Interface SeqFileFormer

  • All Superinterfaces:
    SeqIOListener
    All Known Implementing Classes:
    EmblFileFormer, GenbankFileFormer, ProteinRefSeqFileFormer, SwissprotFileFormer

    public interface SeqFileFormer
    extends SeqIOListener
    Deprecated.
    Use org.biojavax.bio.seq.io framework instead
    Objects implementing the SeqFileFormer interface are responsible for the detailed formatting of sequence data prior to writing to a PrintStream. Some file formats, such as Fasta, are very simple and don't require a SeqFileFormer.
    Since:
    1.2
    Author:
    Keith James
    • Method Detail

      • getPrintStream

        java.io.PrintStream getPrintStream()
        Deprecated.
        getPrintStream returns the PrintStream to which an instance will write the formatted data. If this has not been set, an implementation should default to System.out.
        Returns:
        the PrintStream which will be written to.
      • setPrintStream

        void setPrintStream​(java.io.PrintStream stream)
        Deprecated.
        setPrintStream informs an instance which PrintStream to use.
        Parameters:
        stream - a PrintStream to write to.
      • formatLocation

        java.lang.StringBuffer formatLocation​(java.lang.StringBuffer sb,
                                              Location loc,
                                              StrandedFeature.Strand strand)
        Deprecated.
        formatLocation creates a String representation of a Location. The strand may not be relevant for all formats (e.g. it is relevant for Genbank and EMBL, but not for SwissProt). In such cases the implementation may accept a strand of 'unknown', '0' or '.'. A StringBuffer is used to allow avoidance of expensive String manipulations on (potentially very large numbers of) locations.
        Parameters:
        sb - a StringBuffer to append the location to.
        loc - a Location to format.
        strand - a StrandedFeature.Strand indicating any relevant strandedness.
        Returns:
        a StringBuffer with the location appended.
      • formatLocation

        java.lang.String formatLocation​(Feature theFeature)
        Deprecated.
        Formats the location of a feature. This version is required when formatting remote locations, since the location field of a remote feature is the projection of that feature on the sequence. When a distinction is made between 'order' and 'join' this method will likely be extended for that also.
        Parameters:
        theFeature - The feature with the location to format
        Returns:
        String The formatted location