From b242f3a9e59113b9f1329af553d80a8e0c133b4e Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Mon, 14 Oct 2024 14:16:37 +0100
Subject: [PATCH] register all S3 methods

* even private ones where the generic is not exported and will not be visible to outside users
---
 NAMESPACE              | 10 ++++++++++
 R/hxsurf.R             |  4 ++++
 R/im3d.R               |  2 ++
 R/neuron-io-neuroml.R  |  2 ++
 R/potential_synapses.R |  6 ++++--
 5 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 9d3825b9..bd32d4cf 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,8 @@ S3method("[[",neuronlistz)
 S3method("[[<-",neuronlistfh)
 S3method("boundingbox<-",default)
 S3method("data.frame<-",neuronlist)
+S3method("materials<-",default)
+S3method("materials<-",hxsurf)
 S3method("xyzmatrix<-",character)
 S3method("xyzmatrix<-",default)
 S3method("xyzmatrix<-",dotprops)
@@ -29,6 +31,8 @@ S3method(Ops,dotprops)
 S3method(Ops,hxsurf)
 S3method(Ops,mesh3d)
 S3method(Ops,neuron)
+S3method(PotentialSynapses,default)
+S3method(PotentialSynapses,dotprops)
 S3method(all,equal.dotprops)
 S3method(all,equal.im3d)
 S3method(all,equal.neuron)
@@ -47,6 +51,7 @@ S3method(as.mesh3d,hxsurf)
 S3method(as.neuron,data.frame)
 S3method(as.neuron,default)
 S3method(as.neuron,igraph)
+S3method(as.neuron,morphml_cell)
 S3method(as.neuron,neuron)
 S3method(as.neuron,ngraph)
 S3method(as.neuronlist,default)
@@ -55,6 +60,7 @@ S3method(as.neuronlist,neuronlistz)
 S3method(as.neuronlistfh,neuronlist)
 S3method(as.ngraph,data.frame)
 S3method(as.ngraph,igraph)
+S3method(as.ngraph,morphml_cell)
 S3method(as.ngraph,neuron)
 S3method(as.ngraph,ngraph)
 S3method(as.seglist,default)
@@ -76,6 +82,10 @@ S3method(cmtk.targetvolume,character)
 S3method(cmtk.targetvolume,default)
 S3method(cmtk.targetvolume,im3d)
 S3method(cmtk.targetvolume,list)
+S3method(contains_points,ashape3d)
+S3method(contains_points,boundingbox)
+S3method(contains_points,hxsurf)
+S3method(contains_points,mesh3d)
 S3method(coord2ind,default)
 S3method(dim,im3d)
 S3method(dimnames,neuronlist)
diff --git a/R/hxsurf.R b/R/hxsurf.R
index 1e866628..4e812bd6 100644
--- a/R/hxsurf.R
+++ b/R/hxsurf.R
@@ -738,12 +738,14 @@ pointsinside.default<-function(x, surf, ..., rval=c('logical','distance',
 
 contains_points <- function(obj, points, ...) UseMethod("contains_points")
 
+#' @export
 contains_points.boundingbox <- function(obj, points,  ...) {
   xyz=xyzmatrix(points)
   xyz[,1] >= obj[1,1] & xyz[,2] >= obj[1,2] & xyz[,3] >= obj[1,3] &
     xyz[,1] <= obj[2,1] & xyz[,2] <= obj[2,2] & xyz[,3] <= obj[2,3]
 }
 
+#' @export
 contains_points.mesh3d <- function(obj, points,  ...) {
   xyz=xyzmatrix(points)
   inbb=contains_points(boundingbox(obj), xyz, ...)
@@ -754,8 +756,10 @@ contains_points.mesh3d <- function(obj, points,  ...) {
   res
 }
 
+#' @export
 contains_points.hxsurf<-contains_points.mesh3d
 
+#' @export
 contains_points.ashape3d<-function(obj, points,  ...) {
   alphashape3d::inashape3d(obj, points=xyzmatrix(points), ...)
 }
diff --git a/R/im3d.R b/R/im3d.R
index c8300042..caa9524b 100644
--- a/R/im3d.R
+++ b/R/im3d.R
@@ -1236,10 +1236,12 @@ materials.hxsurf<-function(x, ...) {
 
 `materials<-`<-function(x, value) UseMethod("materials<-")
 
+#' @export
 `materials<-.hxsurf`<-function(x, value) {
   stop("materials<-.hxsurf is not implemented")
 }
 
+#' @export
 `materials<-.default`<-function(x, value) {
   if(!is.data.frame(value))
     stop("materials<- expects a data.frame")
diff --git a/R/neuron-io-neuroml.R b/R/neuron-io-neuroml.R
index db9cc675..35a8ce83 100644
--- a/R/neuron-io-neuroml.R
+++ b/R/neuron-io-neuroml.R
@@ -208,8 +208,10 @@ as.data.frame.morphml_cell<-function(x, ...){
   structure(r[in_names], .Names=out_names)
 }
 
+#' @export
 as.neuron.morphml_cell<-function(x, ...) as.neuron(as.data.frame(x, ...))
 
+#' @export
 as.ngraph.morphml_cell<-function(x, ...) {
   as.ngraph(as.data.frame(x), ...)
 }
diff --git a/R/potential_synapses.R b/R/potential_synapses.R
index 7343d256..052b9915 100644
--- a/R/potential_synapses.R
+++ b/R/potential_synapses.R
@@ -94,7 +94,8 @@ potential_synapses.dotprops<-function(a, b, s, sigma=s, seglength=1, bounds=NULL
 
 PotentialSynapses <- function(a, b, s, sigma, ...) UseMethod("PotentialSynapses")
 
-PotentialSynapses.default <- function(a, b, s=2, sigma=2) {
+#' @export
+PotentialSynapses.default <- function(a, b, s=2, sigma=2, ...) {
   #Compare for matrices of input data rather than neurons
   
   # short circuit if there are no points to check in one list or other!
@@ -144,7 +145,8 @@ PotentialSynapses.default <- function(a, b, s=2, sigma=2) {
   return(rval)
 }
 
-PotentialSynapses.dotprops <- function(a, b, s, sigma, seglength) {
+#' @export
+PotentialSynapses.dotprops <- function(a, b, s, sigma, seglength, ...) {
   # short circuit if there are no points to check in one list or other!
   if(nrow(a$points) * nrow(b$points) == 0) return(0)