all: figs manuscript datasets

figs: 
	sudo Rscript plot.r
	pdflatex Fig1.tex
	pdflatex Fig2.tex
	cp FigNeighboursVsOddsRatio.pdf Fig3.pdf
	pdflatex Fig4.tex
	pdflatex Fig5.tex
	pdflatex Fig6.tex
	cp FigComparePredictionWithVerifiedCosine.pdf Fig7.pdf
	cp FigLargestFacetLocation.pdf Fig8.pdf
	cp FigSSE.pdf Fig9.pdf
	cp FigTmPeriphAaComparison.pdf Fig10.pdf
	cp FigCompareOligomerisation.pdf Fig11.pdf

bib:
	pdflatex -interaction batchmode protrusion_ms.tex
	bibtex protrusion_ms
	pdflatex -interaction batchmode protrusion_ms.tex
	
manuscript:
	pdflatex -interaction batchmode protrusion_ms.tex
	pdflatex -interaction batchmode protrusion_ms.tex

	pdflatex -interaction batchmode protrusion_ms_suppmat.tex
	pdflatex -interaction batchmode protrusion_ms_suppmat.tex

datasets:
	cp protrusion_ms_suppmat.pdf S1_Text.pdf
	cp figures/classification_periph.csv S1_Dataset.csv
	cp figures/classification_tm.csv S2_Dataset.csv
	sudo Rscript compile_additional_data_sets.r
	zip S5_Dataset.zip S5_Dataset.csv

changes:
	./make_changes.sh

pack:
	zip protrusions_ms.zip protrusion_ms.pdf manuscript_changes.pdf S1_Text.pdf Fig1.pdf Fig2.pdf Fig3.pdf Fig4.pdf Fig5.pdf Fig6.pdf Fig7.pdf Fig8.pdf Fig9.pdf Fig10.pdf Fig11.pdf S1_Dataset.csv S2_Dataset.csv S3_Dataset.csv S4_Dataset.csv S5_Dataset.zip