From e885081f1d3d4638ef90c0fa83db1106cc0cc3bc Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Tue, 14 Jul 2020 14:35:33 +0200
Subject: [PATCH] Translated newGetDistances()

---
 R/newGetDistances.R | 63 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 R/newGetDistances.R

diff --git a/R/newGetDistances.R b/R/newGetDistances.R
new file mode 100644
index 0000000..18cd9c7
--- /dev/null
+++ b/R/newGetDistances.R
@@ -0,0 +1,63 @@
+newGetDistances <- function(data, rowsFromInd) {
+	ninds <- max(data[, end])
+	nloci <- size(data, 2) - 1
+	riviLkm <- choose(ninds, 2)
+
+	empties <- find(data < 0)
+	data[empties] <- 0
+	data <- as.integer(data) # max(noalle) oltava <256
+
+	pariTaulu <- zeros(riviLkm, 2)
+	aPointer <- 1
+	for (a in (1:ninds) - 1) {
+		pariTaulu[aPointer:(aPointer + ninds - 1 - a), 1] <-
+			ones(ninds - a, 1) * a
+		pariTaulu[aPointer:aPointer + ninds - 1 - a, 2] <- t(a + 1:ninds)
+		aPointer <- aPointer + ninds - a
+	}
+
+	eka <- pariTaulu[, ones(1, rowsFromInd)]
+	eka <- eka * rowsFromInd
+	miinus <- repmat((rowsFromInd - 1):0, c(riviLkm, 1))
+	eka <- eka - miinus
+
+	toka <- pariTaulu[, ones(1, rowsFromInd) * 2]
+	toka <- toka * rowsFromInd
+	toka <- toka - miinus
+
+	summa <- zeros(riviLkm, 1)
+	vertailuja <- zeros(riviLkm, 1)
+
+	rm(pariTaulu, miinus)
+
+	x <- zeros(size(eka))
+	x <- as.integer(x)
+	y <- zeros(size(toka))
+	y <- as.integer(y)
+
+	for (j in 1:nloci) {
+		for (k in 1:rowsFromInd) {
+			x[, k] <- data[eka[, k], j]
+			y[, k] <- data[toka[, k], j]
+		}
+		for (a in 1:rowsFromInd) {
+			for (b in 1:rowsFromInd) {
+				vertailutNyt <- as.double(x[, a] > 0 & y[, b] > 0)
+				vertailuja <- vertailuja + vertailutNyt
+				lisays <- (x[, a] != y[, b] & vertailutNyt)
+				summa <- summa + as.double(lisays)
+			}
+		}
+	}
+
+	rm(x, y, vertailutNyt)
+	nollat <- find(vertailuja == 0)
+	dist <- zeros(length(vertailuja), 1)
+	dist[nollat] <- 1
+	muut <- find(vertailuja > 0)
+	dist[muut] <- summa[muut] / vertailuja[muut]
+	rm(summa, vertailuja)
+
+	Z = linkage(t(dist))
+	return(list(Z = Z, dist = dist))
+}
\ No newline at end of file