Class DebuggingRichSeqIOListener

All Implemented Interfaces:
Closeable, AutoCloseable, SeqIOListener, RichSeqIOListener

This is purely for debugging purposes. Use it to wrap an input stream then pass it as a parameter to some format to listen for sequence generation events. It will dump out char-by-char what it reads, followed event-by-event the events it receives from the format.
Since:
1.5
Author:
Richard Holland, Mark Schreiber, Michael Heuer
  • Constructor Details

  • Method Details

    • read

      public int read() throws IOException

      Echoes everything that is read to stdout.

      Overrides:
      read in class BufferedInputStream
      Throws:
      IOException
    • setAccession

      public void setAccession(String accession) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the accession of the record being read. It is possible that some records have more than one accession. As a guide the first one sent to the listener should be the primary one.
      Specified by:
      setAccession in interface RichSeqIOListener
      Parameters:
      accession - The accession of the record
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
      See Also:
    • setIdentifier

      public void setIdentifier(String identifier) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the identifier of the record being read. There should be zero or one identifier per bioentry. If there is more than one the Listener should consider throwing an exception. For some formats like fasta the identifier may not exist. For others like GenBank the identifier best maps to the GI.
      Specified by:
      setIdentifier in interface RichSeqIOListener
      Parameters:
      identifier - The identifier of the Bioentry.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
      See Also:
    • setDivision

      public void setDivision(String division) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the division of the record being read. If the source of the calls back is a GenBank parser the division will be a Genbank division. This method would typically be called 0 or 1 times. It should not be called more than once per entry and an exception could be thrown if it is.
      Specified by:
      setDivision in interface RichSeqIOListener
      Parameters:
      division - The division the entry belongs too.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setDescription

      public void setDescription(String description) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the description of the record being read. For example the description line of a FASTA format file would be the description. This method would typically be called 0 or 1 times and may cause an exception if it is called more than once per entry.
      Specified by:
      setDescription in interface RichSeqIOListener
      Parameters:
      description - The description of the record
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setVersion

      public void setVersion(int version) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the version of the record being read. This method would typically be called 0 or 1 times per entry. If it is not called the Listener should assume the version is 0. If it is called more than once per entry an exception should be thrown.
      Specified by:
      setVersion in interface RichSeqIOListener
      Parameters:
      version - the version of the record
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setSeqVersion

      public void setSeqVersion(String version) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the version of the sequence of the record being read. This method would typically be called 0 or 1 times per entry. If it is not called the Listener should assume the version is 0. If it is called more than once per entry an exception should be thrown.
      Specified by:
      setSeqVersion in interface RichSeqIOListener
      Parameters:
      version - the version of the record
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setComment

      public void setComment(String comment) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener about a comment in the record being read. The comment is typically one or more comment lines relevant to the record as a whole and bundled in a Commment object. This method may be called zero or one times per entry. It can be called zero or more times.
      Specified by:
      setComment in interface RichSeqIOListener
      Parameters:
      comment - The comment
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setRankedDocRef

      public void setRankedDocRef(RankedDocRef ref) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener about a literature reference in the record being read. This method may be called zero or more times.
      Specified by:
      setRankedDocRef in interface RichSeqIOListener
      Parameters:
      ref - A literature reference contained in the entry.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setTaxon

      public void setTaxon(NCBITaxon taxon) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the Taxon of the record being read. This method may be called zero or one times. An exception may be thrown if it is called more than once. As a design decision NCBI's taxon model was chosen as it is commonly used and is supported by the BioSQL schema. The setting of an NCBI taxon should be considered entirely optional.
      Specified by:
      setTaxon in interface RichSeqIOListener
      Parameters:
      taxon - The taxon information relevant to this entry.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setNamespace

      public void setNamespace(Namespace namespace) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener the namespace of the record being read. The method can be called zero or one time. If it is called more than once an exception may be thrown.

      The namespace is a concept from the BioSQL schema that enables Bioentries to be disambiguated. It is possible in BioSQL and should be possible in other collections of BioEntries to have records that have the same name, accession and version but different namespaces. This method would be expected to be called if you are reading a sequence from a biosql database or if you are implementing a listener that knows how to write to a biosql database. If you give a sequence a namespace and it is persited to biosql at somepoint in it's life you could expect it to be persisted to that namespace (if possible).

