Uses of Class org.biojava.bio.program.gff.GFFEntrySet (biojava-legacy 1.9.5 API)

Packages that use GFFEntrySet
Package	Description
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.

Methods in org.biojava.bio.program.gff that return GFFEntrySet
Modifier and Type	Method	Description
`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
Modifier and Type	Method	Description
`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 Classorg.biojava.bio.program.gff.GFFEntrySet