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

java.lang.Object
  edu.mssm.crover.tools.tissue.xml.BlastHits

All Implemented Interfaces:

Serializable

public class BlastHits
extends Object
implements Serializable

Class BlastHits.

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

BlastHits()

Method Summary

void	addQuerySequence(int index, QuerySequence vQuerySequence)
void	addQuerySequence(QuerySequence vQuerySequence)
void	deleteBValue()
void	deleteExpectationValue()
void	deleteMaxErrorRate()
void	deleteMinimumLength()
void	deleteVValue()
Enumeration<QuerySequence>	enumerateQuerySequence() Method enumerateQuerySequence.
int	getBValue() Returns the value of field 'bValue'.
String	getDatabase() Returns the value of field 'database'.
double	getExpectationValue() Returns the value of field 'expectationValue'.
double	getMaxErrorRate() Returns the value of field 'maxErrorRate'.
long	getMinimumLength() Returns the value of field 'minimumLength'.
QuerySequence[]	getQuerySequence() Method getQuerySequence.Returns the contents of the collection in an Array.
QuerySequence	getQuerySequence(int index) Method getQuerySequence.
int	getQuerySequenceCount() Method getQuerySequenceCount.
String	getSearchDate() Returns the value of field 'searchDate'.
int	getVValue() Returns the value of field 'vValue'.
boolean	hasBValue() Method hasBValue.
boolean	hasExpectationValue() Method hasExpectationValue.
boolean	hasMaxErrorRate() Method hasMaxErrorRate.
boolean	hasMinimumLength() Method hasMinimumLength.
boolean	hasVValue() Method hasVValue.
boolean	isValid() Method isValid.
Iterator<QuerySequence>	iterateQuerySequence() Method iterateQuerySequence.
void	marshal(ContentHandler handler)
void	marshal(Writer out)
void	removeAllQuerySequence()
boolean	removeQuerySequence(QuerySequence vQuerySequence) Method removeQuerySequence.
QuerySequence	removeQuerySequenceAt(int index) Method removeQuerySequenceAt.
void	setBValue(int bValue) Sets the value of field 'bValue'.
void	setDatabase(String database) Sets the value of field 'database'.
void	setExpectationValue(double expectationValue) Sets the value of field 'expectationValue'.
void	setMaxErrorRate(double maxErrorRate) Sets the value of field 'maxErrorRate'.
void	setMinimumLength(long minimumLength) Sets the value of field 'minimumLength'.
void	setQuerySequence(int index, QuerySequence vQuerySequence)
void	setQuerySequence(QuerySequence[] vQuerySequenceArray)
void	setSearchDate(String searchDate) Sets the value of field 'searchDate'.
void	setVValue(int vValue) Sets the value of field 'vValue'.
static BlastHits	unmarshal(Reader reader) Method unmarshal.
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 IndexOutOfBoundsException

Parameters:

vQuerySequence -

Throws:

IndexOutOfBoundsException - if the index given is outside the bounds of the collection

addQuerySequence

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

Parameters:

index -

vQuerySequence -

Throws:

IndexOutOfBoundsException - if the index given is outside the bounds of the collection

deleteBValue

public void deleteBValue()

deleteExpectationValue

public void deleteExpectationValue()

deleteMaxErrorRate

public void deleteMaxErrorRate()

deleteMinimumLength

public void deleteMinimumLength()

deleteVValue

public void deleteVValue()

enumerateQuerySequence

public Enumeration<QuerySequence> enumerateQuerySequence()

Method enumerateQuerySequence.

Returns:

an Enumeration over all possible elements of this collection

getBValue

public int getBValue()

Returns the value of field 'bValue'.

Returns:

the value of field 'BValue'.

getDatabase

public String getDatabase()

Returns the value of field 'database'.

Returns:

the value of field 'Database'.

getExpectationValue

public double getExpectationValue()

Returns the value of field 'expectationValue'.

Returns:

the value of field 'ExpectationValue'.

getMaxErrorRate

public double getMaxErrorRate()

Returns the value of field 'maxErrorRate'.

Returns:

the value of field 'MaxErrorRate'.

getMinimumLength

public long getMinimumLength()

Returns the value of field 'minimumLength'.

Returns:

the value of field 'MinimumLength'.

getQuerySequence

public QuerySequence getQuerySequence(int index)
                               throws IndexOutOfBoundsException

Method getQuerySequence.

Parameters:

index -

Returns:

the value of the edu.mssm.crover.tools.tissue.xml.QuerySequence at the given index

Throws:

IndexOutOfBoundsException - if the index given is outside the bounds of the collection

getQuerySequence

public QuerySequence[] getQuerySequence()

Method getQuerySequence.Returns the contents of the collection in an Array.

