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)