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[Jmol-commits] SF.net SVN: jmol:[12365] trunk
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From: <eg...@us...> - 2010-02-10 15:56:44
|
Revision: 12365
http://jmol.svn.sourceforge.net/jmol/?rev=12365&view=rev
Author: egonw
Date: 2010-02-10 15:56:35 +0000 (Wed, 10 Feb 2010)
Log Message:
-----------
Added BMC LaTeX template for paper
Added Paths:
-----------
trunk/Jmol-paper/
trunk/Jmol-paper/Makefile
trunk/Jmol-paper/bmc_article.bib
trunk/Jmol-paper/bmc_article.bst
trunk/Jmol-paper/bmc_article.cls
trunk/Jmol-paper/bmc_article.tex
Added: trunk/Jmol-paper/Makefile
===================================================================
--- trunk/Jmol-paper/Makefile (rev 0)
+++ trunk/Jmol-paper/Makefile 2010-02-10 15:56:35 UTC (rev 12365)
@@ -0,0 +1,20 @@
+all: bmc_article.pdf
+ @echo "********* Latex Summary *********"
+ @grep -i error bmc_article.log || true
+ @grep -i warning bmc_article.log || true
+
+update: bmc_article.pdf
+
+bmc_article.bbl: bmc_article.bib
+ pdflatex bmc_article || true
+ bibtex bmc_article || true
+
+bmc_article.pdf: bmc_article.tex bmc_article.bbl
+ pdflatex bmc_article.tex
+ pdflatex bmc_article.tex
+ pdflatex bmc_article.tex
+
+distclean: clean
+
+clean:
+ rm -f *.bbl *.aux bmc_article.pdf *.blg *.log *.ps *.fff *.lof *.lot *.ttt *.dvi *~ *.Rout
Added: trunk/Jmol-paper/bmc_article.bib
===================================================================
--- trunk/Jmol-paper/bmc_article.bib (rev 0)
+++ trunk/Jmol-paper/bmc_article.bib 2010-02-10 15:56:35 UTC (rev 12365)
@@ -0,0 +1,180 @@
+% bmc_article.bib
+%
+% An example of bibtex entries.
+% Entries taken from BMC instructions for authors page.
+
+
+@article{blank,
+ author = {},
+ title = {},
+ journal = {},
+ year = {},
+ month = {},
+ volume= {},
+ number= {},
+ pages = {},
+ note = {}
+}
+
+% Article within a journal
+@ARTICLE{koon,
+ author = {Koonin, E V and Altschul, S F and P Bork},
+ title = {BRCA1 protein products: functional motifs},
+ journal = {Nat Genet},
+ year = {1996},
+ volume = {13},
+ pages = {266-267}
+}
+
+% Article within a journal supplement
+@ARTICLE{oreg,
+ author = {Orengo, C A and Bray, J E and Hubbard,
+ T and LoConte, L and Sillitoe, I},
+ title = {Analysis and assessment of ab initio
+ three-dimensional prediction, secondary
+ structure, and contacts prediction},
+ journal = {Proteins},
+ year = {1999},
+ volume = {Suppl 3},
+ pages = {149-170}
+}
+
+% In press article
+@inpress{khar,
+ author = {Kharitonov, S A and Barnes, P J},
+ title = {Clinical aspects of exhaled nitric oxide},
+ journal = {Eur Respir J},
+ note = {in press}
+}
+
+%
+% Published abstract
+%
+@ARTICLE{zvai,
+ author = {Zvaifler, N J and Burger, J A and Marinova-Mutafchieva,
+ L and Taylor, P and Maini, R N},
+ title = {Mesenchymal cells, stromal derived factor-1 and
+ rheumatoid arthritis [abstract]},
+ journal = {Arthritis Rheum},
+ year = {1999},
+ volume = {42},
+ pages = {s250},
+}
+
+
+%
+% Article within conference proceedings
+%
+@Inproceedings{xjon,
+ author = {X Jones},
+ title = {Zeolites and synthetic mechanisms},
+ booktitle = {Proceedings of the First National Conference on
+ Porous Sieves: 27-30 June 1996; Baltimore},
+ year = {1996},
+ editor = {Y Smith},
+ pages = {16-27},
+ organization = {Stoneham: Butterworth-Heinemann}
+}
+
+%%%%%%%%
+% Book chapter, or article within a book
+%
+@incollection{schn,
+ author = {E Schnepf},
+ title = {From prey via endosymbiont to plastids:
+ comparative studies in dinoflagellates},
+ booktitle = {Origins of Plastids},
+ editor = {R A Lewin},
+ publisher = {Chapman and Hall},
+ pages = {53-76},
+ year = {1993},
+ address = {New York},
+ volume = {2},
+ edition = {2nd}
+}
+
+%%%%%%%%
+% Whole issue of journal
+%
+@wholejournal{pond,
+ editor = {B Ponder and S Johnston and L Chodosh},
+ title = {Innovative oncology},
+ journal = {Breast Cancer Res},
+ year = {1998},
+ volume= {10},
+ pages = {1-72}
+}
+
+
+%%%%%%%%
+% Whole conference proceedings
+%
+@proceedings{smith,
+ editor = {Y Smith},
+ title = {Proceedings of the First National Conference
+ on Porous Sieves: 27-30 June 1996; Baltimore},
+ year = 1996,
+ address= {Stoneham},
+ publisher = {Butterworth-Heinemann},
+}
+
+
+%%%%%%%%
+% Complete book
+%
+@book{marg,
+ author = {L Margulis},
+ title = {Origin of Eukaryotic Cells},
+ publisher = {Yale University Press},
+ year = {1970},
+ address = {New Haven}
+}
+
+
+
+%%%%%%%%
+% Monograph or book in series
+%
+@incollection{hunn,
+ author = {G W Hunninghake and J E Gadek},
+ title = {The alveloar macrophage},
+ booktitle = {Cultured Human Cells and Tissues},
+ publisher = {Academic Press},
+ year = {1995},
+ pages = {54-56},
+ editor = {T J R Harris},
+ address = {New York},
+ note = {Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1}
+}
+
+
+%%%%%%%%
+% Book with institutional author
+@manual{advi,
+ title = {Annual Report},
+ organization = {Advisory Committee on Genetic Modification},
+ address = {London},
+ year = {1999}
+}
+
+
+%%%%%%%%
+% PHD Thesis
+%
+@phdthesis{koha,
+ author = {R Kohavi},
+ title = {Wrappers for performance enhancement and
+ obvious decision graphs},
+ school = {Stanford University, Computer Science Department},
+ year = {1995}
+}
+
+%%%%%%%%
+% Webpage Link / URL
+%
+@webpage{mouse,
+ title = {The Mouse Tumor Biology Database},
+ url = {http://tumor.informatics.jax.org/cancer_links.html}
+}
+
+
Property changes on: trunk/Jmol-paper/bmc_article.bib
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/Jmol-paper/bmc_article.bst
===================================================================
--- trunk/Jmol-paper/bmc_article.bst (rev 0)
+++ trunk/Jmol-paper/bmc_article.bst 2010-02-10 15:56:35 UTC (rev 12365)
@@ -0,0 +1,1880 @@
+%% %
+ % bmc_article.bst ver: 1.01 %
+ % %
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %% %%
+ %% BibTeX BST file for BioMed Central %%
+ %% a style syntax for latex .bib %%
+ %% bibliographies %%
+ %% %%
+ %% <1 September 2003> %%
+ %% %%
+ %% %%
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %
+ %
+ % The order in the reference list is that by which the
+ % works were originally cited in the text, or that in
+ % the database.
+ %
+ %
+ % This file is based on the style 'unsrt.bst'
+ % ------------------------------------------
+ % BibTeX standard bibliography style `unsrt'
+ % version 0.99a for BibTeX versions 0.99a
+ % or later, LaTeX version 2.09.
