org.geworkbench.util.patterns
Class FlexiblePattern

java.lang.Object
  extended by java.util.AbstractCollection<E>
      extended by java.util.AbstractList<E>
          extended by java.util.ArrayList<DSPatternMatch<DSSequence,CSSeqRegistration>>
              extended by 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.