Package org.biojava.bio.program.sax

Class ClustalWAlignmentSAXParser

  • All Implemented Interfaces:
    org.xml.sax.XMLReader
    public class ClustalWAlignmentSAXParser
extends java.lang.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

    • Constructor Summary

      Constructors 
      Constructor Description
      ClustalWAlignmentSAXParser()
      Initialises internal state Sets namespace prefix to "biojava"

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addPrefixMapping​(java.lang.String poPrefix, java.lang.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.
      org.xml.sax.ContentHandler getContentHandler()
      Return the content handler.
      protected java.io.BufferedReader getContentStream​(org.xml.sax.InputSource poSource)
      Create a stream from an an InputSource, picking the correct stream according to order of precedance.
      org.xml.sax.DTDHandler getDTDHandler()
      Do-nothing implementation of interface method
      org.xml.sax.EntityResolver getEntityResolver()
      Do-nothing implementation of interface method
      org.xml.sax.ErrorHandler getErrorHandler()
      Do-nothing implementation of interface method
      boolean getFeature​(java.lang.String poName)
      Do-nothing implementation of interface method
      java.lang.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.
      java.lang.Object getProperty​(java.lang.String name)
      Do-nothing implementation of interface method
      java.lang.String getURIFromPrefix​(java.lang.String poPrefix)
      Gets the URI for a namespace prefix, given that prefix, or null if the prefix is not recognised.
      void parse​(java.lang.String poSystemId)
      Full implementation of interface method.
      void parse​(org.xml.sax.InputSource poSource)
      Describe 'parse' method here.
      java.lang.String prefix​(java.lang.String poElementName)
      Given an unprefixed element name, returns a new element name with a namespace prefix
      void setContentHandler​(org.xml.sax.ContentHandler poHandler)
      Allow an application to register a content event handler.
      void setDTDHandler​(org.xml.sax.DTDHandler handler)
      Do-nothing implementation of interface method
      void setEntityResolver​(org.xml.sax.EntityResolver resolver)
      Do-nothing implementation of interface method
      void setErrorHandler​(org.xml.sax.ErrorHandler handler)
      Do-nothing implementation of interface method
      void setFeature​(java.lang.String poName, boolean value)
      Handles support for ReasoningDomain and Namespace-prefixes
      void setNamespacePrefix​(java.lang.String poPrefix)  
      void setProperty​(java.lang.String name, java.lang.Object value)
      Do-nothing implementation of interface method
      protected void startElement​(org.biojava.bio.program.sax.QName poQName, org.xml.sax.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 org.xml.sax.ContentHandler oHandler

      • tNamespaces

        protected boolean tNamespaces

      • tNamespacePrefixes

        protected boolean tNamespacePrefixes

      • oNamespacePrefix

        protected java.lang.String oNamespacePrefix

      • oFullNamespacePrefix

        protected java.lang.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​(org.xml.sax.InputSource poSource)
           throws java.io.IOException,
                  org.xml.sax.SAXException
        Describe 'parse' method here.
        Specified by:
        parse in interface org.xml.sax.XMLReader
        Parameters:
        poSource - -
        Throws:
        java.io.IOException
        org.xml.sax.SAXException

      • setContentHandler

        public void setContentHandler​(org.xml.sax.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 org.xml.sax.XMLReader
        Parameters:
        poHandler - a ContentHandler The XML content handler
        Throws:
        java.lang.NullPointerException - If the handler argument is null

      • getContentHandler

        public org.xml.sax.ContentHandler getContentHandler()
        Return the content handler.
        Specified by:
        getContentHandler in interface org.xml.sax.XMLReader
        Returns:
        a ContentHandler The current content handler, or null if none has been registered.