+ % Copyright (C) 1985, all rights reserved.
+ % Copying of this file is authorized only if either
+ % (1) you make absolutely no changes to your copy, including name, or
+ % (2) if you do make changes, you name it something other than
+ % btxbst.doc, plain.bst, unsrt.bst, alpha.bst, and abbrv.bst.
+ % This restriction helps ensure that all standard styles are identical.
+ % The file btxbst.doc has the documentation for this style.
+ % ---------------------------------------------------------
+%%
+
+
+
+
+ENTRY
+ { address
+ archive
+ author
+ booktitle
+ chapter
+ edition
+ editor
+ eid
+ howpublished
+ institution
+ journal
+ key
+ month
+ note
+ number
+ organization
+ pages
+ publisher
+ school
+ series
+ title
+ type
+ url
+ volume
+ year
+ }
+ {}
+ { label }
+
+
+% Global variables - most initialised and used locally.
+STRINGS { longest.label }
+STRINGS { cur tag source bibinfo}
+STRINGS { p q r s t z name names }
+STRINGS { lr lp lt ls} % local copys fxns with these call no other fxns.
+INTEGERS { number.label longest.label.width }
+INTEGERS { multiresult nameptr namesleft numnames global.counter}
+INTEGERS { i j k l ll li}
+INTEGERS { output.state before.all mid.sentence after.sentence after.block }
+
+FUNCTION {init.state.consts}
+{ #0 'before.all :=
+ #1 'mid.sentence :=
+ #2 'after.sentence :=
+ #3 'after.block :=
+ #0 'global.counter :=
+}
+
+
+% Logical operators on integers
+FUNCTION {not}
+{ { #0 } { #1 } if$
+}
+FUNCTION {and}
+{ 'skip$ { pop$ #0 } if$
+}
+FUNCTION {or}
+{ { pop$ #1 } 'skip$ if$
+}
+FUNCTION {field.or.null}
+{ duplicate$ empty$ { pop$ "" } 'skip$ if$
+}
+
+FUNCTION {remove.dots}
+{ 'z :=
+ ""
+ { z empty$ not }
+ { z #1 #1 substring$
+ z #2 global.max$ substring$ 'z :=
+ duplicate$ "." = 'pop$
+ { * }
+ if$
+ }
+ while$
+}
+
+%%
+ % myreverse
+ %
+ % Takes 1 string
+ % Returns the myreverse string
+ %
+ % not to be confused with REVERSE (opposite of ITERATE)
+%%
+FUNCTION {myreverse}
+{
+ 'lt :=
+ "" 'ls :=
+ { lt empty$ not }
+ {
+ lt #1 #1 substring$ ls * 'ls :=
+ lt #2 global.max$ substring$ 'lt :=
+ }
+ while$
+ ls
+}
+
+%%
+ % search
+ %
+ % Takes 2 strings (txt, pattern)
+ % Retruns 1 if found 0 if not
+%%
+FUNCTION {search}
+{
+ 'lp := % pattern
+ 'lt := % text to search
+ #0 'i := % result
+ lp text.length$ 'll := % length of the search pattern
+ { lt empty$ not }
+ { lt #1 ll substring$ lp =
+ { #1 'li :=
+ "" 'lt := } % force exit
+ { lt #2 global.max$ substring$ 'lt := } % pop 1 char
+ if$
+ }
+ while$
+ li
+}
+
+
+%%
+ % general replace
+ %
+ % Takes 3 strings (txt, pattern, replace-str)
+ % replaces all instances of pattern
+ % Retruns a new string
+%%
+FUNCTION {replace}
+{
+ 'lr := % replace string
+ 'lp := % pattern
+ 'lt := % text to search
+ "" 'ls := % result string
+ lp text.length$ 'll := % length of the search pattern
+ { lt empty$ not }
+ { lt #1 ll substring$ lp =
+ { ls lr * 'ls :=
+ lt ll #1 + global.max$ substring$ 'lt := }
+ { ls lt #1 #1 substring$ * 'ls :=
+ lt #2 global.max$ substring$ 'lt := }
+ if$
+ }
+ while$
+ ls
+}
+
+
+%%
+ % strip.letters
+ %
+ % Takes 1 arg (string)
+ % if string has letters get rid of them
+ % - useful for 2nd -> 2
+ % Returns string
+%%
+FUNCTION {strip.letters}
+{
+ "" 's :=
+ duplicate$ missing$
+ 'pop$
+ {
+ 't :=
+ { t "" = not }
+ { % ascii '0' = 48, '9' = 57
+ t #1 #1 substring$ chr.to.int$ 'i :=
+ i #47 > i #58 < and
+ { s t #1 #1 substring$ * 's := }
+ 'skip$
+ if$
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ s
+}
+
+FUNCTION {output.nonnull}
+{ 's :=
+ output.state mid.sentence =
+ { ", " * write$ }
+ { output.state after.block =
+ { add.period$ write$
+ newline$
+ "\newblock " write$
+ }
+ { output.state before.all =
+ %{ "OS=(" * output.state int.to.str$ * ") " * write$ }
+ 'write$
+ { add.period$ " " * write$ } % after.sentence
+ if$
+ }
+ if$
+ mid.sentence 'output.state :=
+ }
+ if$
+ s
+}
+
+FUNCTION {output}
+{ duplicate$ empty$
+ 'pop$
+ 'output.nonnull
+ if$
+}
+
+% raises an error (warning message) if type not present.
+FUNCTION {output.check}
+{ 't :=
+ duplicate$ empty$
+ { pop$ "empty " t * " in " * cite$ * warning$ }
+ 'output.nonnull
+ if$
+}
+
+FUNCTION {fin.entry}
+{ add.period$
+ write$
+ newline$
+}
+
+FUNCTION {new.block}
+{ output.state before.all =
+ 'skip$
+ { after.block 'output.state := }
+ if$
+}
+FUNCTION {new.sentence}
+{ output.state after.block =
+ 'skip$
+ { output.state before.all =
+ 'skip$
+ { after.sentence 'output.state := }
+ if$
+ }
+ if$
+}
+FUNCTION {add.blank}
+{ " " * before.all 'output.state :=
+}
+
+FUNCTION {add.bold.colon}
+{ duplicate$ empty$
+ 'skip$
+ { "\textbf{:}" * add.blank }
+ if$
+}
+
+FUNCTION {add.colon}
+{ duplicate$ empty$
+ 'skip$
+ { ":" * add.blank }
+ if$
+}
+FUNCTION {bold}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\textbf{" swap$ * "}" * }
+ if$
+}
+FUNCTION {emphasize}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\emph{" swap$ * "}" * }
+ if$
+}
+FUNCTION {tie.or.space.prefix}
+{ duplicate$ text.length$ #3 <
+ { "~" }
+ { " " }
+ if$
+ swap$
+}
+
+FUNCTION {capitalize}
+{ "u" change.case$ "t" change.case$ }
+
+FUNCTION {space.word}
+{ " " swap$ * " " * }
+
+% if field not entered - push empty string ""
+FUNCTION {bibinfo.check}
+{ swap$
+ duplicate$ missing$
+ { pop$ pop$
+ "" }
+ { duplicate$ empty$
+ { swap$ pop$ }
+ { swap$ pop$ }
+ if$
+ }
+ if$
+}
+FUNCTION {bibinfo.warn}
+{ swap$
+ duplicate$ missing$
+ {
+ swap$ "missing " swap$ * " in " * cite$ * warning$ pop$
+ ""
+ }
+ { duplicate$ empty$
+ {
+ swap$ "empty " swap$ * " in " * cite$ * warning$
+ }
+ { swap$
+ pop$
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.thesis.type}
+{ type duplicate$ empty$
+ 'pop$
+ { swap$ pop$
+ "t" change.case$ "type" bibinfo.check
+ }
+ if$
+}
+
+
+ % Here are the language-specific definitions for explicit words.
