kea.programs.jPrimrose
Class OligoSearchResult

java.lang.Object
  extended by kea.programs.jPrimrose.OligoSearchResult

public class OligoSearchResult
extends java.lang.Object

Stores outcome of database search with specified oligonucleotide.

Version:
2.17.
Author:
Kevin Ashelford.

Constructor Summary
OligoSearchResult(kea.database.Oligo oligo)
          Creates a new instance of OligoSearchResult.
 
Method Summary
 void addSearchResult(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchResult searchResult)
          Stores search result for specified Record object.
 int getDegeneracy()
          Returns the number of degenerate bases within the oligo sequence associated with this object.
 int getHits()
          Returns the total number of database hits (target and non-target).
 int 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.
 int getNumberOfSelfComplementaryBases()
          Returns the number of self complementary bases within the oligonucleotide.
 kea.database.Oligo getOligo()
          Returns Oligo object.
 double getPercentGCContent()
          Returns the percentage GC content of the oligo.
 kea.sequences.nucleicAcid.search.SearchResult getSearchResult(kea.database.Record record)
          Returns SearchResult corresponding to specified Record object.
 int getTargetHits()
          Returns total number of target hits.
 boolean hasFailed()
          Returns true if search has failed (exceeded non-target record limit).
 void setFailed(boolean b)
          Records whether search has failed (exceeded non-target record limit).
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OligoSearchResult

public OligoSearchResult(kea.database.Oligo oligo)
Creates a new instance of OligoSearchResult.

Parameters:
oligo - Oligo object.
Method Detail

getOligo

public kea.database.Oligo getOligo()
Returns Oligo object.

Returns:
Oligo object.

getSearchResult

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

Parameters:
record - Record object.
Returns:
SearchResult.

addSearchResult

public void addSearchResult(kea.database.Record record,
                            kea.sequences.nucleicAcid.search.SearchResult searchResult)
Stores search result for specified Record object.

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

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.

getMeltingTemperature

public int 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.