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


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.