la.bioinformatics

Class Alignment.UPSame

java.lang.Object

la.la.Value

la.la.Function

mml.UPModel

mml.UPSeriesModel

mml.UPSeriesModel.Length

la.bioinformatics.Alignment.UPSame

All Implemented Interfaces:

java.lang.Comparable<Value>

Enclosing class:

Alignment

public static class Alignment.UPSame
extends UPSeriesModel.Length

An UnParameterised SeriesModel of Alignments where both sequences are of the same element Type. It is built from UPsm3, UPsmE and UPx2y. The fully parameterised SeriesModel is Alignment.UPSame.M.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Alignment.UPSame.M The fully parameterised SeriesModel of Alignments.

Nested classes/interfaces inherited from class mml.UPSeriesModel

UPSeriesModel.Est, UPSeriesModel.K, UPSeriesModel.Length

Nested classes/interfaces inherited from class la.la.Function

Function.Cts2Cts, Function.Derivative, Function.Integral, Function.Native, Function.Native2, Function.Native3

Nested classes/interfaces inherited from class la.la.Value

Value.Atomic, Value.Bool, Value.Char, Value.Chars, Value.Cts, Value.Defer, Value.Discrete, Value.Enum, Value.Inc_Or, Value.Int, Value.Lambda, Value.List, Value.Maybe, Value.Option, Value.Real, Value.Scannable, Value.Structured, Value.Triv, Value.Tuple

Field Summary

Fields

Modifier and Type	Field and Description
UPSeriesModel.Length	UPsm3 UPsm3, the UnParameterised SeriesModel of the "flags", (LEFT | RIGHT | BOTH)*.
UPSeriesModel	UPsmE UPsmE, the UnParameterised SeriesModel of elements.
UPFunctionModel	UPx2y UPx2y, the UnParameterised FunctionModel of l→r and r→l.

Fields inherited from class mml.UPModel

dp

Fields inherited from class la.la.Value

C, comparator, CR, E, eight, ffalse, five, fiveR, four, fourR, half, negCR, negOne, negOneR, negTenR, nilVal, nine, None, one, oneR, PI, PIby2, point01, point1, point5, point9, quarter, seven, six, ten, tenR, three, threeR, triv, ttrue, two, twoR, zero, zeroR

Constructor Summary

Constructors

Constructor and Description
UPSame(Value dp)

Method Summary

Modifier and Type	Method and Description
UPSeriesModel.Est	estimator(Value ps) Return the Estimator.
UPModel	lenUPM() UPsm3.lenUPM() provides the UPModel of lengths.
Alignment.UPSame.M	sp2Model(double msg1, double msg2, Value sp) Given two part message lengths, msg1 and msg2, and statistical parameters, sp, return a M.
Value	stats(boolean add, Value ss0, Value ss1) Combine sufficient statisticses 'ss0' and 'ss1' additively (add=true), or remove ss1 from ss0 (add=false).
Value	stats(Vector vs, int lo, int hi) In this case, statistics ss is the data-set vs.

Methods inherited from class mml.UPSeriesModel.Length

lenStats

Methods inherited from class mml.UPSeriesModel

apply

Methods inherited from class mml.UPModel

defnParams, main, stats, stats, toString

Methods inherited from class la.la.Function

bOp, fromBop, fromUop, type, uOp

Methods inherited from class la.la.Value

AoM, bOp, compareTo, cons, cts, elt, errMsg, error, force, isTuple, just, n, nElts, nlAoM, pair, print, quad, real, RTE, triple, tuple, UOE, x

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

UPsm3

public final UPSeriesModel.Length UPsm3

UPsm3, the UnParameterised SeriesModel of the "flags", (LEFT | RIGHT | BOTH)^*.

UPsmE

public final UPSeriesModel UPsmE

UPsmE, the UnParameterised SeriesModel of elements.

UPx2y

public final UPFunctionModel UPx2y

UPx2y, the UnParameterised FunctionModel of l→r and r→l.

Constructor Detail

UPSame

public UPSame(Value dp)

Method Detail

lenUPM

public UPModel lenUPM()

UPsm3.lenUPM() provides the UPModel of lengths.

Specified by:

lenUPM in class UPSeriesModel.Length

stats

public Value stats(Vector vs,
                   int lo,
                   int hi)

In this case, statistics ss is the data-set vs.

Specified by:

stats in class UPModel

stats

public Value stats(boolean add,
                   Value ss0,
                   Value ss1)

Description copied from class: UPModel

Combine sufficient statisticses 'ss0' and 'ss1' additively (add=true), or remove ss1 from ss0 (add=false). Also see stats(ds,lo,hi).

Specified by:

stats in class UPModel

estimator

public UPSeriesModel.Est estimator(Value ps)

Return the Estimator. Parameters ps, if any, are for (UPsm3, UPsmE, UPx2y) respectively.

Overrides:

estimator in class UPModel

sp2Model

public Alignment.UPSame.M sp2Model(double msg1,
                                   double msg2,
                                   Value sp)

Given two part message lengths, msg1 and msg2, and statistical parameters, sp, return a M.

Specified by:

sp2Model in class UPSeriesModel