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java.lang.Objectkea.programs.jPrimrose.OligoSearchResult
public class OligoSearchResult
Stores outcome of database search with specified oligonucleotide.
Constructor Summary | |
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OligoSearchResult(kea.database.Oligo oligo)
Creates a new instance of OligoSearchResult . |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public OligoSearchResult(kea.database.Oligo oligo)
OligoSearchResult
.
oligo
- Oligo object.Method Detail |
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public kea.database.Oligo getOligo()
public kea.sequences.nucleicAcid.search.SearchResult getSearchResult(kea.database.Record record)
record
- Record object.
public void addSearchResult(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchResult searchResult)
record
- Record object.searchResult
- SearchResult object.public int getHits()
public int getTargetHits()
public int getNonTargetHits()
public int getMeltingTemperature(kea.sequences.nucleicAcid.tm.TmCalculatorType tmCalculatorType)
tmCalculatorType
- Melting temperature equation to use.
public int getDegeneracy()
public double getPercentGCContent()
public int getNumberOfSelfComplementaryBases()
public void setFailed(boolean b)
b
- True if failed.public boolean hasFailed()
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