added multiarray2

[jigold]

This is the multiarray2 code from the concordance work.

[cseed]

This should go in its own file in utils/.

[cseed]

Jackie, there's a an Array[Array[T]] in methods/MendelErrors.scala that be a MultiArray2. Go ahead and make that change.

[cseed]

OK, here's some thoughts on rowSlice:

• You did something clever, making a class look like a function. Except to call it, you need to do new a.rowSlice(i) which isn't quite what we want. You could make it a case class or define a companion object with apply.
• However, I think it is clearer as RowSlice: classes are Capitalized, functions and variables are lowerCase.
• so you need a def rowSlice(i: Int) = ....
• RowSlice should be a mutable.IndexedSeq. This will give it an array-like interface. Now would be a good time to read the Scala collections chapter of Introduction to Scala. Make sure you understand the difference between Traversable, Iterable, Iterator and IndexedSeq.

[cseed]

Don't use .toArray. This copies the data. I think getCode should take an IndexedSeq rather than an Array. Or you can pass row(0), row(1), etc. like to MendelError below.

[cseed]

That's all my comments. Back to you.

[jigold]

Cotton -- I fixed the changes you suggested and it should be ready to be merged. For the multiarray of size 0, I tested that you can create the object, but using the apply for (0,0) throws an error.

[cseed]

You still need a check here. If the size is (5, 5), rowSlice(0)(5) will return element (1, 0), but it should throw an error. Basically I'm thinking:

  def apply(j: Int): T = {
    if (j < 0 || j >= n2)
      throw new IndexOutOfBoundsException
      a(...
  }

[cseed]

Perfect re: empty. I had two other minor comments.

[jigold]

Back to you. I hope I understood your comments. If not, then let's discuss in person.

[cseed]

So as we discussed def apply(...) { if (opposite condition) throw new ArrayIndex...; a(i*n2 + j) }. And same below.

[jigold]

All set :)