public class DataCollect
extends java.lang.Object
Constructor and Description |
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DataCollect() |
Modifier and Type | Method and Description |
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void |
addData(java.util.HashMap<java.lang.String,Thermodynamics> parameters)
add all of the mappings from the specified HashMap to the data of DataCollect.
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Thermodynamics |
getAsymmetry()
to get the Thermodynamics object containing the parameters for the internal loop asymmetry.
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Thermodynamics |
getAzobenzeneValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing an
azobenzene ("X_C" or "X_T").
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Thermodynamics |
getBonus(java.lang.String base1,
java.lang.String lastBase,
java.lang.String seqLoop,
java.lang.String type)
to get the Thermodynamics object containing the parameters for a Hairpin loop 'seqLoop' preceded
by the base 'base1' and followed by the base 'lastBase'.
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Thermodynamics |
getBulgeLoopvalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for a bulge loop of size 'size'.
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Thermodynamics |
getClosureValue(java.lang.String base1,
java.lang.String base2)
to get the Thermodynamics object containing the parameters for the base pair (base1, base2) next to the mismatching base pair.
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Thermodynamics |
getCNGvalue(java.lang.String repeats,
java.lang.String seq1)
to get the Thermodynamics object containing the parameters for the CNG pattern 'seq1'.
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Thermodynamics |
getDanglingValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2.
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java.util.HashMap<java.lang.String,Thermodynamics> |
getData()
This method is called to get the data of DataCollect.
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Thermodynamics |
getFirstMismatch(java.lang.String seq1,
java.lang.String seq2,
java.lang.String loop)
to get the Thermodynamics object containing the parameters for the first non canonical pair in the internal loop.
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Thermodynamics |
getHairpinLoopvalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for a Hairpin loop of size 'size'.
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Thermodynamics |
getHydroxyadenosineValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
hydroxyadenine ("A*").
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Thermodynamics |
getInitiation()
to get the Thermodynamics object containing the parameters for the hybridization initiation.
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Thermodynamics |
getInitiation(java.lang.String type)
to get the Thermodynamics object containing the parameters for the initiation with the specified type of initiation.
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Thermodynamics |
getInitiationBulgevalue(java.lang.String size)
to get the Thermodynamics object containing the parameters for the initiation of a bulge loop of size 'size'.
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Thermodynamics |
getInitiationLoopValue()
to get the Thermodynamics object containing the parameters for the initiation of an internal loop.
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Thermodynamics |
getInitiationLoopValue(java.lang.String size)
to get the Thermodynamics object containing the parameters for the initiation of an internal loop with a specified size.
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Thermodynamics |
getInternalLoopValue(java.lang.String size)
to get the Thermodynamics object containing the parameters for an internal loop with a specified size.
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Thermodynamics |
getLockedAcidValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a
locked nucleic acid ("AL", "TL", "GL" or "CL").
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Thermodynamics |
getMismatchParameterValue(java.lang.String base1,
java.lang.String base2)
to get the Thermodynamics object containing the parameters for the mismatching base pair (base1, base2).
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Thermodynamics |
getMismatchValue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the mismatch(es) present in the duplex
composed of seq1 and seq2.
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Thermodynamics |
getMismatchValue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String closing)
to get the Thermodynamics object containing the parameters for the the duplex composed of seq1 and seq2 with the
specified type of closing base pairs.
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Thermodynamics |
getModifiedvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the crick's pair composed of the String seq1 and the String seq2 with
one of the sequences containing a specific nucleic acid.
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Thermodynamics |
getModifiedvalue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String sens)
to get the Thermodynamics object containing the parameters for the String seq1 and the String seq2 with one of the sequences containing a specific
nucleic acid and a dangling end.
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Thermodynamics |
getNNvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics containing the parameters for the crick's pair composed of the String seq1 and the String seq2.
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Thermodynamics |
getPenalty(java.lang.String type)
to get the Thermodynamics object containing the parameters for the penalty of type 'type'.
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Thermodynamics |
getPenalty(java.lang.String type,
java.lang.String parameter)
to get the Thermodynamics object containing the parameters for a penalty of type 'type'
for the specified parameter.
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Thermodynamics |
getSecondDanglingValue(java.lang.String seq1,
java.lang.String seq2,
java.lang.String sens)
to get the Thermodynamics object containing the parameters for the dangling end present in the duplex
composed of seq1 and seq2 with the specified sens.
