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java.lang.Objectkea.programs.jPrimrose.PrimroseOligo
public final class PrimroseOligo
Implementation of Oligo interface.
Constructor Summary | |
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PrimroseOligo(java.lang.String sequence,
kea.sequences.nucleicAcid.Orientation orientation)
Creates a new instance of PrimroseOligo . |
Method Summary | |
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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 |
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public PrimroseOligo(java.lang.String sequence, kea.sequences.nucleicAcid.Orientation orientation) throws kea.exceptions.NonIUBCharacterException, kea.exceptions.IllegalSequenceException, kea.exceptions.NullSequenceException
PrimroseOligo
.
kea.exceptions.NonIUBCharacterException
kea.exceptions.IllegalSequenceException
kea.exceptions.NullSequenceException
Method Detail |
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public kea.sequences.nucleicAcid.Orientation getOrientation()
getOrientation
in interface kea.database.Oligo
public java.lang.String getSequence()
getSequence
in interface kea.database.Oligo
public java.util.regex.Pattern getPattern()
getPattern
in interface kea.database.Oligo
public java.util.regex.Matcher getMatcher()
getMatcher
in interface kea.database.Oligo
public java.util.regex.Matcher getMatcher(java.lang.CharSequence input)
getMatcher
in interface kea.database.Oligo
public void incrementScore(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchResult searchResult)
record
- Record object.searchResult
- SearchResult object.public kea.database.Record[] getRecords()
public kea.database.Record[] getTargetRecords()
public kea.database.Record[] getNonTargetRecords()
public void addSearchOutcome(kea.database.Record record, kea.sequences.nucleicAcid.search.SearchOutcome searchOutcome)
record
- Record object.searchOutcome
- for Record.public void addSequenceLength(kea.database.Record record, int sequenceLength)
record
- Record object.sequenceLength
- Sequence length.public int getSequenceLength(kea.database.Record record)
record
- Record object.
public kea.sequences.nucleicAcid.search.SearchResult getSearchResult(kea.database.Record record)
record
- Record object in question.
public int getStartPosition(kea.database.Record record)
record
- Record object.
public int getEndPosition(kea.database.Record record)
record
- Record object.
public int getHits()
public int getTargetHits()
public int getNonTargetHits()
public float getPercentTargetHits()
public float getPercentNonTargetHits()
public double 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()
public void reset()
public void setSearchComplete(boolean b)
b
- True if search has finished and so data available for display.public boolean searchComplete()
public java.lang.String toString()
toString
in class java.lang.Object
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