Package org.snpeff.nextProt

Class NextProtDb

  • public class NextProtDb
extends java.lang.Object
    Parse NetxProt XML file and build a database http://www.nextprot.org/
    Author:
    pablocingolani

    • Constructor Summary

      Constructors 
      Constructor Description
      NextProtDb​(java.lang.String xmlDirName, Config config)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void fatalError​(java.lang.String message)
      Show an error message and exit
      boolean parse()
      Parse XML file
      void saveDatabase()
      Save nextprot markers as databases
      void setDebug​(boolean debug)  
      void setTrIdFile​(java.lang.String trIdFile)  
      void setVerbose​(boolean verbose)  

      • Methods inherited from class java.lang.Object

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

    • 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

    • Constructor Detail

      • NextProtDb

        public NextProtDb​(java.lang.String xmlDirName,
                  Config config)

    • Method Detail

      • fatalError

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

      • parse

        public boolean parse()
        Parse XML file

      • saveDatabase

        public void saveDatabase()
        Save nextprot markers as databases

      • setDebug

        public void setDebug​(boolean debug)

      • setTrIdFile

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

      • setVerbose

        public void setVerbose​(boolean verbose)