Proposal: new menu layout, with examples

[James Bonfield]

Now that several interfaces to EMBOSS are arriving I feel that it is important 
to have a well structured menu system (as indicated in my last email).

I now have a proposed layout, included as an attachment. It may be hard to see 
the problem with the existing setup, so I've produce a tcl/tk to display a
menu tree and created menu specs for how it is now (1.11.0, so nearly now) and 
my new proposed setup. My new layout still has quite a few questionable
choices, and perhaps I could duplicate more often (although personally I
dislike that) and split into more cascading menus. However it's a start[1].

So if you're interested in developing interfaces to EMBOSS, or you are one of
the developers, please download the following:

    ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/private/emboss_dev/em.tar.gz

See the README file for information on how to run the tcl/tk app. It ought to
work OK even on pretty old tcl/tk installations.

James

[1] I should also point out that in "Spin" the menu labels are actually the
program doc lines with the program command name in brackets (eg "Finds DNA
inverted repeats (einverted)"). However I haven't addressed the issue of a
common language style for doc names yet.

-- 
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/
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+Comparison
+	Global alignment
=		stretcher
=		needle
-
+	Local alignment
=		simplesw
=		water
=		matcher
=		supermatcher
=		est2genome
-
+	Multiple alignment
=		cluster
=		emma
-
+	Dot plots
=		dotmatcher
=		dotpath
=		dottup
=		polydot
-
+	Other
=		megamerger
=		merger
=		diffseq
=		plotcon
=		seqmatchall
=		wordmatch
=		prettyplot
-
-
+Translation
=	backtranseq
=	checktrans
=	coderet
=	cusp
=	getorf
=	plotorf
=	prettyseq
=	showorf
=	showseq
=	transeq
-
+Databases
+	Indexing
=		dbiblast
=		dbifasta
=		dbiflat
=		dbigcg
=		showdb
-
+	SCOP
=		nrscope
=		scope
=		stamps
-
-
+Edit
=	cutseq
=	degapseq
=	descseq
=	extractseq
=	maskfeat
=	maskseq
=	msbar
=	newseq
=	noreturn
=	nthseq
=	pasteseq
=	revseq
=	shuffleseq
=	splitter
=	trimseq
=	vectorstrip
-
+Search
+	Motifs/pattern matching
=		dreg
=		fuzznuc
=		fuzzpro
=		fuzztran
=		helixturnhelix
=		patmatdb
=		patmatmotifs
=		preg
=		printsextract
=		prosextract
=		pscan
=		tfscan
-
+	Repeats
=		einverted
=		equicktandem
=		etandem
=		palindrome
-
+	Profiles
=		cons
=		profit
=		prophecy
=		prophet
-
+	Primers
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=		primersearch
=		stssearch
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+	CPG islands
=		cpgplot
=		cpgreport
=		newcpgreport
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-
+	Restriction enzymes
=		recode
=		redata
=		remap
=		restover
=		restrict
=		silent
-
+	Enzymes
=		findkm
-
+	Misc
=		textsearch
-
-
+Composition
+	DNA
=		banana
=		btwisted
=		chaos
=		chips
=		codcmp
=		complex
=		compseq
=		dan
=		freak
=		geecee
=		isochore
=		marscan
=		syco
=		wobble
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+	Protein
=		antigenic
=		charge
=		compseq
=		digest
=		domainer
=		emowse
=		garnier
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=		hmoment
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=		pepcoil
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=		pepnet
=		pepstats
=		pepwheel
=		pepwindow
=		pepwindowall
=		sigcleave
=		tmap
-
-
+Display
=	cirdna
=	entret
=	infoseq
=	lindna
=	notseq
=	prettyplot
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=	seqretallfeat
=	seqretfeat
=	seqretset
=	seqretsplit
=	seqrettype
=	seqtofeat
=	showfeat
=	showseq
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+Utils
=	embossdata
=	entrails
=	rebaseextract
=	seealso
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=	tfm
=	wossname
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+Test
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=	ajtest2
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=	demosequence
=	demostring
=	demotable
=	histogramtest
=	patmattest
=	plplottest
=	proteinmotifsearch
=	testplot
=	treetypedisplay
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