Class SequencesAsGFF

Method Details

• setShatter

  public void setShatter(boolean b)

  Specify whether features with non-contiguous locations should be broken up such that a GFF feature line is emitted for each contiguous block.

  Parameters:

  b -

  Since:

  1.4

• getShatter

  public boolean getShatter()

  Determine if features with non-contiguous locations will be broken into multiple GFF records.

  Since:

  1.4

• setGenerateSequenceHeader

  public void setGenerateSequenceHeader(boolean b)

  Specify whether a per-sequence header line, giving the length of the sequence, should be generated.

  Since:

  1.4

• getGenerateSequenceHeader

  public boolean getGenerateSequenceHeader()

  Discover if per-sequence header lines will be generated.

  Since:

  1.4

• getFeatureFilter

  public FeatureFilter getFeatureFilter()

  Return the current FeatureFilter.

  This is the object that will accept or reject individual features.

  Returns:

  the current FeatureFilter

• setFeatureFilter

  public void setFeatureFilter(FeatureFilter filter)

  Replace the current FeatureFilter with filter.

  Parameters:

  filter - the new FeatureFilter

• getRecurse

  public boolean getRecurse()

  Return whether features will be filtered recursively or not.

  Returns:

  whether or not to recurse

• setRecurse

  public void setRecurse(boolean recurse)

  Set whether features will be filtered recursively to recurse.

  Parameters:

  recurse - true if you want to recurse, false otherwise

• doPreProcessSequence

  protected void doPreProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) throws BioException

  Emit any per-sequence header information. The default implementation emits sequence-region comment lines.

  Throws:

  BioException

  Since:

  1.4

• doProcessSequence

  protected void doProcessSequence(Sequence seq, GFFDocumentHandler handler, String id) throws BioException

  Internal method to process an individual Sequence.

  Parameters:

  seq - the Sequence to GFFify

  handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seq

  id - the value of the seqName field in any GFFRecords produced

  Throws:

  BioException

• doProcessFeature

  protected void doProcessFeature(Feature feature, GFFDocumentHandler handler, String id) throws BioException

  Internal method to process an individual Feature.

  Parameters:

  feature - the Feature to GFFify

  handler - the GFFDocumentHandler that will receive the GFF for this feature

  id - the value of the seqName field in any GFFRecords produced

  Throws:

  BioException

• createGFFRecord

  protected SimpleGFFRecord createGFFRecord(Feature feature, String id) throws BioException

  Internal method to create a GFFRecord from an individual Feature.

  Parameters:

  feature - the Feature to GFFify

  id - the value of the seqName field in any GFFRecords produced

  Throws:

  BioException

• processSequence

  public void processSequence(Sequence seq, GFFDocumentHandler handler) throws BioException

  Process an individual Sequence, informing handler of any suitable features.

  Parameters:

  seq - the Sequence to GFFify

  handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seq

  Throws:

  BioException

• processDB

  public void processDB(SequenceDB seqDB, GFFDocumentHandler handler) throws BioException

  Process all Sequences within a SequenceDB, informing handler of any suitable features.

  Parameters:

  seqDB - the SequenceDB to GFFify

  handler - the GFFDocumentHandler that will receive the GFF for all suitable features within seqDB

  Throws:

  BioException