level1.go

package gosaca

// After filling in LMS suffixes using the "end of bucket is a counter"
// algorithm from section 4.2, we need to loop over SA and fix any bucket
// counters still left.
func fixLMSBucketCounters(SA []int) {
	for i := len(SA) - 1; i >= 0; i-- {
		if SA[i] == empty || SA[i] >= 0 {
			// SA[i] isn't a counter; move on
			continue
		}
		// right shift all the elements of the bucket, filling the vacated
		// slot with "empty"
		d := SA[i]
		pos := i + d - 1
		prev := empty
		for x := pos + 1; x <= i; x++ {
			SA[x], prev = prev, SA[x]
		}
	}
}

// This helper function implements the logic described in section 4.2 to
// insert an S-type value into its bucket from the end, reusing the ends of
// buckets as counters. If we have to shift a bucket around, the two returned
// integers are the start and end positions of SA that were modified.  If we
// don't have to do any shifting, we return -1, -1.
func insertSTypeUsingCounters(SA []int, index, c int) (int, int) {
	x0, x1 := -1, -1
	n := len(SA)
	switch {
	case SA[c] >= 0:
		// section 4.2 case 2
		prev := SA[c]
		x0, x1 = c, c
		for x := c + 1; x < n; x++ {
			SA[x], prev = prev, SA[x]
			x1 = x
			if prev < 0 && prev != empty {
				break
			}
		}
		fallthrough

	case SA[c] == empty:
		// section 4.2 case 1
		if c-1 >= 0 && SA[c-1] == empty {
			SA[c-1] = index
			SA[c] = -1
		} else {
			SA[c] = index
		}
		break

	default:
		// section 4.2 case 3
		d := SA[c]
		pos := c + d - 1
		if pos >= 0 && SA[pos] == empty {
			SA[pos] = index
			SA[c]--
		} else {
			// right-shift SA[pos+1:c-1], inserting index into SA[pos+1]
			x0, x1 = pos+1, c
			prev := index
			for x := pos + 1; x <= c; x++ {
				SA[x], prev = prev, SA[x]
			}
		}
		break
	}

	return x0, x1
}

// Same style of helper function as above, except for section 4.1 (L-type
// into buckets from head to tail).
func insertLTypeUsingCounters(SA []int, index, c int) (int, int) {
	x0, x1 := -1, -1
	n := len(SA)
	switch {
	case SA[c] >= 0:
		// section 4.1 case 1
		prev := SA[c]
		x0, x1 = c, c
		for x := c - 1; x >= 0; x-- {
			SA[x], prev = prev, SA[x]
			x0 = x
			if prev < 0 && prev != empty {
				break
			}
		}
		fallthrough

	case SA[c] == empty:
		// section 4.1 case 1
		if c+1 < n && SA[c+1] == empty {
			SA[c+1] = index
			SA[c] = -1
		} else {
			SA[c] = index
		}
		break

	default:
		// section 4.1 case 3
		d := SA[c]
		pos := c - d + 1
		if pos < n && SA[pos] == empty {
			SA[pos] = index
			SA[c]--
		} else {
			// left-shift SA[c+1:pos-1], inserting index into SA[pos-1]
			x0, x1 = c, pos-1
			prev := index
			for x := pos - 1; x >= c; x-- {
				SA[x], prev = prev, SA[x]
			}
		}
	}

	return x0, x1
}

// recursive version of ComputeSuffixArray for levels 1+
func computeSuffixArray1(S, SA []int, k int) {
	n := len(S)

	// *********************************************
	// Stage 1: Induced-sort the LMS-substrings of S
	// *********************************************

	// step 1 - initialize SA as empty
	setAllToEmpty(SA)

	// step 2 - put all LMS substrings into buckets based on their first character
	for i := n - 2; i >= 0; i-- {
		if S[i] >= 0 {
			// S[i] is L-type
			continue
		}

		// S[i] is S-type; walk back until S[i-1] is L-type or -1
		for i >= 1 && S[i-1] < 0 {
			// S[i-1] is also S-type
			i--
		}

		if i == 0 {
			// even if S[0] is S-type, it's not LMS - we're done
			break
		}

		// Insertion of the LMS strings is identical to insertions of S-type
		// strings described in section 4.2, but we don't care about the
		// returned values.
		insertSTypeUsingCounters(SA, i, ^S[i])
	}

	// Remove any leftover bucket counters.
	fixLMSBucketCounters(SA)

	// step 3 - induced sort the L-type suffixes of S into their buckets
	induceSortL1(S, SA)

	// step 4 - induced sort the S-type suffixes of S into their buckets
	induceSortS1(S, SA)

	// compact all the now-sorted LMS substrings into the first n1 positions of SA
	n1 := 0
	for _, s := range SA {
		if s != 0 && // S[0] is not LMS by definition
		S[s] < 0 && // S[s] is S-type
		S[s-1] >= 0 { // S[s-1] is L-type
			SA[n1] = s
			n1++
		}
	}

	// *********************************************
	// Stage 2: Rename the LMS substrings
	// *********************************************

