Package org.biojava.bio.seq.io

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 Details

    • getPrintStream

      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(PrintStream stream)
      Deprecated.
      setPrintStream informs an instance which PrintStream to use.
      Parameters:
      stream - a PrintStream to write to.

    • formatLocation

      StringBuffer formatLocation(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

      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