Class FastaSearchSAXParser

Method Details

• parse

  public void parse(InputSource source) throws IOException, SAXException

  Do-nothing implementation of interface method

  Specified by:

  parse in interface XMLReader

  Throws:

  IOException

  SAXException

• getMoreSearches

  public boolean getMoreSearches()

  Description copied from interface: SearchContentHandler

  getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.

  Specified by:

  getMoreSearches in interface SearchContentHandler

  Returns:

  a boolean value.

• setMoreSearches

  public void setMoreSearches(boolean value)

  Description copied from interface: SearchContentHandler

  setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.

  Specified by:

  setMoreSearches in interface SearchContentHandler

  Parameters:

  value - a boolean value.

• setQuerySeq

  public void setQuerySeq(String identifier)

  Deprecated.

  use setQueryID instead.

  setQuerySeq identifies the query sequence by a name, ID or URN.

  Parameters:

  identifier - a String which should be an unique identifer for the sequence.

• setQueryID

  public void setQueryID(String queryID)

  Description copied from interface: SearchContentHandler

  setQueryID identifies the query sequence by a name, ID or URN.

  Specified by:

  setQueryID in interface SearchContentHandler

  Parameters:

  queryID - a String which should be an unique identifer for the sequence.

• setSubjectDB

  public void setSubjectDB(String identifier)

  Deprecated.

  use setDatabaseID instead.

  setSubjectDB identifies the database searched by a name, ID or URN.

  Parameters:

  identifier - a String which should be an unique identifier for the database searched.

• setDatabaseID

  public void setDatabaseID(String databaseID)

  Description copied from interface: SearchContentHandler

  setDatabaseID identifies the database searched by a name, ID or URN.

  Specified by:

  setDatabaseID in interface SearchContentHandler

  Parameters:

  databaseID - a String which should be an unique identifier for the database searched.

• startSearch

  public void startSearch()

  Description copied from interface: SearchContentHandler

  The startSearch method indicates the start of useful search information.

  Specified by:

  startSearch in interface SearchContentHandler

• addSearchProperty

  public void addSearchProperty(Object key, Object value)

  Description copied from interface: SearchContentHandler

  The addSearchProperty method adds a key/value pair containing some property of the overall search result.

  Specified by:

  addSearchProperty in interface SearchContentHandler

  Parameters:

  key - an Object.

  value - an Object.

• endSearch

  public void endSearch()

  Description copied from interface: SearchContentHandler

  The endSearch method indicates the end of useful search information.

  Specified by:

  endSearch in interface SearchContentHandler

• startHeader

  public void startHeader()

  Description copied from interface: SearchContentHandler

  The startHeader method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.

  Specified by:

  startHeader in interface SearchContentHandler

• endHeader

  public void endHeader()

  Description copied from interface: SearchContentHandler

  The endHeader method indicates the end of a formatted header.

  Specified by:

  endHeader in interface SearchContentHandler

• startHit

  public void startHit()

  Description copied from interface: SearchContentHandler

  The startHit method indicates the start of a formatted hit. This could be a single line, or a block of lines.

  Specified by:

  startHit in interface SearchContentHandler

• addHitProperty

  public void addHitProperty(Object key, Object value)

  Description copied from interface: SearchContentHandler

  The addHitProperty method adds a key/value pair containing some property of a particular hit.

  Specified by:

  addHitProperty in interface SearchContentHandler

  Parameters:

  key - an Object.

  value - an Object.

• endHit

  public void endHit()

  Description copied from interface: SearchContentHandler

  The endHit method indicates the end of a formatted hit.

  Specified by:

  endHit in interface SearchContentHandler

• startSubHit

  public void startSubHit()

  Description copied from interface: SearchContentHandler

  The startSubHit method indicates the start of a formatted subhit. There may be zero or more of these per hit.

  Specified by:

  startSubHit in interface SearchContentHandler

• addSubHitProperty

  public void addSubHitProperty(Object key, Object value)

  Description copied from interface: SearchContentHandler

  The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.

  Specified by:

  addSubHitProperty in interface SearchContentHandler

  Parameters:

  key - an Object.

  value - an Object.

• endSubHit

  public void endSubHit()

  Description copied from interface: SearchContentHandler

  The endSubHit method indicates the end of a formatted subhit.

  Specified by:

  endSubHit in interface SearchContentHandler

• setContentHandler

  public void setContentHandler(ContentHandler poHandler)

  Allow an application to register a content event handler. If the application does not register a content handler, all content events reported by the SAX parser will be silently ignored.

  Applications may register a new or different handler in the middle of a parse, and the SAX parser must begin using the new handler immediately.

  Specified by:

  setContentHandler in interface XMLReader

  Parameters:

  poHandler - a ContentHandler The XML content handler

  Throws:

  NullPointerException - If the handler argument is null

• getContentHandler

  public ContentHandler getContentHandler()

  Return the content handler.

