kea.programs.jPrimrose
Class PrimroseOligo

java.lang.Object
  extended by kea.programs.jPrimrose.PrimroseOligo
All Implemented Interfaces:
kea.database.Oligo

public final class PrimroseOligo
extends java.lang.Object
implements kea.database.Oligo

Implementation of Oligo interface.

Version:
2.17.
Author:
Kevin Ashelford.

Constructor Summary
PrimroseOligo(java.lang.String sequence, kea.sequences.nucleicAcid.Orientation orientation)
          Creates a new instance of PrimroseOligo.
 
Method Summary
 void addSearchOutcome(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchOutcome searchOutcome)
          Store Record object and corresponding SearchOutcome.
 void addSequenceLength(kea.database.Record record, int sequenceLength)
          Stores sequence length of record object for display purposes.
 int getDegeneracy()
          Returns the number of degenerate bases within the oligo sequence associated with this object.
 int getEndPosition(kea.database.Record record)
          Returns end position of oligo within specified Record object.
 int getHits()
          Returns the total number of database hits (target and non-target).
 java.util.regex.Matcher getMatcher()
           
 java.util.regex.Matcher getMatcher(java.lang.CharSequence input)
           
 double getMeltingTemperature(kea.sequences.nucleicAcid.tm.TmCalculatorType tmCalculatorType)
          Returns melting temperature of oligo, calculated according to equation indicated by supplied argument.
 int getNonTargetHits()
          Returns total number of non-target hits.
 kea.database.Record[] getNonTargetRecords()
          Returns all non-target Record objects encountered by oligo during search.
 int getNumberOfSelfComplementaryBases()
          Returns the number of self complementary bases within the oligonucleotide.
 kea.sequences.nucleicAcid.Orientation getOrientation()
           
 java.util.regex.Pattern getPattern()
           
 double getPercentGCContent()
          Returns the percentage GC content of the oligo.
 float getPercentNonTargetHits()
          Returns percentage of non-target records hit.
 float getPercentTargetHits()
          Returns percentage of target records hit.
 kea.database.Record[] getRecords()
          Returns all Record objects encountered by oligo during search.
 kea.sequences.nucleicAcid.search.SearchResult getSearchResult(kea.database.Record record)
          Returns search result corresponding to Record object supplied.
 java.lang.String getSequence()
           
 int getSequenceLength(kea.database.Record record)
          Returns sequence length of supplied record object.
 int getStartPosition(kea.database.Record record)
          Returns start position of oligo within specified Record object.
 int getTargetHits()
          Returns total number of target hits.
 kea.database.Record[] getTargetRecords()
          Returns all target Record objects encountered by oligo during search.
 boolean hasFailed()
          Returns true if search has failed (exceeded non-target record limit).
 void incrementScore(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchResult searchResult)
          Scores search result (target/non-target) according specified Record object.
 void reset()
          Resets object - empties all storage.
 boolean searchComplete()
          Returns true if search completed, and therefore record information available for display.
 void setFailed(boolean b)
          Records whether search has failed (exceeded non-target record limit).
 void setSearchComplete(boolean b)
          Sets 'search complete' status for object.
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

PrimroseOligo

public PrimroseOligo(java.lang.String sequence,
                     kea.sequences.nucleicAcid.Orientation orientation)
              throws kea.exceptions.NonIUBCharacterException,
                     kea.exceptions.IllegalSequenceException,
                     kea.exceptions.NullSequenceException
Creates a new instance of PrimroseOligo.

Throws:
kea.exceptions.NonIUBCharacterException
kea.exceptions.IllegalSequenceException
kea.exceptions.NullSequenceException
Method Detail

getOrientation

public kea.sequences.nucleicAcid.Orientation getOrientation()
Specified by:
getOrientation in interface kea.database.Oligo

getSequence

public java.lang.String getSequence()
Specified by:
getSequence in interface kea.database.Oligo

getPattern

public java.util.regex.Pattern getPattern()
Specified by:
getPattern in interface kea.database.Oligo

getMatcher

public java.util.regex.Matcher getMatcher()
Specified by:
getMatcher in interface kea.database.Oligo

getMatcher

public java.util.regex.Matcher getMatcher(java.lang.CharSequence input)
Specified by:
getMatcher in interface kea.database.Oligo

incrementScore

public void incrementScore(kea.database.Record record,
                           kea.sequences.nucleicAcid.search.SearchResult searchResult)
Scores search result (target/non-target) according specified Record object.

