From 17a5ff66d6b588a4b2d6089f392c162bdc2f97c6 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Thu, 22 Dec 2022 08:29:50 +0100
Subject: [PATCH] Translated findCliques() + subfunctions

---
 NAMESPACE            |  1 +
 R/cliques_to_jtree.R |  1 +
 R/elim_order.R       |  1 +
 R/findCliques.R      | 46 +++++++++++++++++++++++++++++++++++++++++++-
 R/myintersect.R      |  1 +
 R/triangulate.R      |  1 +
 6 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 R/cliques_to_jtree.R
 create mode 100644 R/elim_order.R
 create mode 100644 R/myintersect.R
 create mode 100644 R/triangulate.R

diff --git a/NAMESPACE b/NAMESPACE
index 3b8b822..f0dc387 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -74,3 +74,4 @@ importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(utils,read.delim)
 importFrom(vcfR,read.vcfR)
+importFrom(zeallot,"%<-%")
diff --git a/R/cliques_to_jtree.R b/R/cliques_to_jtree.R
new file mode 100644
index 0000000..6b3fd18
--- /dev/null
+++ b/R/cliques_to_jtree.R
@@ -0,0 +1 @@
+cliques_to_jtree <- function(cliques, ns) {}
diff --git a/R/elim_order.R b/R/elim_order.R
new file mode 100644
index 0000000..fe89c56
--- /dev/null
+++ b/R/elim_order.R
@@ -0,0 +1 @@
+elim_order <- function(G, node_sizes) {}
diff --git a/R/findCliques.R b/R/findCliques.R
index eea6d3c..4ff1d8b 100644
--- a/R/findCliques.R
+++ b/R/findCliques.R
@@ -1,3 +1,47 @@
 findCliques <- function(M) {
-   # TODO: translate findCliques() from matlab/spatial/findCliques.m
+  # Muuttaa graafin M kolmioituvaksi ja laskee siitה klikit ja
+  # separaattorit.
+  # Hyצdynnetההn Kevin Murphyn algoritmeja Graph Theory toolboxista.
+  # Pהivitetty 12.8.2005
+  order <- elim_order(M, ones(length(M))) # TODO: translate from findCliques.m
+  c(G, cliques) %<-% triangulate(M, order) # TODO: translate from findCliques.m
+  c(jtree, root) %<-% cliques_to_jtree(cliques, ones(length(M))) # TODO: translate from findCliques.m
+  ncliq <- length(cliques)
+  separators <- cell(ncliq - 1, 1)    # n - solmuisessa puussa n - 1 viivaa
+
+  jono <- zeros(length(ncliq))
+  jono[1] <- root
+  i <- 1
+  pointer <- 2                     # Seuraava tyhjה paikka
+
+  while (!is.null(find(jono != 0))) {  # Puun leveyssuuntainen lהpikהynti) {
+    lapset <- find(jtree[jono[i], ] != 0)
+    jtree[, jono[i]] <- 0         # Klikki kהsitelty
+    jono[pointer:(pointer + length(lapset) - 1)] <- lapset
+    for (j in 1:length(lapset)) {
+      ehdokas <- myintersect(cliques[[jono[i]]], cliques[[lapset[j]]])
+      kelpaa <- 1
+      for (k in 1:(pointer + j - 3)) {
+        # Tutkitaan, ettה separaattoriehdokasta ei vielה kהsitelty
+        if (ehdokas == separators[[k]]) {
+          kelpaa <- 0
+        }
+      }
+      if (kelpaa) {
+        separators[[pointer + j - 2]] <- ehdokas
+      }
+    }
+    jono[i] <- 0
+    pointer <- pointer + length(lapset)
+    i <- i + 1
+  }
+  notEmpty <- zeros(ncliq - 1, 1)
+  for (i in 1:(ncliq - 1)) {
+    if (!is.null(separators[[i]])) {
+      notEmpty[i] <- 1
+    }
+  }
+  notEmpty <- find(notEmpty == 1)
+  separators <- separators(notEmpty)
+  return(list("cliques" = cliques, "separators" = separators, "G" = G))
 }
diff --git a/R/myintersect.R b/R/myintersect.R
new file mode 100644
index 0000000..b2c19f1
--- /dev/null
+++ b/R/myintersect.R
@@ -0,0 +1 @@
+myintersect <- function(A, B) {}
diff --git a/R/triangulate.R b/R/triangulate.R
new file mode 100644
index 0000000..0280b21
--- /dev/null
+++ b/R/triangulate.R
@@ -0,0 +1 @@
+triangulate <- function(G, order) {}