Note: Just in case the collection contents are changing in another thread, we pass a 0-length Array of the correct type into the API call. This way we know that the Array returned is of exactly the correct length.

Returns:

this collection as an Array

getQuerySequenceCount

public int getQuerySequenceCount()

Method getQuerySequenceCount.

Returns:

the size of this collection

getSearchDate

public String getSearchDate()

Returns the value of field 'searchDate'.

Returns:

the value of field 'SearchDate'.

getVValue

public int getVValue()

Returns the value of field 'vValue'.

Returns:

the value of field 'VValue'.

hasBValue

public boolean hasBValue()

Method hasBValue.

Returns:

true if at least one BValue has been added

hasExpectationValue

public boolean hasExpectationValue()

Method hasExpectationValue.

Returns:

true if at least one ExpectationValue has been added

hasMaxErrorRate

public boolean hasMaxErrorRate()

Method hasMaxErrorRate.

Returns:

true if at least one MaxErrorRate has been added

hasMinimumLength

public boolean hasMinimumLength()

Method hasMinimumLength.

Returns:

true if at least one MinimumLength has been added

hasVValue

public boolean hasVValue()

Method hasVValue.

Returns:

true if at least one VValue has been added

isValid

public boolean isValid()

Method isValid.

Returns:

true if this object is valid according to the schema

iterateQuerySequence

public Iterator<QuerySequence> iterateQuerySequence()

Method iterateQuerySequence.

Returns:

an Iterator over all possible elements in this collection

marshal

public void marshal(Writer out)
             throws MarshalException,
                    ValidationException

Parameters:

out -

Throws:

MarshalException - if object is null or if any SAXException is thrown during marshaling

ValidationException - if this object is an invalid instance according to the schema

marshal

public void marshal(ContentHandler handler)
             throws IOException,
                    MarshalException,
                    ValidationException

Parameters:

handler -

Throws:

IOException - if an IOException occurs during marshaling

ValidationException - if this object is an invalid instance according to the schema

MarshalException - if object is null or if any SAXException is thrown during marshaling

removeAllQuerySequence

public void removeAllQuerySequence()

removeQuerySequence

public boolean removeQuerySequence(QuerySequence vQuerySequence)

Method removeQuerySequence.

Parameters:

vQuerySequence -

Returns:

true if the object was removed from the collection.

removeQuerySequenceAt

public QuerySequence removeQuerySequenceAt(int index)

Method removeQuerySequenceAt.

Parameters:

index -

Returns:

the element removed from the collection

setBValue

public void setBValue(int bValue)

Sets the value of field 'bValue'.

Parameters:

bValue - the value of field 'bValue'.

setDatabase

public void setDatabase(String database)

Sets the value of field 'database'.

Parameters:

database - the value of field 'database'.

setExpectationValue

public void setExpectationValue(double expectationValue)

Sets the value of field 'expectationValue'.

Parameters:

expectationValue - the value of field 'expectationValue'

setMaxErrorRate

public void setMaxErrorRate(double maxErrorRate)

Sets the value of field 'maxErrorRate'.

Parameters:

maxErrorRate - the value of field 'maxErrorRate'.

setMinimumLength

public void setMinimumLength(long minimumLength)

Sets the value of field 'minimumLength'.

Parameters:

minimumLength - the value of field 'minimumLength'.

setQuerySequence

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

Parameters:

index -

vQuerySequence -

Throws:

IndexOutOfBoundsException - if the index given is outside the bounds of the collection

setQuerySequence

public void setQuerySequence(QuerySequence[] vQuerySequenceArray)

Parameters:

vQuerySequenceArray -

setSearchDate

public void setSearchDate(String searchDate)

Sets the value of field 'searchDate'.

Parameters:

searchDate - the value of field 'searchDate'.

setVValue

public void setVValue(int vValue)

Sets the value of field 'vValue'.

Parameters:

vValue - the value of field 'vValue'.

unmarshal

public static BlastHits unmarshal(Reader reader)
                           throws MarshalException,
                                  ValidationException

Method unmarshal.

Parameters:

reader -

Returns:

the unmarshaled edu.mssm.crover.tools.tissue.xml.BlastHits

Throws:

MarshalException - if object is null or if any SAXException is thrown during marshaling

ValidationException - if this object is an invalid instance according to the schema

validate

public void validate()
              throws ValidationException

Throws:

ValidationException - if this object is an invalid instance according to the schema