From e9fd51caf9d2f77de3aaf9e43e79d74192886f3e Mon Sep 17 00:00:00 2001
From: monty <velimir.vesselinov@gmail.com>
Date: Wed, 24 Jan 2024 15:52:33 -0700
Subject: [PATCH] work

---
 src/MadsIO.jl   | 32 +++++++++++++++++++++++++++++++-
 src/MadsPlot.jl |  4 ++--
 2 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/src/MadsIO.jl b/src/MadsIO.jl
index 7413a491..be2bc1da 100644
--- a/src/MadsIO.jl
+++ b/src/MadsIO.jl
@@ -1768,8 +1768,38 @@ function testlinks()
 	rm(link)
 end
 
-function jld2append(fname, varname, data)
+function jldappend(fname::AbstractString, varname::AbstractString, data::Any)
+	JLD.jldopen(fname, true, true, true, false, true) do file
+		file[varname] = data
+	end
+end
+
+function jld2append(fname::AbstractString, varname::AbstractString, data::Any)
 	JLD2.jldopen(fname, "a+") do file
 		file[varname] = data
 	end
+end
+
+function jld2haskey(fname::AbstractString, varnames...)
+	flag = true
+	JLD2.jldopen(fname, "r") do file
+		for varname in varnames
+			if !haskey(file, varname)
+				flag = false
+			end
+		end
+	end
+	return flag
+end
+
+function jldhaskey(fname::AbstractString, varnames...)
+	flag = true
+	JLD.jldopen(fname, "r") do file
+		for varname in varnames
+			if !haskey(file, varname)
+				flag = false
+			end
+		end
+	end
+	return flag
 end
\ No newline at end of file
diff --git a/src/MadsPlot.jl b/src/MadsPlot.jl
index 8fb71a7a..68dfa809 100644
--- a/src/MadsPlot.jl
+++ b/src/MadsPlot.jl
@@ -877,7 +877,7 @@ function spaghettiplot(madsdata::AbstractDict, dictarray::AbstractDict; seed::In
 	end
 	spaghettiplot(madsdata::AbstractDict, Y; kw...)
 end
-function spaghettiplot(madsdata::AbstractDict, matrix::AbstractMatrix; plotdata::Bool=true, filename::AbstractString="", keyword::AbstractString="", format::AbstractString="", title::AbstractString="", xtitle::AbstractString="", ytitle::AbstractString="", yfit::Bool=false, obs_plot_dots::Bool=true, linewidth::Measures.AbsoluteLength=2Gadfly.pt, pointsize::Measures.AbsoluteLength=4Gadfly.pt, grayscale::Bool=false, alpha::Number=0.3, xmin::Any=nothing, xmax::Any=nothing, ymin::Any=nothing, ymax::Any=nothing, quiet::Bool=!Mads.graphoutput, colors::AbstractVector=["red", "blue", "green", "cyan", "magenta", "yellow"], plot_nontargets::Bool=false, gm::AbstractVector=[])
+function spaghettiplot(madsdata::AbstractDict, matrix::AbstractMatrix; plotdata::Bool=true, filename::AbstractString="", keyword::AbstractString="", format::AbstractString="", title::AbstractString="", xtitle::AbstractString="", ytitle::AbstractString="", yfit::Bool=false, obs_plot_dots::Bool=true, linewidth::Measures.AbsoluteLength=2Gadfly.pt, pointsize::Measures.AbsoluteLength=4Gadfly.pt, grayscale::Bool=false, alpha::Number=0.2, alphas::AbstractVector=[alpha], xmin::Any=nothing, xmax::Any=nothing, ymin::Any=nothing, ymax::Any=nothing, quiet::Bool=!Mads.graphoutput, colors::AbstractVector=["red", "blue", "green", "cyan", "magenta", "yellow"], plot_nontargets::Bool=false, gm::AbstractVector=[])
 	madsinfo("Spaghetti plots for all the selected model parameter (type != null) ...\n")
 	rootname = getmadsrootname(madsdata)
 	obskeys = Mads.getobskeys(madsdata)
@@ -939,7 +939,7 @@ function spaghettiplot(madsdata::AbstractDict, matrix::AbstractMatrix; plotdata:
 		pl = Gadfly.plot(pa..., Gadfly.layer(Y, x=repeat(t; inner=numberofsamples), y=Gadfly.Col.value(1:numberofsamples...),
 			color=colindex, group=colindex, Gadfly.Geom.line()),
 			Gadfly.Scale.color_discrete(colormap),
-			Gadfly.Theme(key_position=:none, line_width=linewidth, point_size=pointsize, highlight_width=0Gadfly.pt, discrete_highlight_color=c->nothing, alphas=[alpha]),
+			Gadfly.Theme(key_position=:none, line_width=linewidth, point_size=pointsize, highlight_width=0Gadfly.pt, discrete_highlight_color=c->nothing, alphas=alphas),
 			Gadfly.Guide.title(title),
 			Gadfly.Guide.XLabel(xtitle; orientation=:horizontal), Gadfly.Guide.YLabel(ytitle; orientation=:vertical),
 			gm...)