org.geworkbench.util.patterns
Class FlexiblePattern

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<DSPatternMatch<DSSequence,CSSeqRegistration>>
              org.geworkbench.util.patterns.FlexiblePattern

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<DSPatternMatch<DSSequence,CSSeqRegistration>>, java.util.Collection<DSPatternMatch<DSSequence,CSSeqRegistration>>, java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>>, java.util.RandomAccess, DSMatchedPattern<DSSequence,CSSeqRegistration>, DSMatchedSeqPattern, DSNamed, DSPValue

public class FlexiblePattern
extends java.util.ArrayList<DSPatternMatch<DSSequence,CSSeqRegistration>>
implements DSMatchedSeqPattern

Title:

Description:

Copyright: Copyright (c) 2003

Company:

Version:

1.0

Author:

not attributable

See Also:

Serialized Form

Nested Class Summary

class

FlexiblePattern.TwoLocus

Field Summary

java.lang.String	ascii
int	length
int	maxLen
java.util.ArrayList	mLocus
java.util.ArrayList	patterns
double	pValue
int	seqNo

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

FlexiblePattern(CSMatchedSeqPattern p0, CSMatchedSeqPattern p1)

Method Summary

void	addAll(DSMatchedPattern<DSSequence,CSSeqRegistration> matches)
void	buildHistogram(int[] yAxis, int step, int maxBin)
java.lang.String	getASCII()
java.lang.String	getLabel() Gets the label for this object.
int	getLength()
int	getMaxLength()
DSSequence	getObject(int i)
DSPattern<DSSequence,CSSeqRegistration>	getPattern()
double	getPValue()
CSSeqRegistration	getRegistration(int i)
int	getSeqNo()
int	getSupport()
int	getUniqueSupport()
int	hashCode()
java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>>	matches()
java.util.ArrayList	merge(CSMatchedSeqPattern p0, CSMatchedSeqPattern p1)
void	setLabel(java.lang.String label) Sets the label for this object.
void	setPValue(double pValue)
java.lang.String	toString(int i)
void	write(java.io.BufferedWriter writer)

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.geworkbench.bison.datastructure.complex.pattern.DSMatchedPattern

add, get

Methods inherited from interface java.util.List

containsAll, equals, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

seqNo

public int seqNo

patterns

public java.util.ArrayList patterns

mLocus

public java.util.ArrayList mLocus

pValue

public double pValue

ascii

public java.lang.String ascii

length

public int length

maxLen

public int maxLen

Constructor Detail

FlexiblePattern

public FlexiblePattern(CSMatchedSeqPattern p0,
                       CSMatchedSeqPattern p1)

Method Detail

getSupport

public int getSupport()

Specified by:

getSupport in interface DSMatchedPattern<DSSequence,CSSeqRegistration>

getLength

public int getLength()

Specified by:

getLength in interface DSMatchedSeqPattern

getMaxLength

public int getMaxLength()

Specified by:

getMaxLength in interface DSMatchedSeqPattern

getUniqueSupport

public int getUniqueSupport()

Specified by:

getUniqueSupport in interface DSMatchedPattern<DSSequence,CSSeqRegistration>

getSeqNo

public int getSeqNo()

getPValue

public double getPValue()

Specified by:

getPValue in interface DSPValue

setPValue

public void setPValue(double pValue)

Specified by:

setPValue in interface DSPValue

getASCII

public java.lang.String getASCII()

Specified by:

getASCII in interface DSMatchedSeqPattern

write

public void write(java.io.BufferedWriter writer)
           throws java.io.IOException

Specified by:

write in interface DSMatchedSeqPattern

Throws:

java.io.IOException

buildHistogram

public void buildHistogram(int[] yAxis,
                           int step,
                           int maxBin)

merge

public java.util.ArrayList merge(CSMatchedSeqPattern p0,
                                 CSMatchedSeqPattern p1)

toString

public java.lang.String toString(int i)

getRegistration

public CSSeqRegistration getRegistration(int i)
                                  throws java.lang.IndexOutOfBoundsException

Throws:

java.lang.IndexOutOfBoundsException

getObject

public DSSequence getObject(int i)
                     throws java.lang.IndexOutOfBoundsException

Throws:

java.lang.IndexOutOfBoundsException

getPattern

public DSPattern<DSSequence,CSSeqRegistration> getPattern()

Specified by:

getPattern in interface DSMatchedPattern<DSSequence,CSSeqRegistration>

hashCode

public int hashCode()

Specified by:

hashCode in interface java.util.Collection<DSPatternMatch<DSSequence,CSSeqRegistration>>

Specified by:

hashCode in interface java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>>

Overrides:

hashCode in class java.util.AbstractList<DSPatternMatch<DSSequence,CSSeqRegistration>>

addAll

public void addAll(DSMatchedPattern<DSSequence,CSSeqRegistration> matches)

Specified by:

addAll in interface DSMatchedPattern<DSSequence,CSSeqRegistration>

matches

public java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>> matches()

Specified by:

matches in interface DSMatchedPattern<DSSequence,CSSeqRegistration>

setLabel

public void setLabel(java.lang.String label)

Description copied from interface: DSNamed

Sets the label for this object.

Specified by:

setLabel in interface DSNamed

Parameters:

label - the new label for this object.

getLabel

public java.lang.String getLabel()

Description copied from interface: DSNamed

Gets the label for this object.

Specified by:

getLabel in interface DSNamed

Returns:

the label.