Class SequencesAsGFF

java.lang.Object
org.biojava.bio.program.gff.SequencesAsGFF

public class SequencesAsGFF extends Object
Turns a sequence database into a GFF event stream.
Author:
Matthew Pocock, Thomas Down, Len Trigg
  • Constructor Details

  • 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

      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