+ % Each function has a name bbl.xxx where xxx is the English word.
+ % The language selected here is ENGLISH
+FUNCTION {bbl.and}
+{ "and"}
+
+FUNCTION {bbl.etal}
+{ "et~al." }
+
+FUNCTION {bbl.editors}
+{ "(Eds)" }
+%{ "editors" }
+
+FUNCTION {bbl.editor}
+{ "(Ed)" }
+%{ "editor" }
+
+FUNCTION {bbl.edby}
+{ "Edited by" }
+
+FUNCTION {bbl.edition}
+{ "edition" }
+%{ "edn." }
+
+FUNCTION {bbl.volume}
+{ "Volume" }
+%{ "vol." }
+
+FUNCTION {bbl.of}
+{ "of" }
+
+FUNCTION {bbl.number}
+{ "no." }
+
+FUNCTION {bbl.nr}
+{ "no." }
+
+FUNCTION {bbl.in}
+{ "in" }
+
+FUNCTION {bbl.pages}
+{ "" }
+
+FUNCTION {bbl.page}
+{ "" }
+
+FUNCTION {bbl.chapter}
+{ "chap." }
+
+FUNCTION {bbl.techrep}
+{ "Tech. Rep." }
+
+FUNCTION {bbl.mthesis}
+{ "Master's thesis" }
+
+FUNCTION {bbl.phdthesis}
+{ "PhD thesis" }
+
+MACRO {jan} {"Jan."}
+
+MACRO {feb} {"Feb."}
+
+MACRO {mar} {"Mar."}
+
+MACRO {apr} {"Apr."}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"Jun."}
+
+MACRO {jul} {"Jul."}
+
+MACRO {aug} {"Aug."}
+
+MACRO {sep} {"Sep."}
+
+MACRO {oct} {"Oct."}
+
+MACRO {nov} {"Nov."}
+
+MACRO {dec} {"Dec."}
+
+MACRO {acmcs} {"ACM Computing Surveys"}
+
+MACRO {acta} {"Acta Informatica"}
+
+MACRO {cacm} {"Communications of the ACM"}
+
+MACRO {ibmjrd} {"IBM Journal of Research and Development"}
+
+MACRO {ibmsj} {"IBM Systems Journal"}
+
+MACRO {ieeese} {"IEEE Transactions on Software Engineering"}
+
+MACRO {ieeetc} {"IEEE Transactions on Computers"}
+
+MACRO {ieeetcad}
+ {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}
+
+MACRO {ipl} {"Information Processing Letters"}
+
+MACRO {jacm} {"Journal of the ACM"}
+
+MACRO {jcss} {"Journal of Computer and System Sciences"}
+
+MACRO {scp} {"Science of Computer Programming"}
+
+MACRO {sicomp} {"SIAM Journal on Computing"}
+
+MACRO {tocs} {"ACM Transactions on Computer Systems"}
+
+MACRO {tods} {"ACM Transactions on Database Systems"}
+
+MACRO {tog} {"ACM Transactions on Graphics"}
+
+MACRO {toms} {"ACM Transactions on Mathematical Software"}
+
+MACRO {toois} {"ACM Transactions on Office Information Systems"}
+
+MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}
+
+MACRO {tcs} {"Theoretical Computer Science"}
+
+
+% Takes 2 args (author field) and string "author"
+FUNCTION {format.names}
+{ 'bibinfo :=
+ duplicate$ empty$ 'skip$ {
+ 's :=
+ "" 't :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{vv~}{ll}{ f{}}{ jj}"
+ format.name$
+ remove.dots
+ bibinfo bibinfo.check
+ 't :=
+ nameptr #1 >
+ {
+ namesleft #1 >
+ { ", " * t * }
+ {
+ "," *
+ s nameptr "{ll}" format.name$ duplicate$ "others" =
+ { 't := }
+ { pop$ }
+ if$
+ t "others" =
+ {
+ " " * bbl.etal *
+ }
+ { " " * t * }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+ } if$
+}
+
+
+%"{f{~}~}{vv~}{ll}{ jj}"
+FUNCTION {format.names.ed}
+{
+ 'bibinfo :=
+ duplicate$ empty$ 'skip$ {
+ 's :=
+ "" 't :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr
+ "{vv~}{ll}{ f{}}{ jj}"
+ format.name$
+ remove.dots
+ bibinfo bibinfo.check
+ 't :=
+ nameptr #1 >
+ {
+ namesleft #1 >
+ { ", " * t * }
+ {
+ "," *
+ s nameptr "{ll}" format.name$ duplicate$ "others" =
+ { 't := }
+ { pop$ }
+ if$
+ t "others" =
+ {
+
+ " " * bbl.etal *
+ }
+ { " " * t * }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+ } if$
+}
+FUNCTION {format.authors}
+{ author "author" format.names
+}
+FUNCTION {get.bbl.editor}
+{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }
+
+FUNCTION {format.editors}
+{ editor "editor" format.names duplicate$ empty$ 'skip$
+ {
+ " " * get.bbl.editor *
+%% "," * " " * get.bbl.editor *
+ }
+ if$
+}
+FUNCTION {format.note}
+{
+ url empty$
+ 'skip$
+ {
+ "\urlprefix\url{[" url * "]}" * output }
+ if$
+ note empty$
+ { "" }
+ {
+ note "l" change.case$ "in press" =
+ { after.sentence 'output.state :=
+ " in press" }
+ {
+ after.sentence 'output.state :=
+ note #1 #1 substring$
+ duplicate$ "{" =
+ 'skip$
+ { output.state mid.sentence =
+ { "l" }
+ { "u" }
+ if$
+ change.case$ % leave note * As Is *
+ }
+ if$
+ note #2 global.max$ substring$ * "note" bibinfo.check
+ "[" swap$ * "]" *
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {bold.format.title}
+{ title
+ "title" bibinfo.check
+ duplicate$ empty$ 'skip$
+ {
+ bold
+ }
+ if$
+}
+
+FUNCTION {emph.format.title}
+{ title
+ "title" bibinfo.check
+ duplicate$ empty$ 'skip$
+ {
+ emphasize
+ }
+ if$
+}
+
+% Returns ""
+FUNCTION {output.bibitem}
+{ newline$
+ "\bibitem{" write$
+ cite$ write$
+ "}" write$
+ newline$
+ ""
+ before.all 'output.state :=
+}
+
+FUNCTION {output.allinfo.comment}
+{ }
+
+FUNCTION {n.dashify}
+{
+ 't :=
+ ""
+ { t empty$ not }
+ { t #1 #1 substring$ "-" =
+ { t #1 #2 substring$ "--" = not
+ { "--" *
+ t #2 global.max$ substring$ 't :=
+ }
+ { { t #1 #1 substring$ "-" = }
+ { "-" *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+}
+
+FUNCTION {word.in}
+{ bbl.in capitalize
+ " " * }
+
+FUNCTION {format.date}
+{
+ before.all 'output.state :=
+ ""
+ duplicate$ empty$
+ year "year" bibinfo.check duplicate$ empty$
+ { swap$ 'skip$
+ { "there's a month but no year in " cite$ * warning$ }
+ if$
+ *
+ }
+ { swap$ 'skip$
+ {
+ swap$
+ " " * swap$
+ }
+ if$
+ *
+ remove.dots
+ }
+ if$
+
+ duplicate$ "" =
+ 'skip$
+ { " " swap$ * }
+ if$
+}
+
+% Source = book, conference, journal, manual
+% have the source avaliable on the stack
+FUNCTION {format.source}
+{ 'source :=
+ source "source" bibinfo.check
+ duplicate$ empty$ 'skip$
+ {
+ emphasize
+ }
+ if$
+}
+
+FUNCTION {format.title}
+{ title "title" bibinfo.check
+ duplicate$ empty$ 'skip$
+ {
+ bold
+ }
+ if$
+}
+
+
+
+FUNCTION {either.or.check}
+{ empty$
+ 'pop$
