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java.lang.Objectorg.biojava.bio.program.sax.ClustalWAlignmentSAXParser
public class ClustalWAlignmentSAXParser
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 -
Field Summary | |
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protected int |
iState
|
protected java.lang.String |
oFullNamespacePrefix
|
protected org.xml.sax.ContentHandler |
oHandler
|
protected java.lang.String |
oNamespacePrefix
|
protected boolean |
tNamespacePrefixes
|
protected boolean |
tNamespaces
|
Constructor Summary | |
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ClustalWAlignmentSAXParser()
Initialises internal state Sets namespace prefix to "biojava" |
Method Summary | |
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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(org.xml.sax.InputSource poSource)
Describe 'parse' method here. |
void |
parse(java.lang.String poSystemId)
Full implementation of interface method. |
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected org.xml.sax.ContentHandler oHandler
protected boolean tNamespaces
protected boolean tNamespacePrefixes
protected java.lang.String oNamespacePrefix
protected java.lang.String oFullNamespacePrefix
protected int iState
Constructor Detail |
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public ClustalWAlignmentSAXParser()
Method Detail |
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public void parse(org.xml.sax.InputSource poSource) throws java.io.IOException, org.xml.sax.SAXException
parse
in interface org.xml.sax.XMLReader
poSource
- -
java.io.IOException
org.xml.sax.SAXException
public void setContentHandler(org.xml.sax.ContentHandler poHandler)
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.
setContentHandler
in interface org.xml.sax.XMLReader
poHandler
- a ContentHandler
The XML content handler
java.lang.NullPointerException
- If the handler argument is nullpublic org.xml.sax.ContentHandler getContentHandler()
getContentHandler
in interface org.xml.sax.XMLReader
ContentHandler
The current content handler,
or null if none has been registered.public void parse(java.lang.String poSystemId) throws java.io.IOException, org.xml.sax.SAXException
parse
in interface org.xml.sax.XMLReader
java.io.IOException
org.xml.sax.SAXException
public boolean getFeature(java.lang.String poName) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
getFeature
in interface org.xml.sax.XMLReader
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
public void setFeature(java.lang.String poName, boolean value) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
setFeature
in interface org.xml.sax.XMLReader
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
public java.lang.Object getProperty(java.lang.String name) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
getProperty
in interface org.xml.sax.XMLReader
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
public void setProperty(java.lang.String name, java.lang.Object value) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
setProperty
in interface org.xml.sax.XMLReader
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
public void setEntityResolver(org.xml.sax.EntityResolver resolver)
setEntityResolver
in interface org.xml.sax.XMLReader
public org.xml.sax.EntityResolver getEntityResolver()
getEntityResolver
in interface org.xml.sax.XMLReader
public void setDTDHandler(org.xml.sax.DTDHandler handler)
setDTDHandler
in interface org.xml.sax.XMLReader
public org.xml.sax.DTDHandler getDTDHandler()
getDTDHandler
in interface org.xml.sax.XMLReader
public void setErrorHandler(org.xml.sax.ErrorHandler handler)
setErrorHandler
in interface org.xml.sax.XMLReader
public org.xml.sax.ErrorHandler getErrorHandler()
getErrorHandler
in interface org.xml.sax.XMLReader
protected void startElement(org.biojava.bio.program.sax.QName poQName, org.xml.sax.Attributes atts) throws org.xml.sax.SAXException
poQName
- a QName
valueatts
- an Attributes
value
org.xml.sax.SAXException
- if an error occursprotected void endElement(org.biojava.bio.program.sax.QName poQName) throws org.xml.sax.SAXException
poQName
- -
org.xml.sax.SAXException
- thrown if
thrown
- ifprotected void characters(char[] ch, int start, int length) throws org.xml.sax.SAXException
ch
- -start
- -length
- -
org.xml.sax.SAXException
- thrown if
thrown
- ifpublic boolean getNamespaces()
public boolean getNamespacePrefixes()
public void addPrefixMapping(java.lang.String poPrefix, java.lang.String poURI)
poPrefix
- a String
representation of the
namespace prefixpoURI
- a String
representation of the URI
for the namespace prefix.public java.lang.String getURIFromPrefix(java.lang.String poPrefix)
poPrefix
- a String
The namespace prefix.public void setNamespacePrefix(java.lang.String poPrefix)
poPrefix
- a String
valuepublic java.lang.String getNamespacePrefix()
getNamespacePrefix
method here.
String
valuepublic java.lang.String prefix(java.lang.String poElementName)
String
valueprotected java.io.BufferedReader getContentStream(org.xml.sax.InputSource poSource)
poSource
- an InputSource
value
BufferedReader
valueprotected void changeState(int piState)
piState
- an int
value
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