edu.mssm.crover.tools.tissue.xml
Class BlastHits

java.lang.Object
  |
  +--edu.mssm.crover.tools.tissue.xml.BlastHits

All Implemented Interfaces:

java.io.Serializable

public class BlastHits

extends java.lang.Object

implements java.io.Serializable

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

BlastHits()

Method Summary

void	addQuerySequence(int index, QuerySequence vQuerySequence)
void	addQuerySequence(QuerySequence vQuerySequence)
void	clearQuerySequence()
void	deleteBValue()
void	deleteMaxErrorRate()
void	deleteMinimumLength()
void	deleteVValue()
java.util.Enumeration	enumerateQuerySequence()
int	getBValue()
java.lang.String	getDatabase()
double	getExpectationValue()
double	getMaxErrorRate()
int	getMinimumLength()
QuerySequence[]	getQuerySequence()
QuerySequence	getQuerySequence(int index)
int	getQuerySequenceCount()
java.lang.String	getSearchDate()
int	getVValue()
boolean	hasBValue()
boolean	hasExpectationValue()
boolean	hasMaxErrorRate()
boolean	hasMinimumLength()
boolean	hasVValue()
boolean	isValid()
void	marshal(org.xml.sax.DocumentHandler handler)
void	marshal(java.io.Writer out)
boolean	removeQuerySequence(QuerySequence vQuerySequence)
void	setBValue(int bValue)
void	setDatabase(java.lang.String database)
void	setExpectationValue(double expectationValue)
void	setMaxErrorRate(double maxErrorRate)
void	setMinimumLength(int minimumLength)
void	setQuerySequence(int index, QuerySequence vQuerySequence)
void	setQuerySequence(QuerySequence[] querySequenceArray)
void	setSearchDate(java.lang.String searchDate)
void	setVValue(int vValue)
static BlastHits	unmarshal(java.io.Reader reader)
void	validate()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BlastHits

public BlastHits()

Method Detail

addQuerySequence

public void addQuerySequence(QuerySequence vQuerySequence)
                      throws java.lang.IndexOutOfBoundsException

Parameters:

vQuerySequence -

java.lang.IndexOutOfBoundsException

addQuerySequence

public void addQuerySequence(int index,
                             QuerySequence vQuerySequence)
                      throws java.lang.IndexOutOfBoundsException

Parameters:

index -

vQuerySequence -

java.lang.IndexOutOfBoundsException

clearQuerySequence

public void clearQuerySequence()

deleteBValue

public void deleteBValue()

deleteMaxErrorRate

public void deleteMaxErrorRate()

deleteMinimumLength

public void deleteMinimumLength()

deleteVValue

public void deleteVValue()

enumerateQuerySequence

public java.util.Enumeration enumerateQuerySequence()

getBValue

public int getBValue()

getDatabase

public java.lang.String getDatabase()

getExpectationValue

public double getExpectationValue()

getMaxErrorRate

public double getMaxErrorRate()

getMinimumLength

public int getMinimumLength()

getQuerySequence

public QuerySequence getQuerySequence(int index)
                               throws java.lang.IndexOutOfBoundsException

Parameters:

index -

java.lang.IndexOutOfBoundsException

getQuerySequence

public QuerySequence[] getQuerySequence()

getQuerySequenceCount

public int getQuerySequenceCount()

getSearchDate

public java.lang.String getSearchDate()

getVValue

public int getVValue()

hasBValue

public boolean hasBValue()

hasExpectationValue

public boolean hasExpectationValue()

hasMaxErrorRate

public boolean hasMaxErrorRate()

hasMinimumLength

public boolean hasMinimumLength()

hasVValue

public boolean hasVValue()

isValid

public boolean isValid()

marshal

public void marshal(java.io.Writer out)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException

Parameters:

out -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

marshal

public void marshal(org.xml.sax.DocumentHandler handler)
             throws org.exolab.castor.xml.MarshalException,
                    org.exolab.castor.xml.ValidationException

Parameters:

handler -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

removeQuerySequence

public boolean removeQuerySequence(QuerySequence vQuerySequence)

Parameters:

vQuerySequence -

setBValue

public void setBValue(int bValue)

Parameters:

bValue -

setDatabase

public void setDatabase(java.lang.String database)

Parameters:

database -

setExpectationValue

public void setExpectationValue(double expectationValue)

Parameters:

expectationValue -

setMaxErrorRate

public void setMaxErrorRate(double maxErrorRate)

Parameters:

maxErrorRate -

setMinimumLength

public void setMinimumLength(int minimumLength)

Parameters:

minimumLength -

setQuerySequence

public void setQuerySequence(int index,
                             QuerySequence vQuerySequence)
                      throws java.lang.IndexOutOfBoundsException

Parameters:

index -

vQuerySequence -

java.lang.IndexOutOfBoundsException

setQuerySequence

public void setQuerySequence(QuerySequence[] querySequenceArray)

Parameters:

querySequenceArray -

setSearchDate

public void setSearchDate(java.lang.String searchDate)

Parameters:

searchDate -

setVValue

public void setVValue(int vValue)

Parameters:

vValue -

unmarshal

public static BlastHits unmarshal(java.io.Reader reader)
                           throws org.exolab.castor.xml.MarshalException,
                                  org.exolab.castor.xml.ValidationException

Parameters:

reader -

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

validate

public void validate()
              throws org.exolab.castor.xml.ValidationException

org.exolab.castor.xml.ValidationException