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
static GFFEntrySet GFFTools.readGFF(java.lang.String fileName)
          Reads a GFFEntrySet from a file with no filtering
static GFFEntrySet GFFTools.readGFF(java.lang.String fileName, GFFRecordFilter recFilt)
          Reads a GFFEntrySet from a file with the specified filter
static GFFEntrySet GFFTools.readGFF(java.io.BufferedReader gffIn)
           
static GFFEntrySet GFFTools.readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt)
           
static GFFEntrySet GFFTools.gffFromSequence(Sequence seq)
          Creates a GFFEntrySet containing one entry for each feature on a sequence.
 GFFEntrySet GFFEntrySet.filter(GFFRecordFilter filter)
          Filter this entry set into another set.
 

Methods in org.biojava.bio.program.gff with parameters of type GFFEntrySet
static void GFFTools.writeGFF(java.lang.String fileName, GFFEntrySet ents)
          Writes a GFFEntrySet to a file
static void GFFTools.writeGFF(java.io.PrintWriter pw, GFFEntrySet ents)
          Writes a GFFEntrySet to a PrintWriter
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.
 

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

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