Package | Description |
---|---|
org.biojava.bio.program.gff |
GFF manipulation.
|
org.biojava.bio.program.gff3 |
Support for reading and writing GFF3.
|
Modifier and Type | Method and Description |
---|---|
protected GFFRecord |
GFFParser.createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a
GFFRecord and informs
handler.
|
int |
GFFErrorHandler.invalidEnd(java.lang.String token)
The `end' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.SkipRecordErrorHandler.invalidEnd(java.lang.String token) |
int |
GFFErrorHandler.invalidFrame(java.lang.String token)
The `frame' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.SkipRecordErrorHandler.invalidFrame(java.lang.String token) |
double |
GFFErrorHandler.invalidScore(java.lang.String token)
The `score' field of the GFF entry was not a valid value.
|
double |
GFFErrorHandler.SkipRecordErrorHandler.invalidScore(java.lang.String token) |
int |
GFFErrorHandler.invalidStart(java.lang.String token)
The `start' field of the GFF entry was not a valid value.
|
int |
GFFErrorHandler.SkipRecordErrorHandler.invalidStart(java.lang.String token) |
StrandedFeature.Strand |
GFFErrorHandler.invalidStrand(java.lang.String token)
The `strand' field of the GFF entry was not a valid value.
|
StrandedFeature.Strand |
GFFErrorHandler.SkipRecordErrorHandler.invalidStrand(java.lang.String token) |
Modifier and Type | Method and Description |
---|---|
protected GFF3Record |
GFF3Parser.createRecord(GFF3DocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment,
Ontology ontology,
Ontology fallBack)
Actually turns a list of tokens, some value string and a comment into a
GFF3Record and informs
handler.
|