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Packages that use GFFEntrySet | |
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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 |
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Methods in org.biojava.bio.program.gff that return GFFEntrySet | |
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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 | |
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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 |
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Constructors in org.biojava.bio.seq.distributed with parameters of type GFFEntrySet | |
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GFFDataSource(GFFEntrySet gffe)
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