## Uses of Class
org.biojava.bio.program.gff.GFFEntrySet

Packages that use GFFEntrySet
org.biojava.bio.program.gff: GFF manipulation.
org.biojava.bio.seq.distributed: Sequences and SequenceDBs which are composed from data taken from a number of data sources.

Uses of GFFEntrySet in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that return GFFEntrySet
`GFFEntrySet` `GFFEntrySet.filter(GFFRecordFilter filter)` Filter this entry set into another set.
`static GFFEntrySet` `GFFTools.gffFromSeqDB(SequenceDB seqDB)` Creates a GFFEntrySet containing one entry for each feature on each sequence of a SequenceDB.
`static GFFEntrySet` `GFFTools.gffFromSequence(Sequence seq)` Creates a GFFEntrySet containing one entry for each feature on a sequence.
`static GFFEntrySet` `GFFTools.readGFF(BufferedReader gffIn)` Read all GFF entries from a buffered reader.
`static GFFEntrySet` `GFFTools.readGFF(BufferedReader gffIn, GFFRecordFilter recFilt)` Read all GFF entries matching a filter from a buffered reader.
`static GFFEntrySet` `GFFTools.readGFF(File inFile)` Reads a `GFFEntrySet` from a file with no filtering.
`static GFFEntrySet` `GFFTools.readGFF(File inFile, GFFRecordFilter recFilt)` Reads a GFFEntrySet from a file with the specified filter.
`static GFFEntrySet` `GFFTools.readGFF(String fileName)` Deprecated. use: readGff(File)
`static GFFEntrySet` `GFFTools.readGFF(String fileName, GFFRecordFilter recFilt)` Deprecated. use: readGff(File,GFFRecordFilter)

Methods in org.biojava.bio.program.gff with parameters of type GFFEntrySet
`static Sequence` `GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents)` Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
`static Sequence` `GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)` Annotates a sequence with the features from a GFF entry set.
`static SequenceDB` `GFFTools.annotateSequences(SequenceDB seqs, GFFEntrySet ents)` Annotates all sequences in a sequence DB with features from a GFF entry set.
`static void` `GFFTools.writeGFF(File outFile, GFFEntrySet ents)` Writes a GFFEntrySet to a file.
`static void` `GFFTools.writeGFF(PrintWriter pw, GFFEntrySet ents)` Writes a GFFEntrySet to a PrintWriter.
`static void` `GFFTools.writeGFF(String fileName, GFFEntrySet ents)` Writes a GFFEntrySet to a file.

Uses of GFFEntrySet in org.biojava.bio.seq.distributed

Constructors in org.biojava.bio.seq.distributed with parameters of type GFFEntrySet
`GFFDataSource(GFFEntrySet gffe)`