+ { "can't use both " swap$ * " fields in " * cite$ * warning$ }
+ if$
+}
+FUNCTION {format.bvolume}
+{ volume empty$
+ { "" }
+ { bbl.volume volume tie.or.space.prefix
+ "volume" bibinfo.check * *
+ series "series" bibinfo.check
+ duplicate$ empty$ 'pop$
+ { swap$ bbl.of space.word * swap$
+ emphasize * }
+ if$
+ emphasize
+ "volume and number" number either.or.check
+ }
+ if$
+}
+FUNCTION {format.number.series}
+{ volume empty$
+ { number empty$
+ { series field.or.null }
+ { series empty$
+ { number "number" bibinfo.check }
+ { output.state mid.sentence =
+ { bbl.number }
+ { bbl.number capitalize }
+ if$
+ number tie.or.space.prefix "number" bibinfo.check * *
+ bbl.in space.word *
+ series "series" bibinfo.check *
+ }
+ if$
+ }
+ if$
+ }
+ { "" }
+ if$
+}
+
+FUNCTION {format.edition}
+{ edition duplicate$ empty$ 'skip$
+ {
+ output.state mid.sentence =
+ { "l" }
+ { "t" }
+ if$ change.case$
+ "edition" bibinfo.check
+ " " * bbl.edition *
+ }
+ if$
+}
+FUNCTION {multi.page.check}
+{ 't :=
+ #0 'multiresult :=
+ { multiresult not
+ t empty$ not
+ and
+ }
+ { t #1 #1 substring$
+ duplicate$ "-" =
+ swap$ duplicate$ "," =
+ swap$ "+" =
+ or or
+ { #1 'multiresult := }
+ { t #2 global.max$ substring$ 't := }
+ if$
+ }
+ while$
+ multiresult
+}
+
+FUNCTION {format.pages}
+{ pages duplicate$ empty$ 'skip$
+ { duplicate$ multi.page.check
+ {
+ n.dashify
+ }
+ {
+ }
+ if$
+ "pages" bibinfo.check
+ ":" swap$ *
+ }
+ if$
+}
+
+FUNCTION {format.journal.pages}
+{ pages duplicate$ empty$ 'pop$
+ { swap$ duplicate$ empty$
+ { pop$ pop$ format.pages }
+ {
+ ":" *
+ swap$
+ n.dashify
+ "pages" bibinfo.check
+ *
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {format.journal.eid}
+{ eid "eid" bibinfo.check
+ duplicate$ empty$ 'pop$
+ { swap$ duplicate$ empty$ 'skip$
+ {
+ ":" *
+ }
+ if$
+ swap$ *
+ }
+ if$
+}
+
+% ignore issue (num) if == 1
+FUNCTION {format.vol.num.pages}
+{ volume field.or.null
+ duplicate$ empty$ 'skip$
+ {
+ "volume" bibinfo.check bold
+ }
+ if$
+ number "number" bibinfo.check duplicate$ empty$ 'skip$
+ {
+ duplicate$ "1" =
+ {pop$ ""}
+ { swap$ duplicate$ empty$
+ { "there's a number but no volume in " cite$ * warning$ }
+ 'skip$
+ if$
+ swap$
+ "(" swap$ * ")" *
+ }
+ if$
+ }
+ if$ *
+ eid empty$
+ { format.journal.pages }
+ { format.journal.eid }
+ if$
+}
+
+FUNCTION {format.chapter.pages}
+{ chapter empty$
+ 'format.pages
+ { type empty$
+ { bbl.chapter }
+ { type "l" change.case$
+ "type" bibinfo.check
+ }
+ if$
+ chapter tie.or.space.prefix
+ "chapter" bibinfo.check
+ * *
+ pages empty$
+ 'skip$
+ { ", " * format.pages * }
+ if$
+ }
+ if$
+}
+
+
+
+%% FUNCTION {format.in.ed.booktitle}
+%% { booktitle format.source duplicate$ empty$ 'skip$
+%% {
+%% editor "editor" format.names.ed duplicate$ empty$ 'pop$
+%% {
+%% bbl.edby
+%% " " * swap$ *
+%% swap$
+%% "," *
+%% " " * swap$
+%% * }
+%% if$
+%% word.in swap$ *
+%% }
+%% if$
+%% }
+
+FUNCTION{format.edited.by}
+{ editor "editor" format.names.ed duplicate$ empty$
+ 'pop$
+ { bbl.edby
+ " " * swap$ *
+ swap$
+ ". " *
+ swap$
+ * }
+ if$
+}
+
+FUNCTION {format.in.booktitle}
+{ booktitle format.source duplicate$ empty$
+ 'skip$
+ { word.in swap$ * }
+ if$
+}
+FUNCTION {format.in.journal}
+{ journal format.source duplicate$ empty$
+ 'skip$
+ { word.in swap$ * }
+ if$
+}
+FUNCTION {empty.misc.check}
+{ author empty$ title empty$ howpublished empty$
+ month empty$ year empty$ note empty$
+ and and and and and
+ { "all relevant fields are empty in " cite$ * warning$ }
+ 'skip$
+ if$
+}
+FUNCTION {format.tr.number}
+{ number "number" bibinfo.check
+ type duplicate$ empty$
+ { pop$ bbl.techrep }
+ 'skip$
+ if$
+ "type" bibinfo.check
+ swap$ duplicate$ empty$
+ { pop$ "t" change.case$ }
+ { tie.or.space.prefix * * }
+ if$
+}
+FUNCTION {format.article.crossref}
+{
+ key duplicate$ empty$
+ { pop$
+ journal duplicate$ empty$
+ { "need key or journal for " cite$ * " to crossref " * crossref * warning$ }
+ { "journal" bibinfo.check emphasize word.in swap$ * }
+ if$
+ }
+ { word.in swap$ * " " *}
+ if$
+ " \cite{" * crossref * "}" *
+}
+FUNCTION {format.crossref.editor}
+{ editor #1 "{vv~}{ll}" format.name$
+ "editor" bibinfo.check
+ editor num.names$ duplicate$
+ #2 >
+ { pop$
+ "editor" bibinfo.check
+ " " * bbl.etal
+ *
+ }
+ { #2 <
+ 'skip$
+ { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ {
+ "editor" bibinfo.check
+ " " * bbl.etal
+ *
+ }
+ {
+ bbl.and space.word
+ * editor #2 "{vv~}{ll}" format.name$
+ "editor" bibinfo.check
+ *
+ }
+ if$
+ }
+ if$
+ }
+ if$
+}
+FUNCTION {format.book.crossref}
+{ volume duplicate$ empty$
+ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+ pop$ word.in
+ }
+ { bbl.volume
+ capitalize
+ swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
+ }
+ if$
+ editor empty$
+ editor field.or.null author field.or.null =
+ or
+ { key empty$
+ { series empty$
+ { "need editor, key, or series for " cite$ * " to crossref " *
+ crossref * warning$
+ "" *
+ }
+ { series emphasize * }
+ if$
+ }
+ { key * }
+ if$
+ }
+ { format.crossref.editor * }
+ if$
+ " \cite{" * crossref * "}" *
+}
+FUNCTION {format.incoll.inproc.crossref}
+{
+ editor empty$
+ editor field.or.null author field.or.null =
+ or
+ { key empty$
+ { booktitle format.source duplicate$ empty$
+ { "need editor, key, or booktitle for " cite$ * " to crossref " *
+ crossref * warning$
+ }
+ { word.in swap$ * }
+ if$
+ }
+ { word.in key * " " *}
+ if$
+ }
+ { word.in format.crossref.editor * " " *}
+ if$
+ " \cite{" * crossref * "}" *
+}
+
+% Takes 1 arg (publisher or organisation}
+% if present appends address to the front. ie New York: Sachai Ltd
+% returns the formatted string.
