From mantoniotti at common-lisp.net Fri Feb 1 11:33:08 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:33:08 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml In directory tiger.common-lisp.net:/tmp/cvs-serv8689 Added Files: cl-sbml.asd Log Message: .asd file added. --- /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.asd 2013/02/01 11:33:08 NONE +++ /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.asd 2013/02/01 11:33:08 1.1 ;;; -*- Mode: Lisp -*- ;;; cl-sbml.asd ;;; *_cl-xml-load-file* -- ;;; Change this variable to accomodate the location of CL-XML. ;;; If you already have CL-XML loaded in your image, this is optional. (defparameter *_cl-xml-load-file* (merge-pathnames (make-pathname :directory '(:relative "lang" "cl" "cl-xml" "code") :name "load" :type "lisp") (user-homedir-pathname))) (eval-when (:load-toplevel :execute) (unless (find-package "XML-PARSER") (loop while (not (and *_cl-xml-load-file* (probe-file *_cl-xml-load-file*))) do (cerror "Enter the pathanme of CL-XML load file. Use either a string or a pathname." "Cannot find the ~S file.~@ CL-XML is not available and therefore the system cannot~@ be setup." *_cl-xml-load-file*) (format t "> ") (setf *_cl-xml-load-file* (ignore-errors (pathname (read)))) (fresh-line) ) (load *_cl-xml-load-file*))) ;;;; ADD HERE ASDF DIRECTORIES INFO. ;;; CL-SBML asdf system definition. (asdf:defsystem "CL-SBML" :components ((:module "base" :components ("cl-sbml-package" "sid" "sbml-base" "sbml-element" "model" "sbml" "unit" "unit-definition" "unit-kind" "compartment" "event" "event-assignment" "function-definition" "kinetic-law" "species" "parameter" "reaction" "stoichiometry-math" "simple-species-reference" (:file "modifier-species-reference" :depends-on ("simple-species-reference")) (:file "species-reference" :depends-on ("simple-species-reference")) "rule" "algebraic-rule" "rate-rule" "assignment-rule" "sbml-loader" "build-model" "sbml-writer" )) #| #+lispworks (:module "gui" :components ("cl-sbml-interface") :depends-on ("base")) |# ) :depends-on ("cl-xml-ext" "cl-mathml")) (eval-when (:load-toplevel :execute) (format t "~&;;; Setting the CL-SBML LP Translation.~%") (setf (logical-pathname-translations "CL-SBML") `(("*.*" ,(make-pathname :name :wild :type :wild :defaults *load-pathname*)) ("**;*.*" ,(make-pathname :name :wild :type :wild :directory (append (or (pathname-directory *load-pathname*) (list :relative) ; This :RELATIVE may not be right. ) (list :wild-inferiors)) :defaults *load-pathname*)) ))) ;;; end of file -- cl-sbml.asd -- From mantoniotti at common-lisp.net Fri Feb 1 11:39:10 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:39:10 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml/cl-mathml Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml/cl-mathml In directory tiger.common-lisp.net:/tmp/cvs-serv11226 Added Files: cl-mathml.asd Log Message: .asd file added. --- /project/cl-sbml/cvsroot/cl-sbml/cl-mathml/cl-mathml.asd 2013/02/01 11:39:10 NONE +++ /project/cl-sbml/cvsroot/cl-sbml/cl-mathml/cl-mathml.asd 2013/02/01 11:39:10 1.1 ;;; -*- Mode: Lisp -*- ;;; cl-mathml.system (defparameter *_cl-xml-load-file* (pathname ;; "/Users/marcoxa/Projects/Lang/CL/cl-xml/code/load.lisp" "z:/lang/cl/cl-xml/code/load.lisp" ;; "z:/lisp/CL-XML/code/load.lisp" )) (eval-when (:load-toplevel :execute) (unless (find-package "XML-PARSER") (loop while (not (and *_cl-xml-load-file* (probe-file *_cl-xml-load-file*))) do (cerror "Enter the pathanme of CL-XML load file. Use either a string or a pathname." "Cannot find the ~S file.~@ CL-XML is not available and therefore the system cannot~@ be setup." *_cl-xml-load-file*) (format t "> ") (setf *_cl-xml-load-file* (ignore-errors (pathname (read)))) (fresh-line) ) (load *_cl-xml-load-file*))) (asdf:defsystem "CL-MATHML" :components ("cl-mathml-package" "math" "mathml-parser" "mathml-writer" )) (eval-when (:load-toplevel :execute) (format t "Setting the CL-MATHML LP Translation.~%") (setf (logical-pathname-translations "CL-MATHML") `(("*.