Class NextProtDb


  • public class NextProtDb
    extends java.lang.Object
    Parse NetxProt XML file and build a database

    http://www.nextprot.org/

    How this works: - NextProtDb Main class to parse a directory with NextPort XML files. Each XML file is quite large (several GB compressed) so it cannot be fully loaded and parse in memory on a "standard laptop" Once all markers are created (by the marker factory) the database is serialized to a file

    - NextProtMarkerFactory Factory that creates all NextProt Markers. This object is shared across all XML handlers

    - NextProtHandler This is a handler used to extract the relevant data from an XML file. One handler is created for each XML file, all handlers share the NextProtMarkerFactory

    - NextProtSequenceConservation The markers are analyzed for sequence conservation patterns. If the marker type has high conservation, this is set in the NextProtMarker to keep in mind when predicting effects. For instance, a marker that has 100% conservation would be highly affected by a non-synonymous variant.

    - NextProtXmlNode This is the basic "XML" node for the information we need to extract to create the Markers

    - NextProtXmlIsoform: Specified an isoform protein / transcript

    - NextProtXmlAnnotation: An annotation is a controlled vocabulary term (CvTerm) associated with one or more Locations in an Isoform. Example: "For transcript TR_1234, amino acid 25 is a phosphorylation site" In this case we have: "TR_1234": The Isoform "amino acid 25": The Location in the Isoform "phosphorylation site": The controlled vocabulary term

    - NextProtXmlEntry: A set of annotations

    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
      boolean parse()
      Parse all XML files in a directory
      void saveDatabase()  
      void setDebug​(boolean debug)  
      void setVerbose​(boolean verbose)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • NextProtDb

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

      • parse

        public boolean parse()
        Parse all XML files in a directory
      • saveDatabase

        public void saveDatabase()
      • setDebug

        public void setDebug​(boolean debug)
      • setVerbose

        public void setVerbose​(boolean verbose)