https://stackoverflow.com/questions/22796115
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Having read and studied the paper, I can say that C is supposed to be an array holding the alphabet of your strings, where the alphabet size (and, thus, the size of C) is l.
By the looks of your question, however, I feel the need to go deeper on this, because it looks like you didn't get the whole picture yet. What is P[i,j], and why do you need it? The answer is that you don't really need it, but it's an elegant optimization. In page 3, a little bit before Theorem 1, it is said that:
[...] This process ends when j-k = 0 at the k-th step, or a(i) = b(j-k) at the k-th step. Assume that the process stops at the k-th step, and k must be the minimum number that makes a(i) = b(j-k) or j-k = 0. [...]
The recurrence relation in (3) is equivalent to (2), but the fundamental difference is that (2) expands recursively, whereas with (3) you never have recursive calls, provided that you know k. In other words, the magic behind (3) not expanding recursively is that you somehow know the spot where the recursion on (2) would stop, so you look at that cell immediately, rather than recursively approaching it.
Ok then, but how do you find out the value for k? Since k is the spot where (2) reaches a base case, it can be seen that k is the amount of columns that you have to "go back" on B until you are either off the limits (i.e., the first column that is filled with 0's) OR you find a match between a character in B and a character in A (which corresponds to the base case conditions in (2)). Remember that you will be matching the character a(i-1), where i is the current row.
So, what you really want is to find the last position in B before j where the character a(i-1) appears. If no such character ever appears in B before j, then that would be equivalent to reaching the case i = 0 or j-1 = 0 in (2); otherwise, it's the same as reaching a(i) = b(j-1) in (2).
Let's look at an example:
Consider that the algorithm is working on computing the values for i = 2 and j = 3 (the row and column are highlighted in gray). Imagine that the algorithm is working on the cell highlighted in black and is applying (2) to determine the value of S[2,2] (the position to the left of the black one). By applying (2), it would then start by looking at a(2) and b(2). a(2) is C, b(2) is G, to there's no match (this is the same procedure as the original, well-known algorithm). The algorithm now wants to find the value of S[2,2], because it is needed to compute S[2,3] (where we are). S[2,2] is not known yet, but the paper shows that it is possible to determine that value without refering to the row with i = 2. In (2), the 3rd case is chosen: S[2,2] = max(S[1, 2], S[2, 1]). Notice, if you will, that all this formula is doing is looking at the positions that would have been used to calculate S[2,2]. So, to rephrase that: we're computing S[2,3], we need S[2,2] for that, we don't know it yet, so we're going back on the table to see what's the value of S[2,2] in pretty much the same way we did in the original, non-parallel algorithm.
When will this stop? In this example, it will stop when we find the letter C (this is our a(i)) in TGTTCGACA before the second T (the letter on the current column) OR when we reach column 0. Because there is no C before T, we reach column 0. Another example:
Here, (2) would stop with j-1 = 5, because that is the last position in TGTTCGACA where C shows up. Thus, the recursion reaches the base case a(i) = b(j-1) when j-1 = 5.
With this in mind, we can see a shortcut here: if you could somehow know the amount k such that j-1-k is a base case in (2), then you wouldn't have to go through the score table to find the base case.
That's the whole idea behind P[i,j]. P is a table where you lay down the whole alphabet vertically (on the left side); the string B is, once again, placed horizontally in the upper side. This table is computed as part of a preprocessing step, and it will tell you exactly what you will need to know ahead of time: for each position j in B, it says, for each character C[i] in C (the alphabet), what is the last position in B before j where C[i] is found (note that i is used to index C, the alphabet, and not the string A. Maybe the authors should have used another index variable to avoid confusion).
So, you can think of the semantics for an entry P[i,j] as something along the lines of: The last position in B where I saw C[i] before position j. For example, if you alphabet is sigma = {A, E, I, O, U}, and B = "AOOIUEI", thenP` is:
Take the time to understand this table. Note the row for O. Remember: this row lists, for every position in B, where is the last known "O". Only when j = 3 will we have a value that is not zero (it's 2), because that's the position after the first O in AOOIUEI. This entry says that the last position in B where O was seen before is position 2 (and, indeed, B[2] is an O, the one that follows A). Notice, in that same row, that for j = 4, we have the value 3, because now the last position for O is the one that correspnds to the second O in B (and since no more O's exist, the rest of the row will be 3).
Recall that building P is a preprocessing step necessary if you want to easily find the value of k that makes the recursion from equation (2) stop. It should make sense by now that P[i,j] is the k you're looking for in (3). With P, you can determine that value in O(1) time.
Thus, the C[i] in (6) is a letter of the alphabet - the letter that we are currently considering. In the example above, C = [A,E,I,O,U], and C[1] = A, C[2] = E, etc. In equaton (7), c is the position in C where a(i) (the current letter of string A being considered) lives. It makes sense: after all, when building the score table position S[i,j], we want to use P to find the value of k - we want to know where was the last time we saw an a(i) in B before j. We do that by reading P[index_of(a(i)), j].
Ok, now that you understand the use of P, let's see what's happening with your implementation.
About your specific case
In the paper, P is shown as a table that lists the whole alphabet. It is a good idea to iterate through the alphabet because the typical uses of this algorithm are in bioinformatics, where the alphabet is much, much smaller than the string A, making the iteration through the alphabet cheaper.
Because your strings are sequences of objects, your C would be the set of all possible objects, so you'd have to build a table P with the set of all possible object instance (nonsense, of course). This is definitely a case where the alphabet size is huge when compared to your string size. However, note that you will only be indexing P in those rows that correspond to letters from A: any row in P for a letter C[i] that is not in A is useless and will never be used. This makes your life easier, because it means you can build P with the string A instead of using the alphabet of every possible object.
Again, an example: if your alphabet is AEIOU, A is EEI and B is AOOIUEI, you will only be indexing P in the rows for E and I, so that's all you need in P:
This works and suffices, because in (7), P[c,j] is the entry in P for the character c, and c is the index of a(i). In other words: C[c] always belongs to A, so it makes perfect sense to build P for the characters of A instead of using the whole alphabet for the cases where the size of A is considerably smaller than the size of C.
All you have to do now is to apply the same principle to whatever your objects are.
I really don't know how to explain it any better. This may be a little dense at first. Make sure to re-read it until you really get it - and I mean every little detail. You have to master this before thinking about implementing it.
NOTE: You said you were looking for a credible and / or official source. I'm just another CS student, so I'm not an official source, but I think I can be considered "credible". I've studied this before and I know the subject. Happy coding!
