Package org.biojava.bio.seq.io
Interface SeqFileFormer
- All Superinterfaces:
SeqIOListener
- All Known Implementing Classes:
EmblFileFormer
,GenbankFileFormer
,ProteinRefSeqFileFormer
,SwissprotFileFormer
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 Summary
Modifier and TypeMethodDescriptionformatLocation
(StringBuffer sb, Location loc, StrandedFeature.Strand strand) Deprecated.formatLocation
creates a String representation of aLocation
.formatLocation
(Feature theFeature) Deprecated.Formats the location of a feature.Deprecated.getPrintStream
returns thePrintStream
to which an instance will write the formatted data.void
setPrintStream
(PrintStream stream) Deprecated.setPrintStream
informs an instance whichPrintStream
to use.Methods inherited from interface org.biojava.bio.seq.io.SeqIOListener
addFeatureProperty, addSequenceProperty, addSymbols, endFeature, endSequence, setName, setURI, startFeature, startSequence
-
Method Details
-
getPrintStream
Deprecated.getPrintStream
returns thePrintStream
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
Deprecated.setPrintStream
informs an instance whichPrintStream
to use.- Parameters:
stream
- aPrintStream
to write to.
-
formatLocation
Deprecated.formatLocation
creates a String representation of aLocation
. 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 '.'. AStringBuffer
is used to allow avoidance of expensiveString
manipulations on (potentially very large numbers of) locations.- Parameters:
sb
- aStringBuffer
to append the location to.loc
- aLocation
to format.strand
- aStrandedFeature.Strand
indicating any relevant strandedness.- Returns:
- a
StringBuffer
with the location appended.
-
formatLocation
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
-