      • parse

        public void parse​(java.lang.String poSystemId)
           throws java.io.IOException,
                  org.xml.sax.SAXException
        Full implementation of interface method.
        Specified by:
        parse in interface org.xml.sax.XMLReader
        Throws:
        java.io.IOException
        org.xml.sax.SAXException

      • getFeature

        public boolean getFeature​(java.lang.String poName)
                   throws org.xml.sax.SAXNotRecognizedException,
                          org.xml.sax.SAXNotSupportedException
        Do-nothing implementation of interface method
        Specified by:
        getFeature in interface org.xml.sax.XMLReader
        Throws:
        org.xml.sax.SAXNotRecognizedException
        org.xml.sax.SAXNotSupportedException

      • setFeature

        public void setFeature​(java.lang.String poName,
                       boolean value)
                throws org.xml.sax.SAXNotRecognizedException,
                       org.xml.sax.SAXNotSupportedException
        Handles support for ReasoningDomain and Namespace-prefixes
        Specified by:
        setFeature in interface org.xml.sax.XMLReader
        Throws:
        org.xml.sax.SAXNotRecognizedException
        org.xml.sax.SAXNotSupportedException

      • getProperty

        public java.lang.Object getProperty​(java.lang.String name)
                             throws org.xml.sax.SAXNotRecognizedException,
                                    org.xml.sax.SAXNotSupportedException
        Do-nothing implementation of interface method
        Specified by:
        getProperty in interface org.xml.sax.XMLReader
        Throws:
        org.xml.sax.SAXNotRecognizedException
        org.xml.sax.SAXNotSupportedException

      • setProperty

        public void setProperty​(java.lang.String name,
                        java.lang.Object value)
                 throws org.xml.sax.SAXNotRecognizedException,
                        org.xml.sax.SAXNotSupportedException
        Do-nothing implementation of interface method
        Specified by:
        setProperty in interface org.xml.sax.XMLReader
        Throws:
        org.xml.sax.SAXNotRecognizedException
        org.xml.sax.SAXNotSupportedException

      • setEntityResolver

        public void setEntityResolver​(org.xml.sax.EntityResolver resolver)
        Do-nothing implementation of interface method
        Specified by:
        setEntityResolver in interface org.xml.sax.XMLReader

      • getEntityResolver

        public org.xml.sax.EntityResolver getEntityResolver()
        Do-nothing implementation of interface method
        Specified by:
        getEntityResolver in interface org.xml.sax.XMLReader

      • setDTDHandler

        public void setDTDHandler​(org.xml.sax.DTDHandler handler)
        Do-nothing implementation of interface method
        Specified by:
        setDTDHandler in interface org.xml.sax.XMLReader

      • getDTDHandler

        public org.xml.sax.DTDHandler getDTDHandler()
        Do-nothing implementation of interface method
        Specified by:
        getDTDHandler in interface org.xml.sax.XMLReader

      • setErrorHandler

        public void setErrorHandler​(org.xml.sax.ErrorHandler handler)
        Do-nothing implementation of interface method
        Specified by:
        setErrorHandler in interface org.xml.sax.XMLReader

      • getErrorHandler

        public org.xml.sax.ErrorHandler getErrorHandler()
        Do-nothing implementation of interface method
        Specified by:
        getErrorHandler in interface org.xml.sax.XMLReader

      • startElement

        protected void startElement​(org.biojava.bio.program.sax.QName poQName,
                            org.xml.sax.Attributes atts)
                     throws org.xml.sax.SAXException
        Utility method to centralize sending of a SAX startElement message to document handler
        Parameters:
        poQName - a QName value
        atts - an Attributes value
        Throws:
        org.xml.sax.SAXException - if an error occurs

      • endElement

        protected void endElement​(org.biojava.bio.program.sax.QName poQName)
                   throws org.xml.sax.SAXException
        Utility method to centralize the sending of a SAX endElement message a document handler.
        Parameters:
        poQName - -
        Throws:
        org.xml.sax.SAXException - thrown if
        thrown - if

      • characters

        protected void characters​(char[] ch,
                          int start,
                          int length)
                   throws org.xml.sax.SAXException
        Utility method to centralize the sending of a SAX characters message a document handler.
        Parameters:
        ch - -
        start - -
        length - -
        Throws:
        org.xml.sax.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​(java.lang.String poPrefix,
                             java.lang.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 java.lang.String getURIFromPrefix​(java.lang.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​(java.lang.String poPrefix)
        Parameters:
        poPrefix - a String value

      • getNamespacePrefix

        public java.lang.String getNamespacePrefix()
        Describe getNamespacePrefix method here.
        Returns:
        a String value

      • prefix

        public java.lang.String prefix​(java.lang.String poElementName)
        Given an unprefixed element name, returns a new element name with a namespace prefix
        Returns:
        a String value

      • getContentStream

        protected java.io.BufferedReader getContentStream​(org.xml.sax.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