+FUNCTION {format.org.or.pub}
+{ 't :=
+ t empty$
+ { address empty$
+ 'skip$
+ { address "address" bibinfo.check 't := }
+ if$ }
+ { address empty$
+ 'skip$
+ { address "address" bibinfo.check ": " * t * 't :=}
+ if$
+ }
+ if$
+ t
+}
+
+FUNCTION {format.publisher.address}
+{ publisher "publisher" bibinfo.warn format.org.or.pub
+}
+
+FUNCTION {format.organization.address}
+{ organization "organization" bibinfo.check format.org.or.pub
+}
+
+FUNCTION {article}
+{ output.bibitem
+ author empty$
+ { format.editors "author or editor" output.check
+ add.colon
+ }
+ { format.authors output.nonnull
+ add.colon
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ bold.format.title "title" output.check
+ new.sentence
+ crossref missing$
+ {
+ journal "journal" bibinfo.check
+ format.source "journal" output.check
+ format.date "year" output.check
+ format.vol.num.pages output
+ }
+ { format.article.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+FUNCTION {wholejournal}
+{ output.bibitem
+ author empty$
+ { format.editors "author or editor" output.check
+ add.colon
+ }
+ { format.authors output.nonnull
+ add.colon
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ bold.format.title "title" output.check
+ new.sentence
+ crossref missing$
+ {
+ journal emphasize word.in swap$ * "journal" output.check
+ format.date "year" output.check
+ format.vol.num.pages output
+ }
+ { format.article.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ format.note output
+ fin.entry
+}
+FUNCTION {book}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ add.colon
+ }
+ { format.authors output.nonnull
+ add.colon
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ title format.source "source" output.check
+ crossref missing$
+ { format.bvolume output
+ new.sentence
+ format.number.series output
+ format.publisher.address output
+ }
+ {
+ new.sentence
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.edition output
+ format.date "year" output.check
+ format.note output
+ fin.entry
+}
+
+FUNCTION {inbook}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check
+ add.colon
+ }
+ { format.authors output.nonnull
+ add.colon
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ title format.source "title" output.check
+ crossref missing$
+ {
+ format.publisher.address output
+ format.bvolume output
+ new.sentence
+ format.number.series output
+ }
+ {
+ new.sentence
+ format.book.crossref output.nonnull
+ }
+ if$
+ format.edition output
+ format.date "year" output.check
+ add.blank
+ format.chapter.pages "chapter and/or pages" output.check
+ format.note output
+ fin.entry
+}
+
+% In <source> . Volume X. y edition. Edited by <ed>.
+% Add: Pub; date:pages.
+FUNCTION {incollection}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title "title" output.check
+ new.sentence
+ crossref missing$
+ { format.in.booktitle "booktitle" output.check
+ %format.in.ed.booktitle "booktitle" output.check
+ format.bvolume output
+ format.number.series output
+ format.edition output
+ booktitle empty$
+ 'skip$
+ {format.edited.by}
+ if$
+ format.publisher.address output
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ }
+ if$
+ format.date "year" output.check
+ before.all 'output.state := %no space,comma,etc.. -> 1991:23
+ format.pages output
+ format.note output
+ fin.entry
+}
+
+
+FUNCTION {inproceedings}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title "title" output.check
+ new.sentence
+ crossref missing$
+ % In <source> . Volume X. x nd edition. Edited by <ed>.
+ { format.in.booktitle "booktitle" output.check
+ format.bvolume output
+ format.edition output
+ format.number.series output
+ booktitle missing$
+ 'skip$
+ { booktitle missing$
+ 'skip$
+ {format.edited.by}
+ if$
+ }
+ if$
+ publisher missing$
+ { format.organization.address output }
+ { organization "organization" bibinfo.check output
+ format.publisher.address output
+ }
+ if$
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ }
+ if$
+ format.date "year" output.check
+ before.all 'output.state := %no space,comma,etc..
+ format.pages output
+ format.note output
+ fin.entry
+}
+
+FUNCTION {conference} {inproceedings}
+
+
+FUNCTION {mastersthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title
+ "title" output.check
+ new.sentence
+ bbl.mthesis format.thesis.type format.source output.nonnull
+ school "school" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ format.note output
+ fin.entry
+}
+
+% old manual style syntax
+% all optional: (author, title, howpublished, month, year, note)
+% maybe missing: (organization, address, edition)
+FUNCTION {misc}
+{ output.bibitem
+ author empty$
+ { organization missing$ 'skip$
+ { organization output }
+ if$
+ }
+ { format.authors output }
+ if$
+ add.colon
+ bold.format.title output
+ new.sentence
+ howpublished "howpublished" bibinfo.check format.source output
+ new.sentence
+ edition missing$ 'skip$
+ {edition output}
+ if$
+ author empty$
+ 'skip$
+ { organization missing$
+ 'skip$
+ {organization output}
+ if$
+ }
+ if$
+ address missing$ 'skip$
+ {address output}
+ if$
+ format.date output
+ format.note output
+ fin.entry
+ empty.misc.check
+}
+
+FUNCTION {webpage}
+{ output.bibitem
+ author empty$
+ { organization missing$ 'skip$
+ { organization output }
+ if$
+ }
+ { format.authors output }
+ if$
+ add.colon
+ bold.format.title " " * output
+ new.sentence
+ howpublished "howpublished" bibinfo.check format.source output
+ new.sentence
+ edition missing$ 'skip$
+ {edition output}
+ if$
+ author empty$
+ 'skip$
+ { organization missing$
+ 'skip$
+ {organization output}
+ if$
+ }
+ if$
+ address missing$ 'skip$
+ {address output}
+ if$
+ format.date output
+ format.note output
+ fin.entry
+ empty.misc.check
+}
+
+
+FUNCTION {inpress}
+{ output.bibitem
+ author empty$
+ { organization missing$ 'skip$
+ { organization output }
+ if$
+ }
+ { format.authors output }
+ if$
+ add.colon
+ bold.format.title output
+ new.sentence
+ journal emphasize output
+ "in press" output
+ fin.entry
+ empty.misc.check
+}
+
+
+
+FUNCTION {manual}
+{ output.bibitem
+ author empty$
+ { organization missing$ 'skip$
+ { organization output }
+ if$
+ }
+ { format.authors output }
+ if$
+ add.colon
+ title output
+ emphasize
+ new.sentence
+ howpublished "howpublished" bibinfo.check format.source output
+ new.sentence
+ edition missing$ 'skip$
+ {edition output}
+ if$
+ author empty$
+ 'skip$
+ { organization missing$
+ 'skip$
+ {organization output}
+ if$
+ }
+ if$
+ address missing$ 'skip$
+ {address output}
+ if$
+ format.date output
+ format.note output
+ fin.entry
+ empty.misc.check
+}
+
+FUNCTION {booklet}{misc}
+
+
+FUNCTION {phdthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title
+ "title" output.check
+ new.sentence
+ bbl.phdthesis format.thesis.type format.source output.nonnull
+ school "school" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ format.note output
+ fin.entry
+}
+
+FUNCTION {proceedings}
+{ output.bibitem
+ editor empty$
+ { organization "organization" bibinfo.check output
+ }
+ { format.editors output.nonnull }
+ if$
+ add.colon
+ title format.source "source" output.check
+ format.bvolume output
+ format.number.series output
+ editor empty$
+ { publisher empty$
+ 'skip$
+ {
+ format.publisher.address output
+ }
+ if$
+ }
+ { publisher empty$
+ {
+ format.organization.address output }
+ {
+ organization "organization" bibinfo.check output
+ format.publisher.address output
+ }
+ if$
+ }
+ if$
+ format.date "year" output.check
+ format.note output
+ fin.entry
+}
+
+FUNCTION {techreport}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title
+ "title" output.check
+ new.sentence
+ format.tr.number output.nonnull
+ institution "institution" bibinfo.warn output
+ address "address" bibinfo.check output
+ format.date "year" output.check
+ format.note output
+ fin.entry
+}
+
+FUNCTION {unpublished}
+{ output.bibitem
+ format.authors "author" output.check
+ add.colon
+ bold.format.title "title" output.check
+ format.date output
+ format.note "note" output.check
+ fin.entry
+}
+
+FUNCTION {default.type} { misc }
+
+
+
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %% %%%% %%% %%%%%%% %% %%%%%%%%%
+%% %%%% %% %%%% % %%%%% % %% %%%%%%%%%
+%% %%%%% %%%%% %% %%% %% %% %%%%%%%%%
+%% %%%%%% %%%%%% %%% % %%% %% %%%%%%%%%
+%% %%%%% %%%%% %%%% %%%% %% %%%%%%%%%
+%% %%%% %% %%%% %%%%%%%%%%% %% %%%%%%%%%
+%% %% %%%% %%% %%%%%%%%%%% %% %%
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %
+ % Function for printing out all data in xml format.