*" ,(make-pathname :name :wild :type :wild :defaults *load-pathname*)) ("**;*.*" ,(make-pathname :name :wild :type :wild :directory (append (pathname-directory *load-pathname*) (list :wild-inferiors)) :defaults *load-pathname*)) ))) ;;; end of file -- cl-mathml.system -- From mantoniotti at common-lisp.net Fri Feb 1 11:39:57 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:39:57 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml/cl-xml-ext Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml/cl-xml-ext In directory tiger.common-lisp.net:/tmp/cvs-serv11320 Added Files: cl-xml-ext.asd Log Message: cl-xml-ext.asd file added. --- /project/cl-sbml/cvsroot/cl-sbml/cl-xml-ext/cl-xml-ext.asd 2013/02/01 11:39:57 NONE +++ /project/cl-sbml/cvsroot/cl-sbml/cl-xml-ext/cl-xml-ext.asd 2013/02/01 11:39:57 1.1 ;;; -*- Mode: Lisp -*- (eval-when (:load-toplevel :execute) (unless (find-package "XML-PARSER") (error "CL-XML.EXTENSION error: the CL-XML library is not available, ~ therefore it cannot be extended."))) (asdf:defsystem "CL-XML-EXT" :components ("cl-xml-ext-package" "cl-xml-ext")) ;;; end of file -- cl-xml-ext.asdf -- From mantoniotti at common-lisp.net Fri Feb 1 11:41:15 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:41:15 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml In directory tiger.common-lisp.net:/tmp/cvs-serv11523 Modified Files: simple-species-reference.lisp Log Message: Fixed a few glitches that made the system not loadable (some bit-rot). Copyright Notice also updated. --- /project/cl-sbml/cvsroot/cl-sbml/simple-species-reference.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/simple-species-reference.lisp 2013/02/01 11:41:15 1.2 @@ -1,7 +1,6 @@ (in-package "CL-SBML") -(defstruct (simple-species-reference (:include sbml-base) - (:constructor nil)) +(defstruct (simple-species-reference (:include sbml-base)) "The SBML Simple Species Reference Structure Class." (species nil :type (or symbol string)) ) From mantoniotti at common-lisp.net Fri Feb 1 11:41:36 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:41:36 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml In directory tiger.common-lisp.net:/tmp/cvs-serv11586 Modified Files: COPYING build-model.lisp cl-sbml-package.lisp cl-sbml.system species-reference.lisp species.lisp unit-kind.lisp Log Message: Fixed a few glitches that made the system not loadable (some bit-rot). Copyright Notice also updated. --- /project/cl-sbml/cvsroot/cl-sbml/COPYING 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/COPYING 2013/02/01 11:41:36 1.2 @@ -1,5 +1,7 @@ -Copyright (c) 2004-2005 Marco Antoniotti, Bioinformatics Group, Courant -Institute of Mathematical Sciences, New York University +Copyright (c) 2004-2013 Marco Antoniotti, Bioinformatics Group, Courant +Institute of Mathematical Sciences, New York University, New York, USA and +Dipartimento di Informatica, Sistemistica e Comunicazione, Universita` +degli Studi di Milano Bicocca, Milan, Italy. All rights reserved. Permission is hereby granted, without written agreement and without @@ -9,19 +11,22 @@ copies of this software. IN NO EVENT SHALL THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT -INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY BE LIABLE -TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR -CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS -DOCUMENTATION, EVEN IF THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE -COURANT INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY -HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF -MATHEMATICAL SCIENCES, AND NEW YORK UNIVERSITY SPECIFICALLY DISCLAIMS -ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES -OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE -PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE AUTHOR(S), THE +INSTITUTE OF MATHEMATICAL SCIENCES, NEW YORK UNIVERSITY, DIPARTIMENTO +DI INFORMATICA, SISTEMISTICA E COMUNICAZIONE, OR UNIVERSITA` DEGLI STUDI +DI MILANO BICOCCA, BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, +SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE +OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF MATHEMATICAL SCIENCES, -OR NEW YORK UNIVERSITY HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, -SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. +OR NEW YORK UNIVERSITY HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH +DAMAGE. +THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE COURANT INSTITUTE OF +MATHEMATICAL SCIENCES, NEW YORK UNIVERSITY, DIPARTIMENTO DI +INFORMATICA, SISTEMISTICA E COMUNICAZIONE, AND UNIVERSITA` DEGLI STUDI +DI MILANO BICOCCA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, +BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND +FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS +ON AN "AS IS" BASIS, AND THE AUTHOR(S), THE BIOINFORMATICS GROUP, THE +COURANT INSTITUTE OF MATHEMATICAL SCIENCES, OR NEW YORK UNIVERSITY +HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, +ENHANCEMENTS, OR MODIFICATIONS. --- /project/cl-sbml/cvsroot/cl-sbml/build-model.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/build-model.lisp 2013/02/01 11:41:36 1.2 @@ -1,9 +1,7 @@ -;;; +;;;; -*- Mode: Emacs -*- (in-package "CL-SBML") -(use-package "CL-XML-EXT") - ;;;=========================================================================== ;;; System dependencies. @@ -23,7 +21,7 @@ #+(and lispworks win32) (eval-when (:load-toplevel :execute) (warn "Automatic and silent stack group extension not implemented ~@ - for LWW. INFIX may not work rpoperly.") + for LWW. INFIX may not work properly.") (setf sys::*stack-overflow-behaviour* nil)) --- /project/cl-sbml/cvsroot/cl-sbml/cl-sbml-package.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/cl-sbml-package.lisp 2013/02/01 11:41:36 1.2 @@ -1,6 +1,6 @@ ;;; -*- Mode: Lisp -*- -(defpackage "EDU.NYU.BIOINFORMATICS.MARCOXA.CL-SBML" (:use "COMMON-LISP") +(defpackage "EDU.NYU.BIOINFORMATICS.MARCOXA.CL-SBML" (:use "COMMON-LISP" "CL-XML-EXT") (:nicknames "CL-SBML") (:documentation "The CL-SBML Package.") --- /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.system 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/cl-sbml.system 2013/02/01 11:41:36 1.2 @@ -74,10 +74,11 @@ "build-model" "sbml-writer" )) - #+lispworks + #| #+lispworks (:module "gui" :components ("cl-sbml-interface") :depends-on ("base")) + |# ) :depends-on ("cl-xml-ext" "cl-mathml")) --- /project/cl-sbml/cvsroot/cl-sbml/species-reference.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/species-reference.lisp 2013/02/01 11:41:36 1.2 @@ -2,7 +2,7 @@ (defstruct (species-reference (:include simple-species-reference)) "The SBML Species Reference Structure Class." - (stoichiometry 0.0d0 :type double) + (stoichiometry 0.0d0 :type double-float) (stoichiometry-math () :type (or null cons stoichiometry-math)) ) --- /project/cl-sbml/cvsroot/cl-sbml/species.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/species.lisp 2013/02/01 11:41:36 1.2 @@ -14,7 +14,7 @@ (has-only-substance-units-p nil :type boolean) - (boundary-condition-p nil :type boolean) + (boundary-condition nil :type boolean) (charge 0 :type fixnum) (constant-p nil :type boolean) ) --- /project/cl-sbml/cvsroot/cl-sbml/unit-kind.lisp 2005/05/12 17:21:30 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/unit-kind.lisp 2013/02/01 11:41:36 1.2 @@ -1,44 +1,45 @@ (in-package "CL-SBML") -(defconstant +unit-kinds+ - '( - :AMPERE - :BECQUEREL - :CANDELA - :CELSIUS - :COULOMB - :DIMENSIONLESS - :FARAD - :GRAM - :GRAY - :HENRY - :HERTZ - :ITEM - :JOULE - :KATAL - :KELVIN - :KILOGRAM - :LITER - :LITRE - :LUMEN - :LUX - :METER - :METRE - :MOLE - :NEWTON - :OHM - :PASCAL - :RADIAN - :SECOND - :SIEMENS - :SIEVERT - :STERADIAN - :TESLA - :VOLT - :WATT - :WEBER - :INVALID) - ) +(eval-when (:load-toplevel :compile-toplevel :execute) + (defconstant +unit-kinds+ + '( + :AMPERE + :BECQUEREL + :CANDELA + :CELSIUS + :COULOMB + :DIMENSIONLESS + :FARAD + :GRAM + :GRAY + :HENRY + :HERTZ + :ITEM + :JOULE + :KATAL + :KELVIN + :KILOGRAM + :LITER + :LITRE + :LUMEN + :LUX + :METER + :METRE + :MOLE + :NEWTON + :OHM + :PASCAL + :RADIAN + :SECOND + :SIEMENS + :SIEVERT + :STERADIAN + :TESLA + :VOLT + :WATT + :WEBER + :INVALID) + )) (deftype unit-kind () From mantoniotti at common-lisp.net Fri Feb 1 11:42:34 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:42:34 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml In directory tiger.common-lisp.net:/tmp/cvs-serv11763 Added Files: ChangeLog Log Message: ChangeLog updated. --- /project/cl-sbml/cvsroot/cl-sbml/ChangeLog 2013/02/01 11:42:34 NONE +++ /project/cl-sbml/cvsroot/cl-sbml/ChangeLog 2013/02/01 11:42:34 1.1 2013-02-01 author * COPYING, build-model.lisp, cl-sbml-package.lisp, cl-sbml.system, species-reference.lisp, species.lisp, unit-kind.lisp, simple-species-reference.lisp: Fixed a few glitches that made the system not loadable (some bit-rot). Copyright Notice also updated. * cl-xml-ext/cl-xml-ext.asd: cl-xml-ext.asd file added. * cl-mathml/cl-mathml.asd, cl-sbml.asd: .asd file added. 2005-05-12 author * tests/100Yeast.xml.gz: Added the (large) 100Yeast.xml.gz test file. * docs/html/images/header_bg.gif, docs/html/images/header_bg_1.gif, docs/html/images/shim.gif, tests/CellCycle-1991Tys-2.xml, tests/CellCycle-1997Nov.xml, tests/Metabolism-2002Lam.xml, docs/html/cl-sbml-dictionary.html, docs/html/dictionary/algebraic-rule.html, docs/html/dictionary/assignment-rule.html, docs/html/dictionary/build-model-from-sbml.html, docs/html/dictionary/cl-sbml-package.html, docs/html/dictionary/compartment.html, docs/html/dictionary/event-assignment.html, docs/html/dictionary/event.html, docs/html/dictionary/function-definition.html, docs/html/dictionary/kinetic-law.html, docs/html/dictionary/load-sbml.html, docs/html/dictionary/model.html, docs/html/dictionary/modifier-species-reference.html, docs/html/dictionary/parameter.html, docs/html/dictionary/rate-rule.html, docs/html/dictionary/reaction.html, docs/html/dictionary/rule.html, docs/html/dictionary/sbml-base.html, docs/html/dictionary/sbml-element.html, docs/html/dictionary/sbml.html, docs/html/dictionary/sid.html, docs/html/dictionary/simple-species-reference.html, docs/html/dictionary/species-reference.html, docs/html/dictionary/species.html, docs/html/dictionary/stoichiometry-math.html, docs/html/dictionary/unit-definition.html, docs/html/dictionary/unit-kind-p.html, docs/html/dictionary/unit-kind.html, docs/html/dictionary/unit-kinds-constant.html, docs/html/dictionary/unit.html, docs/html/downloads.html, docs/html/index.html, docs/html/installation.html, docs/html/links.html, docs/html/main.css, docs/usage.txt, COPYING, INSTALL, README, algebraic-rule.lisp, assignment-rule.lisp, build-model.lisp, cl-mathml/cl-mathml-package.lisp, cl-mathml/cl-mathml.system, cl-mathml/math.lisp, cl-mathml/mathml-parser.lisp, cl-mathml/mathml-writer.lisp, cl-sbml-package.lisp, cl-sbml.system, cl-xml-ext/cl-xml-ext-package.lisp, cl-xml-ext/cl-xml-ext.lisp, cl-xml-ext/cl-xml-ext.system, compartment.lisp, event-assignment.lisp, event.lisp, function-definition.lisp, kinetic-law.lisp, model.lisp, modifier-species-reference.lisp, parameter.lisp, rate-rule.lisp, reaction.lisp, rule.lisp, sbml-base.lisp, sbml-element.lisp, sbml-loader.lisp, sbml-writer.lisp, sbml.lisp, sid.lisp, simple-species-reference.lisp, species-reference.lisp, species.lisp, stoichiometry-math.lisp, unit-definition.lisp, unit-kind.lisp, unit.lisp: Initial manual import of CL-SBML sources and documentation. From mantoniotti at common-lisp.net Fri Feb 1 11:47:17 2013 From: mantoniotti at common-lisp.net (CVS User mantoniotti) Date: Fri, 01 Feb 2013 03:47:17 -0800 Subject: [cl-sbml-cvs] CVS cl-sbml/docs/html Message-ID: Update of /project/cl-sbml/cvsroot/cl-sbml/docs/html In directory tiger.common-lisp.net:/tmp/cvs-serv13831 Modified Files: downloads.html index.html installation.html links.html Log Message: Added link to CVS tarball and undated copyrights. --- /project/cl-sbml/cvsroot/cl-sbml/docs/html/downloads.html 2005/05/12 17:21:41 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/docs/html/downloads.html 2013/02/01 11:47:17 1.2 @@ -43,18 +43,17 @@

