Package de.julielab.jules.ae.genemapping.resources.ncbigene

Class GeneXMLUtils

  • public class GeneXMLUtils
extends java.lang.Object

    • Constructor Summary

      Constructors 
      Constructor Description
      GeneXMLUtils()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.Set<java.lang.String> determineMissingTaxIds​(java.io.File taxIdFile, java.io.File storageDirectory, java.io.File dbFile, java.io.File downloadedTaxIdsFile)  
      static java.util.List<GeneXmlExtract> extractAndWriteGeneInfoToFile​(java.io.OutputStream osSummaries, java.io.OutputStream osProtnames, java.io.OutputStream ofRefSeqAndTracStatus, java.io.InputStream is)  
      static java.util.List<GeneXmlExtract> extractGeneInfoFromXml​(java.io.InputStream openStream)  
      static java.util.List<java.io.File> getMetaFiles​(java.io.File storageDirectory)
      Returns the file objects for the meta information files retrieved from NCBI Gene XML data.
      static void writeGeneInfoToFile​(java.util.List<GeneXmlExtract> geneExtractList, java.io.OutputStream osSummaries, java.io.OutputStream osProtnames, java.io.OutputStream osRefSeqAndTrackStatus)  

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • EG2ENTREZGENE_PROT_FILENAME

        public static final java.lang.String EG2ENTREZGENE_PROT_FILENAME
        See Also:
        Constant Field Values

      • EG2SUMMARY_FILENAME

        public static final java.lang.String EG2SUMMARY_FILENAME
        See Also:
        Constant Field Values

    • Constructor Detail

      • GeneXMLUtils

        public GeneXMLUtils()

    • Method Detail

      • writeGeneInfoToFile

        public static void writeGeneInfoToFile​(java.util.List<GeneXmlExtract> geneExtractList,
                                       java.io.OutputStream osSummaries,
                                       java.io.OutputStream osProtnames,
                                       java.io.OutputStream osRefSeqAndTrackStatus)
                                throws java.io.IOException
        Throws:
        java.io.IOException

      • extractGeneInfoFromXml

        public static java.util.List<GeneXmlExtract> extractGeneInfoFromXml​(java.io.InputStream openStream)
                                                             throws javax.xml.stream.XMLStreamException,
                                                                    java.io.IOException
        Throws:
        javax.xml.stream.XMLStreamException
        java.io.IOException

      • extractAndWriteGeneInfoToFile

        public static java.util.List<GeneXmlExtract> extractAndWriteGeneInfoToFile​(java.io.OutputStream osSummaries,
                                                                           java.io.OutputStream osProtnames,
                                                                           java.io.OutputStream ofRefSeqAndTracStatus,
                                                                           java.io.InputStream is)
                                                                    throws javax.xml.stream.XMLStreamException,
                                                                           java.io.IOException
        Throws:
        javax.xml.stream.XMLStreamException
        java.io.IOException

      • determineMissingTaxIds

        public static java.util.Set<java.lang.String> determineMissingTaxIds​(java.io.File taxIdFile,
                                                                     java.io.File storageDirectory,
                                                                     java.io.File dbFile,
                                                                     java.io.File downloadedTaxIdsFile)
                                                              throws java.io.IOException
        Throws:
        java.io.IOException

      • getMetaFiles

        public static java.util.List<java.io.File> getMetaFiles​(java.io.File storageDirectory)
        Returns the file objects for the meta information files retrieved from NCBI Gene XML data. The list of files contains
        1. gene summaries file
        2. gene protein names file
        3. taxonomy ID list of organisms for which the other files contain records
        4. gene RefSeq status
        Parameters:
        storageDirectory - The base directory where to find/store the meta data.
        Returns:
        An ordered list of gene meta data files.