+ % { address archive author booktitle chapter edition editor
+ % howpublished institution journal key month note number
+ % organization pages publisher school series title
+ % type url volume year
+ % }
+ %
+%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+%%
+ % output.xml
+ %
+%%
+FUNCTION {output.xml}
+{ duplicate$ "" =
+ 'pop$
+ { " " swap$ * write$ newline$ }
+ if$
+}
+
+%%
+ % markup.xml
+ %
+ % Takes 2 args text & tag {"the text " "tag"}
+ % Returns 1 string {"<tag>the text <\tag>"}
+%%
+FUNCTION {markup.xml}
+{
+ "" 'r := % result
+ 't := % tag
+ duplicate$ missing$
+ 'pop$
+ { 'r := }
+ if$
+ r "" =
+ 'skip$
+ { "<" t * ">" * r * "</" * t * ">" * 'r := }
+ if$
+ r
+}
+
+%% Takes 2 args - tag, string
+FUNCTION{markup.xml.title}
+{ pop$ % tag
+ duplicate$ missing$
+ 'pop$
+ {
+ 's := % string
+ s "\&" "&" replace 's :=
+ s "p" markup.xml 's :=
+ s "title" markup.xml output.xml
+ }
+ if$
+}
+
+
+%%
+ % markup.xml.pages
+ %
+ % Takes 1 arg (pages string)
+ % seperates into <fpage> and <lpage> if
+ % there is a - seperator. else no lpage.
+ %
+ % need to remove others
+%%
+FUNCTION{markup.xml.pages}
+{
+ "" 'r := % fpage
+ "" 's := % lpage
+ duplicate$ missing$
+ 'pop$
+ {
+ 't :=
+ t " " "" replace 't := % remove all spaces. pgs must be - seperated
+ { t empty$ not }
+ {
+ t #1 #1 substring$ "-" =
+ {
+ t #2 global.max$ substring$ 's :=
+ "" 't := % break while loop
+ }{
+ r t #1 #1 substring$ * 'r :=
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+ }
+ if$
+ r "fpage" markup.xml output.xml
+ s "lpage" markup.xml output.xml
+}
+
+
+%%
+ % markup.xml.names
+ %
+ % Takes 2 args
+ % tag, namefield (eg. author "au")
+ % splits fields into <fnm> and <snm>
+ % writes info
+ % returns nothing
+%%
+FUNCTION {markup.xml.names}
+{
+ 't := % tag
+ "" 'r :=
+ "" 's :=
+ duplicate$ empty$
+ { pop$
+ organization missing$
+ { institution "cnm" markup.xml
+ "au" markup.xml "aug" markup.xml output.xml }
+ { organization "cnm" markup.xml
+ "au" markup.xml "aug" markup.xml output.xml }
+ if$ }
+ {
+ " <aug>" write$ newline$
+ 'names := % names string
+ names num.names$ 'j := % num of names
+ #1 'i := % init counter
+ { i #1 j + < } % while (i <= j)
+ {
+ " <au>" write$
+
+ % Initial first names
+ % if first name all in capitals
+ % - assume is initial list of first names.
+ names i "{ff{ }}" format.name$
+ duplicate$ "u" change.case$ =
+ { names i "{ff{ }}" format.name$ }
+ { names i "{f{}}" format.name$ }
+ if$
+
+ % if last name but no first name use cnm; else snm
+ duplicate$ "" =
+ { names i "{ll{ }}" format.name$ % last names space seperated.
+ "cnm" markup.xml write$ }
+ { names i "{ll{ }}" format.name$ % last names space seperated.
+ "snm" markup.xml write$ }
+ if$
+
+ "fnm" markup.xml write$
+
+ "</au>" write$ newline$
+ i #1 + 'i :=
+ }
+ while$
+ " </aug>" write$ newline$
+ }
+ if$
+}
+
+
+%%
+ % markup.xml.pub
+ %
+ % Takes 4 args (school address publisher tag)
+ % prints concatenation
+ % returns nothing
+%%
+FUNCTION {markup.xml.pub}
+{
+ 't := % Tag
+ "" 'p := % Publisher
+ "" 'q := % Address
+ "" 'r := % School
+ "" 's := % Answer
+ duplicate$ missing$ 'pop$ { 'p := } if$
+ duplicate$ missing$ 'pop$ { 'q := } if$
+ duplicate$ missing$ 'pop$ { 'r := } if$
+ "" r = not % school not empty
+ { r 's := } % return school as publisher
+ { % else
+ "" p = "" q = and % address and pub empty
+ 'skip$
+ {
+ "" q =
+ { p 's := } % return pub
+ { "" p =
+ { q 's := } % return add
+ { q ": " * p * 's := } % return add : pub
+ if$
+ }
+ if$
+ }
+ if$
+ }
+ if$
+ s t markup.xml output.xml
+}
+
+%%
+ % xml.phd
+ %
+ % Takes nothing
+ % Returns type (phd/msc) of empty string
+%%
+FUNCTION {xml.phd}
+{
+ "phdthesis" type$ =
+ "mastersthesis" type$ = OR
+ { "phdthesis" type$ =
+ { bbl.phdthesis format.thesis.type }
+ { bbl.mthesis format.thesis.type }
+ if$
+ }
+ { type } % usually empty
+ if$
+}
+
+% markup.xml.edition
+%
+% edition is a numeric value. ie "2"
+% if format 2nd 1st etc.. strip letters.
