la.bioinformatics

Class Alignment

java.lang.Object

la.la.Value

la.la.Value.Structured

la.maths.Vector

la.bioinformatics.Alignment

All Implemented Interfaces:

java.lang.Comparable<Value>, Value.Scannable

public abstract class Alignment
extends Vector

This is experimental code, not a production application. You are welcome to look, but consider it to be ephemeral. An Alignment of two sequences is seen primarily as a Vector of Inc_Or t1 t2 where t1 is the element type of sequence 1 and t2 is the element type of sequence 2. Of course t1 and t2 may be the same.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Alignment.UPSame An UnParameterised SeriesModel of Alignments where both sequences are of the same element Type.

Nested classes/interfaces inherited from class la.maths.Vector

Vector.Derived, Vector.Doubles, Vector.GP, Vector.Ints, Vector.Slice, Vector.Strings, Vector.Weighted

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 inherited from class la.maths.Vector

empty

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
Alignment()

Method Summary

Modifier and Type	Method and Description
static Alignment.UPSame.M	a2m(Alignment al, Estimator e) Estimate a SeriesModel to suit the Alignment al.
static Alignment	algnmnt(Value.Inc_Or[] Inc_Ors) One way to create an Alignment, as a given.
abstract Value.Inc_Or	elt(int i) elt(i) must be an Value.Inc_Or.
static Alignment	EM(Vector s1, Vector s2, Estimator e)
Value.Scannable	flags() The Scannable Int(n())s of this Alignment.
static Value.Scannable	flags(Value.Scannable sv) The Scannable Int(n())s of a Scannable of Inc_OR.
static void	main(java.lang.String[] args) A very rudimentary test.
Value.Scannable	side(int sel) sel = LEFT | RIGHT | BOTH.
static Value.Scannable	side(Value.Scannable sv, int sel) sel = LEFT | RIGHT | BOTH.
static Alignment	simple(Vector s1, Vector s2, Alignment.UPSame.M m) Given two sequences, s1 and s2, and a SeriesModel of Alignments, m, return an optimal global Alignment of s1 and s2.

Methods inherited from class la.maths.Vector

addMore, addMore, append, append, as_1xn, as_nx1, asDiagonal, asMatrix, asQ, asQrotn, bOp, closes, col, cols, combine, compareTo, constAoM, constNlAoM, constWt, csv, csv, delete, delete, dot, doubles, doubles, doubles, drop, drop, dropLast, elt, elts, eltType, foldl, foldl, foldr, foldr, fromScannable, ints, ints, isRectangular, isSquare, map, match, merge, nCols, nearlySymmetric, nearlySymmetric, nElts, nElts, nlAoM, nlAoM, norm_Cts, norm, normalised, normalised1, normalised2, opens, repeat, rotate, rotate, rowLength, scaled, shape, singleton, slice, sorted, sorted, sorted, strings, sumSq, take, takeLast, times, toSeries, type, uniqueElts, unzip, unzip, uOp, values, weight, weight, weight, weightLike, weightLike, wt, wtMedian, wtNlAoM, wtNlAoM, wts, wts, zip, zip

Methods inherited from class la.la.Value.Structured

AoM, elts, frth, fst, print, separator, snd, thrd, toString

Methods inherited from class la.la.Value

apply, cons, cts, errMsg, error, force, isTuple, just, n, pair, quad, real, RTE, triple, tuple, UOE, x

Methods inherited from class java.lang.Object

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

Constructor Detail

Alignment

public Alignment()

Method Detail

elt

public abstract Value.Inc_Or elt(int i)

elt(i) must be an Value.Inc_Or.

Specified by:

elt in class Vector

side

public Value.Scannable side(int sel)

sel = LEFT | RIGHT | BOTH. The Scannable elements of the sel-ected side or sides (pairs) of this Alignment.

flags

public Value.Scannable flags()

The Scannable Int(n())s of this Alignment. That is of 0|1|2 for LEFT|RIGHT|BOTH repectively.

algnmnt

public static Alignment algnmnt(Value.Inc_Or[] Inc_Ors)

One way to create an Alignment, as a given.

simple

public static Alignment simple(Vector s1,
                               Vector s2,
                               Alignment.UPSame.M m)

Given two sequences, s1 and s2, and a SeriesModel of Alignments, m, return an optimal global Alignment of s1 and s2. It is required that m.sm3 incorporates simple costs — constant for each of insert, delete, match.

a2m

public static Alignment.UPSame.M a2m(Alignment al,
                                     Estimator e)

Estimate a SeriesModel to suit the Alignment al.

EM

public static Alignment EM(Vector s1,
                           Vector s2,
                           Estimator e)

side

public static Value.Scannable side(Value.Scannable sv,
                                   int sel)

sel = LEFT | RIGHT | BOTH. The elements on the sel-ected side or sides of the Scannable Value sv.

flags

public static Value.Scannable flags(Value.Scannable sv)

The Scannable Int(n())s of a Scannable of Inc_OR.

main

public static void main(java.lang.String[] args)

A very rudimentary test.