You can access the CL-SBML (anonymous) CVS repository using the instructions for generic common-lisp.net projects.

+ href="http://www.common-lisp.net">common-lisp.net + projects.

-

Otherwise, you can try one of the .tar.gz releases - listed hereafter in chronological order: -

    -
  • Sorry, none yet. Please wait.
    • -
+

The CVS repository is here. You + can download a tarball directly from there.

-
-

Questions? Queries? Suggestions? Comments? Please direct them - at me. -

- @@ -83,16 +77,6 @@
-

News

- -

News in chronological order, most recent on top. -

- -
    -
  • 2004-05-05
    - Started the site. -
    • -
@@ -108,7 +92,7 @@
- © 2003-2004, Marco Antoniotti, all rights reserved. + © 2003-2013, Marco Antoniotti, all rights reserved.
--- /project/cl-sbml/cvsroot/cl-sbml/docs/html/index.html 2005/05/12 17:21:41 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/docs/html/index.html 2013/02/01 11:47:17 1.2 @@ -242,19 +242,6 @@
-

News

- -

News in chronological order, most recent on top. -

- -
    -
  • 2005-05-05
    - Page updated. -
    • -
  • 2004-05-05
    - Started the site. -
    • -
@@ -270,7 +257,7 @@
- © 2003-2005, Marco Antoniotti, all rights reserved. + © 2003-2013, Marco Antoniotti, all rights reserved.
--- /project/cl-sbml/cvsroot/cl-sbml/docs/html/installation.html 2005/05/12 17:21:41 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/docs/html/installation.html 2013/02/01 11:47:17 1.2 @@ -151,7 +151,7 @@
- © 2003-2005, Marco Antoniotti, all rights reserved. + © 2003-2013, Marco Antoniotti, all rights reserved.
--- /project/cl-sbml/cvsroot/cl-sbml/docs/html/links.html 2005/05/12 17:21:41 1.1 +++ /project/cl-sbml/cvsroot/cl-sbml/docs/html/links.html 2013/02/01 11:47:17 1.2 @@ -47,7 +47,7 @@