+%
+FUNCTION {markup.xml.edition}
+{ pop$ pop$ %clear stack
+ edition strip.letters duplicate$ "" =
+ { pop$ edition }
+ 'skip$
+ if$
+ "edition" markup.xml output.xml
+}
+
+
+%% [bmc@xmlcomment]
+ % this is an environment that returns nothing
+ % so although it will be embedded in the bbl file it
+ % will not display anything
+%%
+FUNCTION{begin.bmcxmlcomment}{
+ newline$
+ "\newcommand{\BMCxmlcomment}[1]{}" write$ newline$
+ newline$
+ "\BMCxmlcomment{" write$ newline$
+ newline$ "<refgrp>" write$ newline$
+}
+
+FUNCTION{end.bmcxmlcomment}{
+ newline$
+ "</refgrp>" write$ newline$
+ "} % end of \BMCxmlcomment" write$ newline$
+}
+
+%%
+ % export.xml
+ %
+ % done for each entry referenced in the BibTeX database
+%%
+FUNCTION {export.xml}{
+ newline$
+ global.counter #1 + 'global.counter :=
+ "<bibl id=" quote$ * "B" * global.counter int.to.str$ * quote$ * ">" *
+ write$ newline$
+% title "\&" "&" replace "title" markup.xml.title
+ title "title" markup.xml.title
+ author "aug" markup.xml.names % org. and inst. here
+ howpublished missing$
+ { booktitle missing$
+ { journal missing$
+ { xml.phd } % <type> Phd/Msc
+ {journal}
+ if$
+ } {booktitle}
+ if$
+ } { howpublished }
+ if$ "source" markup.xml output.xml
+ school
+ address
+ publisher "publisher" markup.xml.pub
+ editor "editor" markup.xml output.xml
+ edition "edition" markup.xml.edition
+ series "p" markup.xml
+ "title" markup.xml
+ "series" markup.xml output.xml
+ chapter "p" markup.xml
+ "title" markup.xml
+ "section" markup.xml output.xml
+ % month % ignore
+ year "pubdate" markup.xml output.xml
+
+ note missing$
+ { volume "volume" markup.xml output.xml
+ number "issue" markup.xml output.xml
+ pages markup.xml.pages
+ url "url" markup.xml output.xml }
+ { note "l" change.case$ "in press" =
+ { " <inpress />" write$ newline$ }
+ { volume "volume" markup.xml output.xml
+ number "issue" markup.xml output.xml
+ pages markup.xml.pages
+ url "url" markup.xml output.xml
+ note "note" markup.xml output.xml
+ }
+ if$
+ }
+ if$
+ "</bibl>" write$ newline$
+}
+
+% xml fields not used
+% suppliment conference xrefbib issn issb archive key
+% BioMed_Central_Tex_Template_v1.01
+
+
+%%%%%%%%%%%%%%%%
+% %
+% Main %
+% %
+%%%%%%%%%%%%%%%%
+
+READ
+
+FUNCTION {initialize.longest.label}
+{ "" 'longest.label :=
+ #1 'number.label :=
+ #0 'longest.label.width :=
+}
+FUNCTION {longest.label.pass}
+{ number.label int.to.str$ 'label :=
+ number.label #1 + 'number.label :=
+ label width$ longest.label.width >
+ { label 'longest.label :=
+ label width$ 'longest.label.width :=
+ }
+ 'skip$
+ if$
+}
+EXECUTE {initialize.longest.label}
+ITERATE {longest.label.pass}
+FUNCTION {begin.bib}
+{ "%% BioMed_Central_Bib_Style_v1.01" write$ newline$ newline$
+ preamble$ empty$
+ 'skip$
+ { preamble$ write$ newline$ }
+ if$
+ "\begin{thebibliography}{" longest.label * "}" *
+ write$ newline$
+ "\providecommand{\url}[1]{[#1]}"
+ write$ newline$
+ "\providecommand{\urlprefix}{}"
+ write$ newline$
+}
+
+EXECUTE {begin.bib}
+EXECUTE {init.state.consts}
+ITERATE {call.type$}
+FUNCTION {end.bib}
+{ newline$
+ "\end{thebibliography}" write$ newline$
+}
+EXECUTE {end.bib}
+EXECUTE {begin.bmcxmlcomment}
+ITERATE {export.xml}
+EXECUTE {end.bmcxmlcomment}
+%% End of customized bst file
+%%
+%% End of file `basic.bst'.
Property changes on: trunk/Jmol-paper/bmc_article.bst
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/Jmol-paper/bmc_article.cls
===================================================================
--- trunk/Jmol-paper/bmc_article.cls (rev 0)
+++ trunk/Jmol-paper/bmc_article.cls 2010-02-10 15:56:35 UTC (rev 12365)
@@ -0,0 +1,138 @@
+%% %
+ % bmc_article.cls ver: 1.03 %
+ % %
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % %%
+ % A Style Class based on article for %%
+ % formating towards BioMed Central %%
+ % guidelines %%
+ % %%
+ % <1 September 2003> %%
+ % %%
+ % %%
+ % %%
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %
+ % See Readme.txt for ToDo list.
+%%
+%
+
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesClass{bmc_article}[2003/09/01 v1.01 BioMed Central article class]
+\LoadClassWithOptions{article}
+
+\renewcommand\@biblabel[1]{#1.}
+\def\hi{}
+\def\pb{\\*[0.42cm]}
+
+
+\AtBeginDocument{}
+
+\def\@abstractline{\textwidth}
+
+\newcounter{bmc@correspondingauthor}
+\setcounter{bmc@correspondingauthor}{0} %never changes
+\newcounter{bmc@emailcounter} \setcounter{bmc@emailcounter}{0}
+
+
+% Corresponding Authors.
+% adds an asterisk * as a marker.
+\def\correspondingauthor{$^*$}
+\def\@corresponding{\footnotesize\correspondingauthor Corresponding author}
+
+
+% Email.
+% A variable to store names and emails.
+\gdef\bmc@email{Email: }
+\newcommand\bmc@curname{}
+\newcommand\email[1]{\relax
+ \g@addto@macro\bmc@email{#1; }} % has trailing ;
+
+\def\@bmc@email{\relax\footnotesize{\bmc@email}}
+
+% Address
+\def\address#1{ \def\@address{\begin{hi}\footnotesize#1\end{hi}}}
+\def\iid(#1){\hi$^#1$}
+
+% Thanks
+\def\thempfootnote{\normalfont\@arabic\c@mpfootnote}
+\def\thanks#1{%
+ \stepcounter{footnote}%
+ \hbox{\@textsuperscript{\normalfont\thefootnote}}%
+ \protected@xdef\@thanks{\@thanks%
+ \protect\footnotetext[\the\c@footnote]{#1}}%
+ }
+
+% Maketitle
+\let\old@maketitle\maketitle
+\renewcommand\maketitle{
+ \begin{flushleft}\mbox{
+ \global\let\@date\@empty % @date = null.