  Specified by:

  getContentHandler in interface XMLReader

  Returns:

  a ContentHandler The current content handler, or null if none has been registered.

• parse

  public void parse(String poSystemId) throws IOException, SAXException

  Full implementation of interface method.

  Specified by:

  parse in interface XMLReader

  Throws:

  IOException

  SAXException

• getFeature

  public boolean getFeature(String poName) throws SAXNotRecognizedException, SAXNotSupportedException

  Do-nothing implementation of interface method

  Specified by:

  getFeature in interface XMLReader

  Throws:

  SAXNotRecognizedException

  SAXNotSupportedException

• setFeature

  public void setFeature(String poName, boolean value) throws SAXNotRecognizedException, SAXNotSupportedException

  Handles support for ReasoningDomain and Namespace-prefixes

  Specified by:

  setFeature in interface XMLReader

  Throws:

  SAXNotRecognizedException

  SAXNotSupportedException

• getProperty

  public Object getProperty(String name) throws SAXNotRecognizedException, SAXNotSupportedException

  Do-nothing implementation of interface method

  Specified by:

  getProperty in interface XMLReader

  Throws:

  SAXNotRecognizedException

  SAXNotSupportedException

• setProperty

  public void setProperty(String name, Object value) throws SAXNotRecognizedException, SAXNotSupportedException

  Do-nothing implementation of interface method

  Specified by:

  setProperty in interface XMLReader

  Throws:

  SAXNotRecognizedException

  SAXNotSupportedException

• setEntityResolver

  public void setEntityResolver(EntityResolver resolver)

  Do-nothing implementation of interface method

  Specified by:

  setEntityResolver in interface XMLReader

• getEntityResolver

  public EntityResolver getEntityResolver()

  Do-nothing implementation of interface method

  Specified by:

  getEntityResolver in interface XMLReader

• setDTDHandler

  public void setDTDHandler(DTDHandler handler)

  Do-nothing implementation of interface method

  Specified by:

  setDTDHandler in interface XMLReader

• getDTDHandler

  public DTDHandler getDTDHandler()

  Do-nothing implementation of interface method

  Specified by:

  getDTDHandler in interface XMLReader

• setErrorHandler

  public void setErrorHandler(ErrorHandler handler)

  Do-nothing implementation of interface method

  Specified by:

  setErrorHandler in interface XMLReader

• getErrorHandler

  public ErrorHandler getErrorHandler()

  Do-nothing implementation of interface method

  Specified by:

  getErrorHandler in interface XMLReader

• startElement

  protected void startElement(org.biojava.bio.program.sax.QName poQName, Attributes atts) throws SAXException

  Utility method to centralize sending of a SAX startElement message to document handler

  Parameters:

  poQName - a QName value

  atts - an Attributes value

  Throws:

  SAXException - if an error occurs

• endElement

  protected void endElement(org.biojava.bio.program.sax.QName poQName) throws SAXException

  Utility method to centralize the sending of a SAX endElement message a document handler.

  Parameters:

  poQName - -

  Throws:

  SAXException - thrown if

  thrown - if

• characters

  protected void characters(char[] ch, int start, int length) throws SAXException

  Utility method to centralize the sending of a SAX characters message a document handler.

  Parameters:

  ch - -

  start - -

  length - -

  Throws:

  SAXException - thrown if

  thrown - if

• getNamespaces

  public boolean getNamespaces()

  Support SAX2 configuration of namespace support of parser.

• getNamespacePrefixes

  public boolean getNamespacePrefixes()

  Support SAX2 configuration of namespace support of parser.

• addPrefixMapping

  public void addPrefixMapping(String poPrefix, String poURI)

  Adds a namespace prefix to URI mapping as (key,value) pairs. This mapping can be looked up later to get URIs on request using the getURIFromPrefix method.

  Parameters:

  poPrefix - a String representation of the namespace prefix

  poURI - a String representation of the URI for the namespace prefix.

• getURIFromPrefix

  public String getURIFromPrefix(String poPrefix)

  Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.

  Parameters:

  poPrefix - a String The namespace prefix.

• setNamespacePrefix

  public void setNamespacePrefix(String poPrefix)

  Parameters:

  poPrefix - a String value

• getNamespacePrefix

  public String getNamespacePrefix()

  Describe getNamespacePrefix method here.

  Returns:

  a String value

• prefix

  public String prefix(String poElementName)

  Given an unprefixed element name, returns a new element name with a namespace prefix

  Returns:

  a String value

• getContentStream

  protected BufferedReader getContentStream(InputSource poSource)

  Create a stream from an an InputSource, picking the correct stream according to order of precedance.

  Parameters:

  poSource - an InputSource value

  Returns:

  a BufferedReader value

• changeState

  protected void changeState(int piState)

  Centralise chaining of iState field to help with debugging. E.g. printing out value etc. All changes to iState should be made through this method.

  Parameters:

  piState - an int value