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## org.biojava.bio.program.sax
Class ClustalWAlignmentSAXParser

    java.lang.Object
      org.biojava.bio.program.sax.ClustalWAlignmentSAXParser

All Implemented Interfaces:
  XMLReader

    public class ClustalWAlignmentSAXParser

extends Object

A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format. For example,

      K1C0_XENLA/125-441      DKVHALETANTELERKIKEWYEKQRPGSSSGDGAKDYSKYYT
      K1C4_XENLA/81-396       EKVRALEAANADLELKIREWYEKQK-GSGIGAGSKDFSKYFE
      K1C5_XENLA/73-384       DRVRSLEQANHELELKIREYLDKK-----AAVGSLDYSGYYN
      keratin15               DKVRALEEANADLEVKIHDWYQKQTP----ASPECDYSQYFK

      K1C0_XENLA/125-441      -----AKFLLQNDNARLAADDFKMKFEN--------------
      K1C4_XENLA/81-396       -----SRVVLQIDNAKLAADDFRLKFEN--------------
      K1C5_XENLA/73-384       -----TRLVLSIDNAKLAADDFKIKYES--------------
      keratin15               -----SRVILEIDNARLAADDFRLKYEN--------------

Please note, this parser reads the whole alignment in to core memory and thus does not scale to work with very large alignments on low-end hardware.

Please also note that this class has not been tested with many version of CLUSTAL W. Copyright © 2000,2001 Cambridge Antibody Technology.

Primary author -

- Simon Brocklehurst (CAT)

Other authors -

- Neil Benn (CAT)
- Lawrence Bower (CAT)
- Derek Crockford (CAT)
- Tim Dilks (CAT)
- Colin Hardman (CAT)
- Stuart Johnston (CAT)

Version:
  1.0
Author:
  Cambridge Antibody Technology (CAT), Greg Cox

Field Summary
`protected int` | `iState`
`protected String` | `oFullNamespacePrefix`
`protected ContentHandler` | `oHandler`
`protected String` | `oNamespacePrefix`
`protected boolean` | `tNamespacePrefixes`
`protected boolean` | `tNamespaces`

Constructor Summary
`ClustalWAlignmentSAXParser()` Initialises internal state Sets namespace prefix to "biojava"

Method Summary
`void` | `addPrefixMapping(String poPrefix, String poURI)` Adds a namespace prefix to URI mapping as (key,value) pairs.
`protected void` | `changeState(int piState)` Centralise chaining of iState field to help with debugging.
`protected void` | `characters(char[] ch, int start, int length)` Utility method to centralize the sending of a SAX characters message a document handler.
`protected void` | `endElement(org.biojava.bio.program.sax.QName poQName)` Utility method to centralize the sending of a SAX endElement message a document handler.
`ContentHandler` | `getContentHandler()` Return the content handler.
`protected BufferedReader` | `getContentStream(InputSource poSource)` Create a stream from an an InputSource, picking the correct stream according to order of precedance.
`DTDHandler` | `getDTDHandler()` Do-nothing implementation of interface method
`EntityResolver` | `getEntityResolver()` Do-nothing implementation of interface method
`ErrorHandler` | `getErrorHandler()` Do-nothing implementation of interface method
`boolean` | `getFeature(String poName)` Do-nothing implementation of interface method
`String` | `getNamespacePrefix()` Describe `getNamespacePrefix` method here.
`boolean` | `getNamespacePrefixes()` Support SAX2 configuration of namespace support of parser.
`boolean` | `getNamespaces()` Support SAX2 configuration of namespace support of parser.
`Object` | `getProperty(String name)` Do-nothing implementation of interface method
`String` | `getURIFromPrefix(String poPrefix)` Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.
`void` | `parse(InputSource poSource)` Describe 'parse' method here.
`void` | `parse(String poSystemId)` Full implementation of interface method.
`String` | `prefix(String poElementName)` Given an unprefixed element name, returns a new element name with a namespace prefix
`void` | `setContentHandler(ContentHandler poHandler)` Allow an application to register a content event handler.
`void` | `setDTDHandler(DTDHandler handler)` Do-nothing implementation of interface method
`void` | `setEntityResolver(EntityResolver resolver)` Do-nothing implementation of interface method
`void` | `setErrorHandler(ErrorHandler handler)` Do-nothing implementation of interface method
`void` | `setFeature(String poName, boolean value)` Handles support for ReasoningDomain and Namespace-prefixes
`void` | `setNamespacePrefix(String poPrefix)`
`void` | `setProperty(String name, Object value)` Do-nothing implementation of interface method
`protected void` | `startElement(org.biojava.bio.program.sax.QName poQName, Attributes atts)` Utility method to centralize sending of a SAX startElement message to document handler

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

### oHandler

    protected ContentHandler oHandler

### tNamespaces

    protected boolean tNamespaces

### tNamespacePrefixes

    protected boolean tNamespacePrefixes

### oNamespacePrefix

    protected String oNamespacePrefix

### oFullNamespacePrefix

    protected String oFullNamespacePrefix

### iState

    protected int iState

Constructor Detail

### ClustalWAlignmentSAXParser

    public ClustalWAlignmentSAXParser()

  Initialises internal state Sets namespace prefix to "biojava"

Method Detail

### parse

    public void parse(InputSource poSource)
               throws IOException,
                      SAXException

  Describe 'parse' method here.

  Specified by:
    `parse` in interface `XMLReader`
  Parameters:
    `poSource` - -
  Throws:
    `IOException`
    `SAXException`

### 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

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