	// provably, n1 is at most floor(n/2), so the following overlapping works
	SA1 := SA[:n1]  // SA1 overlaps the front of SA
	work := SA[n1:] // workspace overlaps the rest of SA
	S1 := SA[n-n1:] // S1 overlaps the end of SA (including part of "work", but rename deals with that correctly)
	k1 := rename1(S, SA1, work, S1)

	// *********************************************
	// Stage 3: Sort recursively
	// *********************************************
	sortRecursively(S1, SA1, k1)

	// NOT DESCRIBED IN PAPER BUT STILL NECESSARY (see SA-IS)
	// We need to undo the renaming of the LMS suffixes.
	// We no longer need S1, so reuse it to hold all the LMS indices.
	j := n1 - 1
	for i := n - 2; i >= 0; i-- {
		if S[i] >= 0 {
			// L-type; ignore
			continue
		}
		// S[i] is S-type; walk backwards to find LMS
		for i >= 1 && S[i-1] < 0 {
			// S[i-1] is also S-type; keep moving back
			i--
		}
		// S[0] is not LMS by definition, but otherwise S[i] is LMS
		if i > 0 {
			S1[j] = i
			j--
		}
	}
	if j != -1 {
		panic("didn't find all the LMS characters we expected")
	}
	// Now convert SA1 from renamed values to true values.
	for i, s := range SA1 {
		SA1[i] = S1[s]
	}

	// *********************************************
	// Stage 4: Induced-sort SA(S) from SA1(S1)
	// *********************************************

	// step 1 - initialize SA[n1:] as empty
	setAllToEmpty(SA[n1:])

	// step 2 - put all the sorted LMS suffixes of S into their buckets in SA
	for i := n1 - 1; i >= 0; i-- {
		j := SA[i]
		SA[i] = empty
		c := ^S[j]
		if j == 0 {
			panic("unexpected j == 0")
		}
		// If we've worked our way back to c == i, then all the remaining
		// SA[0,c] values are already correct, and going into the loop below
		// with bucket counters will just screw things up.
		if c == i {
			SA[c] = j // restore it (we just emptied it out above...)
			break
		}

		// Same explanation for what's going on here as in Stage 1 step 2.
		insertSTypeUsingCounters(SA, j, c)
	}

	// Remove any leftover bucket counters.
	fixLMSBucketCounters(SA)

	// step 3 - induced sort the L-type suffixes of S into their buckets
	induceSortL1(S, SA)

	// step 4 - induced sort the S-type suffixes of S into their buckets
	induceSortS1(S, SA)
}

// TODO pre-post
func induceSortL1(S, SA []int) {
	n := len(S)

	// special case to deal with the (virtual) sentinel:
	// S[n-1] is L-type because of the sentinel, and if we were treating
	// the sentinel as a real character, it would be at the front of SA[]
	// (it's effectively stored in "SA[-1]").
	//
	// Because c is L-type, we know SA[c] is empty, so we're in case 1 of section 4.1
	c := S[n-1]
	if c+1 < n && SA[c+1] == empty {
		SA[c+1] = n - 1
		SA[c] = -1
	} else {
		SA[c] = n - 1
	}

	for i := 0; i < n; i++ {
		if SA[i] < 0 {
			// SA[i] is empty or being used as a counter; nothing to do
			continue
		}
		j := SA[i] - 1
		// if we just grabbed the character before an LMS suffix, we need to clear
		// out that LMS suffix (induceSortS1 assumes only L-type suffixes are in SA)
		if S[SA[i]] < 0 {
			SA[i] = empty
		}
		if j < 0 {
			// SA[i] was == 0; there is no preceding character to look at
			continue
		}
		c := S[j]
		if c < 0 {
			// S[j] is S-type; move on
			continue
		}

		// insert j into its bucket; if we overwrite SA[i], we need to stay
		// here and look at it again in the next pass
		x0, x1 := insertLTypeUsingCounters(SA, j, c)
		if i >= x0 && i <= x1 {
			i--
		}
	}

	// NOT MENTIONED IN PAPER: We need to go back over SA and fix
	// any leftover counter values via left shifting the buckets appropriately.
	// This is the moral equivalent of fixLMSBucketCounters, but we only ever
	// do this once, so didn't bother extracting it into its own function.
	for i, d := range SA {
		if d == empty || d >= 0 {
			continue
		}
		pos := i - d + 1
		prev := empty
		for x := pos - 1; x >= i; x-- {
			SA[x], prev = prev, SA[x]
		}
	}
}

// TODO pre-post
func induceSortS1(S, SA []int) {
	n := len(S)

	for i := n - 1; i >= 0; i-- {
		if SA[i] <= 0 {
			// SA[i] is empty or being used as a counter; nothing to do
			continue
		}
		j := SA[i] - 1
		c := ^S[j]
		if c < 0 {
			// S[j]==c is L-type; move on
			continue
		}

		// insert j into its bucket; if we overwrite SA[i], we need to stay
		// here and look at it again in the next pass
		x0, x1 := insertSTypeUsingCounters(SA, j, c)
		if i >= x0 && i <= x1 {
			i++
		}
	}
}