Parameters:
record - Record object.
searchResult - SearchResult object.

getRecords

public kea.database.Record[] getRecords()
Returns all Record objects encountered by oligo during search.

Returns:
Array of Record objects.

getTargetRecords

public kea.database.Record[] getTargetRecords()
Returns all target Record objects encountered by oligo during search.

Returns:
Array of Record objects.

getNonTargetRecords

public kea.database.Record[] getNonTargetRecords()
Returns all non-target Record objects encountered by oligo during search.

Returns:
Array of Record objects.

addSearchOutcome

public void addSearchOutcome(kea.database.Record record,
                             kea.sequences.nucleicAcid.search.SearchOutcome searchOutcome)
Store Record object and corresponding SearchOutcome.

Parameters:
record - Record object.
searchOutcome - for Record.

addSequenceLength

public void addSequenceLength(kea.database.Record record,
                              int sequenceLength)
Stores sequence length of record object for display purposes.

Parameters:
record - Record object.
sequenceLength - Sequence length.

getSequenceLength

public int getSequenceLength(kea.database.Record record)
Returns sequence length of supplied record object.

Parameters:
record - Record object.
Returns:
Sequence length.

getSearchResult

public kea.sequences.nucleicAcid.search.SearchResult getSearchResult(kea.database.Record record)
Returns search result corresponding to Record object supplied.

Parameters:
record - Record object in question.
Returns:
Outcome of search between oligo and Record object.

getStartPosition

public int getStartPosition(kea.database.Record record)
Returns start position of oligo within specified Record object.

Parameters:
record - Record object.
Returns:
Start position.

getEndPosition

public int getEndPosition(kea.database.Record record)
Returns end position of oligo within specified Record object.

Parameters:
record - Record object.
Returns:
End position.

getHits

public int getHits()
Returns the total number of database hits (target and non-target).

Returns:
Hits.

getTargetHits

public int getTargetHits()
Returns total number of target hits.

Returns:
Target hits.

getNonTargetHits

public int getNonTargetHits()
Returns total number of non-target hits.

Returns:
Non-target hits.

getPercentTargetHits

public float getPercentTargetHits()
Returns percentage of target records hit.

Returns:
Percentage.

getPercentNonTargetHits

public float getPercentNonTargetHits()
Returns percentage of non-target records hit.

Returns:
Percentage.

getMeltingTemperature

public double getMeltingTemperature(kea.sequences.nucleicAcid.tm.TmCalculatorType tmCalculatorType)
Returns melting temperature of oligo, calculated according to equation indicated by supplied argument.

Parameters:
tmCalculatorType - Melting temperature equation to use.
Returns:
Melting temperature.

getDegeneracy

public int getDegeneracy()
Returns the number of degenerate bases within the oligo sequence associated with this object.

Returns:
number of degenerate bases.

getPercentGCContent

public double getPercentGCContent()
Returns the percentage GC content of the oligo.

Returns:
Percentage GC content.

getNumberOfSelfComplementaryBases

public int getNumberOfSelfComplementaryBases()
Returns the number of self complementary bases within the oligonucleotide.

Returns:
Number of self complementary bases.

setFailed

public void setFailed(boolean b)
Records whether search has failed (exceeded non-target record limit).

Parameters:
b - True if failed.

hasFailed

public boolean hasFailed()
Returns true if search has failed (exceeded non-target record limit).

Returns:
True if failed.

reset

public void reset()
Resets object - empties all storage.


setSearchComplete

public void setSearchComplete(boolean b)
Sets 'search complete' status for object.

Parameters:
b - True if search has finished and so data available for display.

searchComplete

public boolean searchComplete()
Returns true if search completed, and therefore record information available for display.

Returns:
True if record-related information is available.

toString

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