE_REFSEQ
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ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID
protected java.lang.String ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID
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Constructor Detail
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NextProtParser
public NextProtParser(Config config)
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Method Detail
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defineNextProtXmlTerms
protected void defineNextProtXmlTerms()
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fatalError
protected void fatalError(java.lang.String message)
Show an error message and exit
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getAaEnd
protected int getAaEnd(org.w3c.dom.Node posNode)
Get AA end position from position node
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getAaStart
protected int getAaStart(org.w3c.dom.Node posNode)
Get AA start position from position node
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getIsoformRefFromPos
protected java.lang.String getIsoformRefFromPos(org.w3c.dom.Node posNode)
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getMarkers
public Markers getMarkers()
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parse
public void parse(org.w3c.dom.Node doc)
Parse XML document
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setDebug
public void setDebug(boolean debug)
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setTrIdFile
public void setTrIdFile(java.lang.String trIdFile)
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setVerbose
public void setVerbose(boolean verbose)
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