Package org.biojava.bio.program.gff

Class GFFFilterer

java.lang.Object
org.biojava.bio.program.gff.GFFFilterer
All Implemented Interfaces:
GFFDocumentHandler
public class GFFFilterer extends Object implements GFFDocumentHandler
An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.

The choice to forward or drop is made by a GFFRecordFilter.

Unless otherwise stated, all methods forward to the listening handler without altering the arguments in any way.

Author:
Matthew Pocock

  • Constructor Details

    • GFFFilterer

      public GFFFilterer(GFFDocumentHandler handler, GFFRecordFilter filter)
      Create a new GFFFilterer that will forward to handler everything that filter accepts.
      Parameters:
      handler - the listening GFFDocumentHandler
      filter - the GFFRecordFilter that decides what is forwarded to handler

  • Method Details

    • startDocument

      public void startDocument(String locator)
      Description copied from interface: GFFDocumentHandler
      Indicates that a new GFF document has been started. This gives you a hook to set up per-document resources.
      Specified by:
      startDocument in interface GFFDocumentHandler
      Parameters:
      locator - A URI for the stream being parsed.

    • endDocument

      public void endDocument()
      Description copied from interface: GFFDocumentHandler
      Indicates that the current GFF document has now ended.

      This gives you the chance to flush results, or do calculations if you wish.

      Specified by:
      endDocument in interface GFFDocumentHandler

    • commentLine

      public void commentLine(String comment)
      Description copied from interface: GFFDocumentHandler
      A comment line has been encountered.

      comment has already had the leading '#' removed, and may have had leading-and-trailing whitespace trimmed.

      Specified by:
      commentLine in interface GFFDocumentHandler
      Parameters:
      comment - the comment String

    • recordLine

      public void recordLine(GFFRecord record)
      Only forward the GFFRecords that match a filter.
      Specified by:
      recordLine in interface GFFDocumentHandler
      Parameters:
      record - the GFFRecord containing all the info