Package org.snpeff.nextProt

Class NextProtParser

  • 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

    • Field Detail

      • HIGHLY_CONSERVED_AA_PERCENT

        public static final double HIGHLY_CONSERVED_AA_PERCENT
        See Also:
        Constant Field Values

      • HIGHLY_CONSERVED_AA_COUNT

        public static final int HIGHLY_CONSERVED_AA_COUNT
        See Also:
        Constant Field Values

      • CATAGORY_BLACK_LIST_STR

        public static final java.lang.String[] CATAGORY_BLACK_LIST_STR

      • NODE_NAME_PROTEIN

        protected java.lang.String NODE_NAME_PROTEIN

      • NODE_NAME_GENE

        protected java.lang.String NODE_NAME_GENE

      • NODE_NAME_TRANSCRIPT

        protected java.lang.String NODE_NAME_TRANSCRIPT

      • NODE_NAME_ANNOTATION

        protected java.lang.String NODE_NAME_ANNOTATION

      • NODE_NAME_ANNOTATION_LIST

        protected java.lang.String NODE_NAME_ANNOTATION_LIST

      • NODE_NAME_POSITION

        protected java.lang.String NODE_NAME_POSITION

      • NODE_NAME_PROPERTY

        protected java.lang.String NODE_NAME_PROPERTY

      • NODE_NAME_DESCRIPTION

        protected java.lang.String NODE_NAME_DESCRIPTION

      • NODE_NAME_CVNAME

        protected java.lang.String NODE_NAME_CVNAME

      • NODE_NAME_SEQUENCE

        protected java.lang.String NODE_NAME_SEQUENCE

      • NODE_NAME_XREF

        protected java.lang.String NODE_NAME_XREF

      • ATTR_NAME_UNIQUE_NAME

        protected java.lang.String ATTR_NAME_UNIQUE_NAME

      • ATTR_NAME_DATABASE

        protected java.lang.String ATTR_NAME_DATABASE

      • ATTR_NAME_ACCESSION

        protected java.lang.String ATTR_NAME_ACCESSION

      • ATTR_NAME_ANNOTATION_LIST

        protected java.lang.String ATTR_NAME_ANNOTATION_LIST

      • ATTR_NAME_CATAGORY

        protected java.lang.String ATTR_NAME_CATAGORY

      • ATTR_NAME_FIRST

        protected java.lang.String ATTR_NAME_FIRST

      • ATTR_NAME_LAST

        protected java.lang.String ATTR_NAME_LAST

      • ATTR_NAME_ISOFORM_REF

        protected java.lang.String ATTR_NAME_ISOFORM_REF

      • ATTR_NAME_PROPERTY_NAME

        protected java.lang.String ATTR_NAME_PROPERTY_NAME

      • ATTR_NAME_VALUE

        protected java.lang.String ATTR_NAME_VALUE

      • ATTR_VALUE_ENSEMBL

        protected java.lang.String ATTR_VALUE_ENSEMBL

      • ATTR_VALUE_REFSEQ

        protected java.lang.String ATTR_VALUE_REFSEQ

      • ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID

        protected java.lang.String ATTR_VALUE_NUCLEOTIDE_SEQUENCE_ID

    • Constructor Detail

      • NextProtParser

        public NextProtParser​(Config config)

    • Method Detail

      • defineNextProtXmlTerms

        protected void defineNextProtXmlTerms()

      • fatalError

        protected void fatalError​(java.lang.String message)
        Show an error message and exit

      • getAaEnd

        protected int getAaEnd​(org.w3c.dom.Node posNode)
        Get AA end position from position node

      • getAaStart

        protected int getAaStart​(org.w3c.dom.Node posNode)
        Get AA start position from position node

      • getIsoformRefFromPos

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

      • getMarkers

        public Markers getMarkers()

      • parse

        public void parse​(org.w3c.dom.Node doc)
        Parse XML document

      • setDebug

        public void setDebug​(boolean debug)

      • setTrIdFile

        public void setTrIdFile​(java.lang.String trIdFile)

      • setVerbose

        public void setVerbose​(boolean verbose)