Package org.biojava.bio.program.gff

Class GFFWriter

  • All Implemented Interfaces:
    GFFDocumentHandler
    public class GFFWriter
extends java.lang.Object
implements GFFDocumentHandler
    Listens to a stream of GFF events and writes the lines to a PrintWriter.

    This will ignore all exceptions. Perhaps the error-handling needs to move into an error handling interface?

    Author:
    Matthew Pocock, Keith James (docs)

    • Constructor Summary

      Constructors 
      Constructor Description
      GFFWriter​(java.io.PrintWriter out)
      Create a new GFFWriter that will write to out.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void commentLine​(java.lang.String comment)
      Prints the comment directly to the PrintWriter after adding a leading '#'.
      void endDocument()
      Flushes the PrintWriter to make sure that everything is written.
      void invalidEnd​(java.lang.String token, java.lang.NumberFormatException nfe)  
      void invalidFrame​(java.lang.String token, java.lang.NumberFormatException nfe)  
      void invalidScore​(java.lang.String token, java.lang.NumberFormatException nfe)  
      void invalidStart​(java.lang.String token, java.lang.NumberFormatException nfe)  
      void invalidStrand​(java.lang.String token)  
      void recordLine​(GFFRecord record)
      Prints record to the PrintWriter.
      void startDocument​(java.lang.String locator)
      Indicates that a new GFF document has been started.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • GFFWriter

        public GFFWriter​(java.io.PrintWriter out)
        Create a new GFFWriter that will write to out.
        Parameters:
        out - the PrintWriter to write to

    • Method Detail

      • startDocument

        public void startDocument​(java.lang.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()
        Flushes the PrintWriter to make sure that everything is written.
        Specified by:
        endDocument in interface GFFDocumentHandler

      • commentLine

        public void commentLine​(java.lang.String comment)
        Prints the comment directly to the PrintWriter after adding a leading '#'.
        Specified by:
        commentLine in interface GFFDocumentHandler
        Parameters:
        comment - the comment String

      • recordLine

        public void recordLine​(GFFRecord record)
        Prints record to the PrintWriter.
        Specified by:
        recordLine in interface GFFDocumentHandler
        Parameters:
        record - the GFFRecord containing all the info

      • invalidStart

        public void invalidStart​(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
        Throws:
        BioException

      • invalidEnd

        public void invalidEnd​(java.lang.String token,
                       java.lang.NumberFormatException nfe)
                throws BioException
        Throws:
        BioException

      • invalidScore

        public void invalidScore​(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
        Throws:
        BioException

      • invalidFrame

        public void invalidFrame​(java.lang.String token,
                         java.lang.NumberFormatException nfe)
                  throws BioException
        Throws:
        BioException