      Specified by:
      setNamespace in interface RichSeqIOListener
      Parameters:
      namespace - The namespace of the entry.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setRelationship

      public void setRelationship(BioEntryRelationship relationship) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry. This may be called zero or more times.
      Specified by:
      setRelationship in interface RichSeqIOListener
      Parameters:
      relationship - The relationship
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setRankedCrossRef

      public void setRankedCrossRef(RankedCrossRef crossRef) throws ParseException
      Description copied from interface: RichSeqIOListener
      Call back method so the event emitter can tell the listener about a cross reference. This could be called zero or more times per entry.
      Specified by:
      setRankedCrossRef in interface RichSeqIOListener
      Parameters:
      crossRef - the cross reference
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • setURI

      public void setURI(String uri) throws ParseException
      Description copied from interface: RichSeqIOListener
      Notify the listener of a URI identifying the current sequence.
      Specified by:
      setURI in interface RichSeqIOListener
      Specified by:
      setURI in interface SeqIOListener
      Throws:
      ParseException
    • getCurrentFeature

      Description copied from interface: RichSeqIOListener
      Gets the feature currently being created.
      Specified by:
      getCurrentFeature in interface RichSeqIOListener
      Returns:
      the feature under construction.
      Throws:
      ParseException - if a feature is not currently being created.
    • setCircular

      public void setCircular(boolean circular) throws ParseException
      Description copied from interface: RichSeqIOListener
      Defined this sequence being parser as circular. It is best to call this as early as possible during parsing. It should definitely be called before doing anything with locations or features.
      Specified by:
      setCircular in interface RichSeqIOListener
      Parameters:
      circular - set this to true if you want it to be circular.
      Throws:
      ParseException - If the Listener cannot understand the event, is unable to deal with the event or is not expecting the event.
    • startSequence

      public void startSequence() throws ParseException
      Description copied from interface: SeqIOListener
      Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.
      Specified by:
      startSequence in interface SeqIOListener
      Throws:
      ParseException
    • endSequence

      public void endSequence() throws ParseException
      Description copied from interface: SeqIOListener
      Notify the listener that processing of the sequence is complete.
      Specified by:
      endSequence in interface SeqIOListener
      Throws:
      ParseException
    • setName

      public void setName(String name) throws ParseException
      Description copied from interface: SeqIOListener
      Notify the listener that the current sequence is generally known by a particular name.
      Specified by:
      setName in interface SeqIOListener
      Parameters:
      name - the String that should be returned by getName for the sequence being parsed
      Throws:
      ParseException
    • addSymbols

      public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
      Description copied from interface: SeqIOListener
      Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception
      Specified by:
      addSymbols in interface SeqIOListener
      Parameters:
      alpha - The alphabet of the symbol data
      syms - An array containing symbols
      start - The start offset of valid data within the array
      length - The number of valid symbols in the array
      Throws:
      IllegalAlphabetException - if we can't cope with this alphabet.
    • addSequenceProperty

      public void addSequenceProperty(Object key, Object value) throws ParseException
      Description copied from interface: SeqIOListener
      Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.
      Specified by:
      addSequenceProperty in interface SeqIOListener
      Throws:
      ParseException
    • startFeature

      public void startFeature(Feature.Template templ) throws ParseException
      Description copied from interface: SeqIOListener
      Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.
      Specified by:
      startFeature in interface SeqIOListener
      Throws:
      ParseException
    • endFeature

      public void endFeature() throws ParseException
      Description copied from interface: SeqIOListener
      Mark the end of data associated with one specific feature.
      Specified by:
      endFeature in interface SeqIOListener
      Throws:
      ParseException
    • addFeatureProperty

      public void addFeatureProperty(Object key, Object value) throws ParseException
      Description copied from interface: SeqIOListener
      Notify the listener of a feature property.
      Specified by:
      addFeatureProperty in interface SeqIOListener
      Throws:
      ParseException