java.lang.Object
- org.biojava.bio.program.sax.FastaSearchSAXParser

All Implemented Interfaces:

SearchContentHandler, XMLReader
```
public class FastaSearchSAXParser
extends Object
implements SearchContentHandler
```
FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).

Versions of Fasta supported are as follows. Note that the compile time option -DM10_CONS should be used to allow correct reporting of the number of matches in HSPSummary elements
- 33t07
- 33t08 (current tests are against output from this version)
The SAX2 events produced are as if the input to the parser was an XML file validating against the BioJava BlastLikeDataSetCollection DTD. There is no requirement for an intermediate conversion of native output to XML format.
Since:

1.2

Author:

Keith James

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`iState`
`protected String`	`oFullNamespacePrefix`
`protected ContentHandler`	`oHandler`
`protected String`	`oNamespacePrefix`
`protected boolean`	`tNamespacePrefixes`
`protected boolean`	`tNamespaces`

Constructor Summary

Constructors
Constructor Description

FastaSearchSAXParser()
Creates a new FastaSearchSAXParser instance.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`addHitProperty(Object key, Object value)`	The `addHitProperty` method adds a key/value pair containing some property of a particular hit.
`void`	`addPrefixMapping(String poPrefix, String poURI)`	Adds a namespace prefix to URI mapping as (key,value) pairs.
`void`	`addSearchProperty(Object key, Object value)`	The `addSearchProperty` method adds a key/value pair containing some property of the overall search result.
`void`	`addSubHitProperty(Object key, Object value)`	The `addSubHitProperty` method adds a key/value pair containing some property of a particular subhit.
`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.
`void`	`endHeader()`	The `endHeader` method indicates the end of a formatted header.
`void`	`endHit()`	The `endHit` method indicates the end of a formatted hit.
`void`	`endSearch()`	The `endSearch` method indicates the end of useful search information.
`void`	`endSubHit()`	The `endSubHit` method indicates the end of a formatted subhit.
`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
`boolean`	`getMoreSearches()`	`getMoreSearches` returns the state of the `SearchContentHandler` with respect to further searches from its data source.
`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(String poSystemId)`	Full implementation of interface method.
`void`	`parse(InputSource source)`	Do-nothing 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`	`setDatabaseID(String databaseID)`	`setDatabaseID` identifies the database searched by a name, ID or URN.
`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`	`setMoreSearches(boolean value)`	`setMoreSearches` sets the state of the `SearchContentHandler`'s expectation of receiving more results.
`void`	`setNamespacePrefix(String poPrefix)`
`void`	`setProperty(String name, Object value)`	Do-nothing implementation of interface method
`void`	`setQueryID(String queryID)`	`setQueryID` identifies the query sequence by a name, ID or URN.
`void`	`setQuerySeq(String identifier)`	Deprecated. use `setQueryID` instead.
`void`	`setSubjectDB(String identifier)`	Deprecated. use `setDatabaseID` instead.
`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
`void`	`startHeader()`	The `startHeader` method indicates the start of a formatted header.
`void`	`startHit()`	The `startHit` method indicates the start of a formatted hit.
`void`	`startSearch()`	The `startSearch` method indicates the start of useful search information.
`void`	`startSubHit()`	The `startSubHit` method indicates the start of a formatted subhit.

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
  - FastaSearchSAXParser
```
public FastaSearchSAXParser()
```
    Creates a new FastaSearchSAXParser instance.
- Method Detail
  - 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

Class FastaSearchSAXParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

oHandler

tNamespaces

tNamespacePrefixes

oNamespacePrefix

oFullNamespacePrefix

iState

Constructor Detail

FastaSearchSAXParser

Method Detail

parse

getMoreSearches

setMoreSearches

setQuerySeq

setQueryID

setSubjectDB

setDatabaseID

startSearch

addSearchProperty

endSearch

startHeader

endHeader

startHit

addHitProperty

endHit

startSubHit

addSubHitProperty

endSubHit

setContentHandler

getContentHandler

parse

getFeature

setFeature

getProperty

setProperty

setEntityResolver

getEntityResolver

setDTDHandler

getDTDHandler

setErrorHandler

getErrorHandler

startElement

endElement

characters

getNamespaces

getNamespacePrefixes

addPrefixMapping

getURIFromPrefix

setNamespacePrefix

getNamespacePrefix

prefix

getContentStream

changeState