public interface SeqFileFormer extends SeqIOListener
SeqFileFormerinterface 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
|Modifier and Type||Method and Description|
Formats the location of a feature.
PrintStreamto which an instance will write the formatted data. If this has not been set, an implementation should default to System.out.
PrintStreamwhich will be written to.
void setPrintStream(PrintStream stream)
setPrintStreaminforms an instance which
PrintStreamto write to.
StringBuffer formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand)
formatLocationcreates 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
StringBufferis used to allow avoidance of expensive
Stringmanipulations on (potentially very large numbers of) locations.
StringBufferto append the location to.
StrandedFeature.Strandindicating any relevant strandedness.
StringBufferwith the location appended.
String formatLocation(Feature theFeature)
theFeature- The feature with the location to format
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