Modifier and Type | Method and Description |
---|---|
NucleotidSequences |
Environment.getSequences()
This method is called to get the sequences NucleotidSequences of Environment.
|
Modifier and Type | Method and Description |
---|---|
ThermoResult |
PatternComputationMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
PatternComputationMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2)
Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern
at the positions pos1 and pos2.
|
Modifier and Type | Method and Description |
---|---|
abstract ThermoResult |
PatternComputation.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
PatternComputation.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Broda05CNGRepeats.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Broda05CNGRepeats.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Breslauer86.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Freier86.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Xia98.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto96.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto95.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
CricksNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Tanaka04.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantalucia97.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia96.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Breslauer86.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Freier86.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Xia98.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto96.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto95.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
CricksNNMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Tanaka04.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantalucia97.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia96.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko071x2Loop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04InternalLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Znosko071x2Loop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06InternalLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04InternalLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04LongBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Turner99_06LongBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04LongBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto02RNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SugimotoLongDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Sugimoto02DNADanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Sugimoto02RNADanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SugimotoLongDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Sugimoto02DNADanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Serra05DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06DoubleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SecondDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Serra05DoubleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra06DoubleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SecondDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Tanaka04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99_06SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Santalucia04SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
GlobalSingleBulgeLoopMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra07SingleBulgeLoop.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Tanaka04SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner99_06SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Santalucia04SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
GlobalSingleBulgeLoopMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra07SingleBulgeLoop.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Bommarito00SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra06_08SingleDanglingEnd.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
SingleDanglingEndMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Bommarito00SingleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra06_08SingleDanglingEnd.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
SingleDanglingEndMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Znosko08mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
ZnoskoMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Watkins11mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner06mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99mm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
ZnoskoMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Watkins11mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner06mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99mm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Sugimoto01Hydroxyadenine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Asanuma05Azobenzene.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
McTigue04LockedAcid.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Sugimoto01Hydroxyadenine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Asanuma05Azobenzene.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
McTigue04LockedAcid.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Turner99_06tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
AllawiSantaluciaPeyret97_98_99tanmm.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Turner99_06tanmm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
AllawiSantaluciaPeyret97_98_99tanmm.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
ThermoResult |
Santalucia05Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
InosineNNMethod.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Turner99Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Znosko07Inosine.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
ThermoResult |
Serra12Wobble.computeThermodynamics(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Turner99Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
protected ThermoResult |
Serra12Wobble.getGUThermoResult(NucleotidSequences sequences,
int pos1,
int pos2,
ThermoResult result) |
boolean |
Santalucia05Inosine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
InosineNNMethod.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Turner99Wobble.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Znosko07Inosine.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
boolean |
Serra12Wobble.isMissingParameters(NucleotidSequences sequences,
int pos1,
int pos2) |
Modifier and Type | Method and Description |
---|---|
static NucleotidSequences |
NucleotidSequences.buildSymetricSequences(String seq1,
String seq2)
creates a NucleotidSequences with two symmetric sequences String created from the
seq1 String an seq2 String.
|
NucleotidSequences |
NucleotidSequences.getEquivalentSequences(String hybridizationType)
This method is called when the same NucleotidSequences is required but with the sequences converted in the new
hybridization type "hybridizationType"
|
Constructor and Description |
---|
NucleotidSequences(String hybridizationType,
NucleotidSequences sequences)
Creates a new NucleotidSequences object from a reference nucleotiDSequences object.
|