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Thermodynamics |
getSingleBulgeLoopvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the single bulge (seq1, seq2).
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Thermodynamics |
getsymmetry()
to get the Thermodynamics object containing the parameters for the symmetry correction.
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Thermodynamics |
getTerminal(java.lang.String type)
to get the Thermodynamics containing the parameters for the specified type of terminal base pair.
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Thermodynamics |
getTerminalMismatchvalue(java.lang.String seq1,
java.lang.String seq2)
to get the Thermodynamics object containing the parameters for the terminal mismatching base pair (seq1, seq2)
of a hairpin loop.
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public java.util.HashMap<java.lang.String,Thermodynamics> getData()
public void addData(java.util.HashMap<java.lang.String,Thermodynamics> parameters)
public Thermodynamics getTerminal(java.lang.String type)
type
- : type of the terminal base pair.public Thermodynamics getNNvalue(java.lang.String seq1, java.lang.String seq2)
seq1
- : nucleic acids from the sequence (5'3') in the Crick's pair.seq2
- : nucleic acids from the complementary sequence (3'5') in the Crick's pair.public Thermodynamics getInitiation()
public Thermodynamics getInitiation(java.lang.String type)
type
- : type of initiationpublic Thermodynamics getsymmetry()
public Thermodynamics getModifiedvalue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getModifiedvalue(java.lang.String seq1, java.lang.String seq2, java.lang.String sens)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').sens
- : sens of the dangling endpublic Thermodynamics getAzobenzeneValue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getLockedAcidValue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getHydroxyadenosineValue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getSecondDanglingValue(java.lang.String seq1, java.lang.String seq2, java.lang.String sens)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').sens
- : sens of the dangling endpublic Thermodynamics getDanglingValue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getMismatchValue(java.lang.String seq1, java.lang.String seq2)
seq1
- : sequence (5'3').seq2
- : complementary sequence (3'5').public Thermodynamics getInternalLoopValue(java.lang.String size)
size
- : size of the internal loop.public Thermodynamics getInitiationLoopValue(java.lang.String size)
size
- : size of the internal loop.public Thermodynamics getInitiationLoopValue()
public Thermodynamics getMismatchParameterValue(java.lang.String base1, java.lang.String base2)
base1
- : from the sequence (5'3')base2
- : from the complementary sequence (3'5')public Thermodynamics getClosureValue(java.lang.String base1, java.lang.String base2)
base1
- : from the sequence (5'3')base2
- : from the complementary sequence (3'5')public Thermodynamics getMismatchValue(java.lang.String seq1, java.lang.String seq2, java.lang.String closing)
seq1
- : from the sequence (5'3')seq2
- : from the complementary sequence (3'5')closing
- : type of the base pair next to the mismatching base pair..public Thermodynamics getPenalty(java.lang.String type)
type
- : type of the penaltypublic Thermodynamics getAsymmetry()
public Thermodynamics getFirstMismatch(java.lang.String seq1, java.lang.String seq2, java.lang.String loop)
seq1
- : from the sequence (5'3')seq2
- : from the complementary sequence (3'5')loop
- : type of internal loop.public Thermodynamics getHairpinLoopvalue(java.lang.String size)
size
- : size of the hairpin loop.public Thermodynamics getBonus(java.lang.String base1, java.lang.String lastBase, java.lang.String seqLoop, java.lang.String type)
base1
- : base preceding the hairpin loop. (from the sequence (5'3'))lastBase
- : base following the hairpin loop. (from the sequence (5'3'))seqLoop
- : hairpin loop sequence.type
- : type of hairpin looppublic Thermodynamics getPenalty(java.lang.String type, java.lang.String parameter)
type
- : type of penaltyparameter
- public Thermodynamics getTerminalMismatchvalue(java.lang.String seq1, java.lang.String seq2)
seq1
- : (5'3') orientationseq2
- : (3'5') orientationpublic Thermodynamics getCNGvalue(java.lang.String repeats, java.lang.String seq1)
repeats
- : number of CNG repeats in the sequence.seq1
- : CNG pattern (5'3')public Thermodynamics getSingleBulgeLoopvalue(java.lang.String seq1, java.lang.String seq2)
seq1
- : from the sequence (5'3')seq2
- : from the complementary sequence (3'5')public Thermodynamics getBulgeLoopvalue(java.lang.String size)
size
- : size of the bulge looppublic Thermodynamics getInitiationBulgevalue(java.lang.String size)
size
- : size of the bulge loop