org.geworkbench.util.patterns
Class CSMatchedSeqPattern

java.lang.Object
  extended by org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern<DSSequence,CSSeqRegistration>
      extended by org.geworkbench.util.patterns.CSMatchedSeqPattern
All Implemented Interfaces:
java.io.Serializable, DSMatchedPattern<DSSequence,CSSeqRegistration>, DSMatchedSeqPattern, DSNamed, DSPValue

public final class CSMatchedSeqPattern
extends CSMatchedPattern<DSSequence,CSSeqRegistration>
implements DSMatchedSeqPattern, java.io.Serializable

Version:
$Id: CSMatchedSeqPattern.java 10008 2012-10-08 19:44:14Z zji $
Author:
not attributable
See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
zScore
 
Constructor Summary
CSMatchedSeqPattern(DSSequenceSet<DSSequence> seqDB)
           
CSMatchedSeqPattern(java.lang.String s)
           
 
Method Summary
 DSPatternMatch<DSSequence,CSSeqRegistration> get(int i)
           
 java.lang.String getASCII()
           
 int getLength()
           
 int getMaxLength()
           
 int getOffset(int j)
           
 int getSupport()
           
 int getUniqueSupport()
           
 java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>> matches()
           
 void setIdNo(int value)
           
 void setLocus(byte[] locus)
           
 void setOffset(java.util.ArrayList<PatternOfflet> offset)
           
 void setSeqNo(int value)
           
 java.lang.String toString()
           
 void updateASCII()
          update the ascii representation.
 void write(java.io.BufferedWriter writer)
           
 
Methods inherited from class org.geworkbench.bison.datastructure.complex.pattern.CSMatchedPattern
containsObject, containsSupport, getLabel, getPValue, setLabel, setPValue
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.geworkbench.bison.util.DSPValue
getPValue, setPValue
 
Methods inherited from interface org.geworkbench.bison.datastructure.properties.DSNamed
getLabel, setLabel
 

Constructor Detail

CSMatchedSeqPattern

public CSMatchedSeqPattern(DSSequenceSet<DSSequence> seqDB)

CSMatchedSeqPattern

public CSMatchedSeqPattern(java.lang.String s)
Method Detail

setLocus

public void setLocus(byte[] locus)

setOffset

public void setOffset(java.util.ArrayList<PatternOfflet> offset)

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

updateASCII

public void updateASCII()
update the ascii representation. Method to replace PatternOperations.fill method.


getLength

public int getLength()
Specified by:
getLength in interface DSMatchedSeqPattern

getSupport

public int getSupport()
Specified by:
getSupport in interface DSMatchedPattern<DSSequence,CSSeqRegistration>
Overrides:
getSupport in class CSMatchedPattern<DSSequence,CSSeqRegistration>

getUniqueSupport

public int getUniqueSupport()
Specified by:
getUniqueSupport in interface DSMatchedPattern<DSSequence,CSSeqRegistration>
Overrides:
getUniqueSupport in class CSMatchedPattern<DSSequence,CSSeqRegistration>

getMaxLength

public int getMaxLength()
Specified by:
getMaxLength in interface DSMatchedSeqPattern

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

getOffset

public int getOffset(int j)

get

public DSPatternMatch<DSSequence,CSSeqRegistration> get(int i)
Specified by:
get in interface DSMatchedPattern<DSSequence,CSSeqRegistration>
Overrides:
get in class CSMatchedPattern<DSSequence,CSSeqRegistration>

matches

public java.util.List<DSPatternMatch<DSSequence,CSSeqRegistration>> matches()
Specified by:
matches in interface DSMatchedPattern<DSSequence,CSSeqRegistration>
Overrides:
matches in class CSMatchedPattern<DSSequence,CSSeqRegistration>

setIdNo

public void setIdNo(int value)

setSeqNo

public void setSeqNo(int value)