+ {\sffamily\begin{minipage}{\textwidth}%
+ \@maketitle
+ {\raggedright%
+ {\noindent\@address}\\ \hbox{}
+ {\noindent\@bmc@email}\\ \hbox{}
+ {\noindent\@corresponding}%
+ }%end \raggedright
+ \end{minipage}%
+ }
+ \renewcommand\thefootnote{\old@thefootnote} %
+ } % \mbox
+ \end{flushleft}
+}
+
+\def\and{, }
+
+\def\@maketitle{%
+ \newpage
+ \null
+ \vskip 2em%
+ {\noindent\LARGE \bfseries\@title \par}%
+ \vskip 1.5em%
+ {\large
+ %\lineskip .5em%
+ \noindent\@author
+ \par}%
+ \vskip 1em%
+ \par
+ \vskip 1.5em}
+
+
+% reformats abstract to BMC looks
+\let\old@abstract\abstract
+\renewenvironment{abstract}
+ {
+ \ifhmode\begingroup\parskip0pt\par\noindent\endgroup\fi%
+ \begin{sffamily}
+ \vspace{1cm} % use \topsep in list
+ {\noindent\bfseries\large\abstractname\vspace{-0.5em}}
+ {\par\vbox{\hrule width \@abstractline}}
+ }{
+ \ifhmode\begingroup\parskip0pt\par\noindent\endgroup\fi %
+ \vbox{\hrule width \@abstractline} \vspace{1cm} %
+ \end{sffamily}
+ }
+
+
+
+%% \@startsection{sec-name}{level}{indent}{pre-skip}
+%% {post-skip}{style}*[srt title]{title}
+\renewcommand\section{\@startsection {section}{1}{\z@}%
+ {-0.84cm \@plus -1ex \@minus -.2ex} {.2ex \@plus.2ex} %%
+ {\normalfont\large\bfseries\sffamily}}
+\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
+ {-0.84cm \@plus -1ex \@minus -.2ex} {.2ex \@plus.2ex} %%
+ {\normalfont\normalsize\bfseries\sffamily}}
+\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
+ {-0.84cm \@plus -1ex \@minus -.2ex} {.2ex \@plus.2ex} %%
+ {\normalfont\normalsize\sffamily\itshape}}
+\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
+ {-.2em \@plus1ex \@minus.2ex} {-0.5em} %%
+ {\normalfont\small\bfseries\sffamily}}
+\renewcommand\subparagraph{\@startsection{subparagraph}{5}{\parindent}%
+ {-.2em \@plus1ex \@minus.2ex} {-0.5em} %%
+ {\normalfont\normalsize\sffamily}}
+
+\endinput
+%% end of bmc_article.cls
Property changes on: trunk/Jmol-paper/bmc_article.cls
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/Jmol-paper/bmc_article.tex
===================================================================
--- trunk/Jmol-paper/bmc_article.tex (rev 0)
+++ trunk/Jmol-paper/bmc_article.tex 2010-02-10 15:56:35 UTC (rev 12365)
@@ -0,0 +1,383 @@
+%% BioMed_Central_Tex_Template_v1.05
+%% %
+% bmc_article.tex ver: 1.05 %
+% %
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% LaTeX template for BioMed Central %%
+%% journal article submissions %%
+%% %%
+%% <27 January 2006> %%
+%% %%
+%% %%
+%% Uses: %%
+%% cite.sty, url.sty, bmc_article.cls %%
+%% ifthen.sty. multicol.sty %%
+%% %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% For instructions on how to fill out this Tex template %%
+%% document please refer to Readme.pdf and the instructions for %%
+%% authors page on the biomed central website %%
+%% http://www.biomedcentral.com/info/authors/ %%
+%% %%
+%% Please do not use \input{...} to include other tex files. %%
+%% Submit your LaTeX manuscript as one .tex document. %%
+%% %%
+%% All additional figures and files should be attached %%
+%% separately and not embedded in the \TeX\ document itself. %%
+%% %%
+%% BioMed Central currently use the MikTex distribution of %%
+%% TeX for Windows) of TeX and LaTeX. This is available from %%
+%% http://www.miktex.org %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\documentclass[10pt]{bmc_article}
+
+
+
+% Load packages
+\usepackage{cite} % Make references as [1-4], not [1,2,3,4]
+\usepackage{url} % Formatting web addresses
+\usepackage{ifthen} % Conditional
+\usepackage{multicol} %Columns
+\usepackage[utf8]{inputenc} %unicode support
+%\usepackage[applemac]{inputenc} %applemac support if unicode package fails
+%\usepackage[latin1]{inputenc} %UNIX support if unicode package fails
+\urlstyle{rm}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% If you wish to display your graphics for %%
+%% your own use using includegraphic or %%
+%% includegraphics, then comment out the %%
+%% following two lines of code. %%
+%% NB: These line *must* be included when %%
+%% submitting to BMC. %%
+%% All figure files must be submitted as %%
+%% separate graphics through the BMC %%
+%% submission process, not included in the %%
+%% submitted article. %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\def\includegraphic{}
+\def\includegraphics{}
+
+
+
+\setlength{\topmargin}{0.0cm}
+\setlength{\textheight}{21.5cm}
+\setlength{\oddsidemargin}{0cm}
+\setlength{\textwidth}{16.5cm}
+\setlength{\columnsep}{0.6cm}
+
+\newboolean{publ}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% You may change the following style settings %%
+%% Should you wish to format your article %%
+%% in a publication style for printing out and %%
+%% sharing with colleagues, but ensure that %%
+%% before submitting to BMC that the style is %%
+%% returned to the Review style setting. %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%Review style settings
+\newenvironment{bmcformat}{\begin{raggedright}\baselineskip20pt\sloppy\setboolean{publ}{false}}{\end{raggedright}\baselineskip20pt\sloppy}
+
+%Publication style settings
+%\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy}
+
+
+
+% Begin ...
+\begin{document}
+\begin{bmcformat}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% Enter the title of your article here %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\title{A sample article title}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% Enter the authors here %%
+%% %%
+%% Ensure \and is entered between all but %%
+%% the last two authors. This will be %%
+%% replaced by a comma in the final article %%
+%% %%
+%% Ensure there are no trailing spaces at %%
+%% the ends of the lines %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\author{Charles A Darwin\correspondingauthor$^{1,2}$%
+ \email{Charles A Darwin\correspondingauthor - ch...@lo...}%
+ \and
+ Jane E Doe\correspondingauthor$^2$%
+ \email{Jane E Doe\correspondingauthor - jan...@ca...}
+ and
+ John RS Smith$^3$%
+ \email{John RS Smith - joh...@ca...}%
+ }
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% Enter the authors' addresses here %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\address{%
+ \iid(1)Life Sciences Department, Kings College London, Cornwall House,%
+ Waterloo Road, London, UK\\
+ \iid(2)Department of Zoology, Cambridge, Waterloo Road, London, UK\\
+ \iid(3)Marine Ecology Department, Institute of Marine Sciences Kiel, %
+ D\"{u}sternbrooker Weg 20, 24105 Kiel, Germany
+}%
+
+\maketitle
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% The Abstract begins here %%
+%% %%
+%% The Section headings here are those for %%
+%% a Research article submitted to a %%
+%% BMC-Series journal. %%
+%% %%
+%% If your article is not of this type, %%
+%% then refer to the Instructions for %%
+%% authors on http://www.biomedcentral.com %%
+%% and change the section headings %%
+%% accordingly. %%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\begin{abstract}
+ % Do not use inserted blank lines (ie \\) until main body of text.
+ \paragraph*{Background:} Text for this section of the abstract.
+
+ \paragraph*{Results:} Text for this section of the abstract \ldots
+
+ \paragraph*{Conclusions:} Text for this section of the abstract \ldots
+\end{abstract}
+
+
+
+\ifthenelse{\boolean{publ}}{\begin{multicols}{2}}{}
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% %%
+%% The Main Body begins here %%
+%% %%
+%% The Section headings here are those for %%
+%% a Research article submitted to a %%
+%% BMC-Series journal. %%
+%% %%
+%% If your article is not of this type, %%
+%% then refer to the instructions for %%
+%% authors on: %%
+%% http://www.biomedcentral.com/info/authors%%
+%% and change the section headings %%
+%% accordingly. %%
+%% %%
+%% See the Results and Discussion section %%
+%% for details on how to create sub-sections%%
+%% %%
+%% use \cite{...} to cite references %%
+%% \cite{koon} and %%
+%% \cite{oreg,khar,zvai,xjon,schn,pond} %%
+%% \nocite{smith,marg,hunn,advi,koha,mouse}%%
+%% %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+
+%%%%%%%%%%%%%%%%
+%% Background %%
+%%
+\section*{Background}
+ Text for this section.\cite{koon,oreg,khar,zvai,xjon,schn,pond,smith,marg,hunn,advi,koha,mouse}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Results and Discussion %%
+%%
+\section*{Results and Discussion}
+ \subsection*{Results sub-heading}
+ \subsubsection*{This is a sub-sub-heading}
+ Sub-sub-sub...
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