[Jsbml-svn] SF.net SVN: jsbml:[2407] trunk/core/doc

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Revision: 2407
          http://sourceforge.net/p/jsbml/code/2407
Author:   niko-rodrigue
Date:     2015-11-26 16:32:15 +0000 (Thu, 26 Nov 2015)
Log Message:
-----------
small updates to the user guide, incorporating some of the comments from Andreas

Modified Paths:
--------------
    trunk/core/doc/common/tex/literature.bib
    trunk/core/doc/user_guide/JSBML_getting_started.tex
    trunk/core/doc/user_guide/JSBMLdoc.cls
    trunk/core/doc/user_guide/User_Guide.tex

Modified: trunk/core/doc/common/tex/literature.bib
===================================================================

--- trunk/core/doc/common/tex/literature.bib	2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/common/tex/literature.bib	2015-11-26 16:32:15 UTC (rev 2407)
@@ -658,7 +658,7 @@
   title = {Java\texttrademark},
   howpublished = {Available on the World Wide Web at \url{http://www.java.com/en/download/manual.jsp}},
   url = {http://www.java.com/en/download/manual.jsp},
-  year = {2012}, 
+  year = {2015}, 
 }
 
 @MISC{SBMLspecs,
@@ -666,7 +666,7 @@
   title = {The {SBML} Specifications},
   howpublished = {Available on the World Wide Web at \url{http://sbml.org/Documents/Specifications/}},
   url = {http://sbml.org/Documents/Specifications/},
-  year = 2012
+  year = 2015
 }
 
 @MISC{SBMLFAQ,
@@ -674,7 +674,7 @@
   title = {The {SBML} Frequently Asked Questions and Answers},
   howpublished = {Available on the World Wide Web at \url{http://sbml.org/Documents/FAQ}},
   url = {http://sbml.org/Documents/FAQ},
-  year = 2012
+  year = 2015
 }
 
 @MISC{SBMLforums,
@@ -682,7 +682,7 @@
   title = {The {SBML} discussion forums and mailing lists},
   howpublished = {Available on the World Wide Web at \url{http://sbml.org/Forums/}},
   url = {http://sbml.org/Forums/},
-  year = 2012, 
+  year = 2015 
 }
 
 @MISC{JSBMLdownload,
@@ -690,7 +690,7 @@
   title = {The {JSBML} Downloads},
   howpublished = {Available on the World Wide Web at \url{http://sourceforge.net/projects/jsbml/files/}},
   url = {http://sourceforge.net/projects/jsbml/files/},
-  year = {2012}, 
+  year = 2015, 
 }
 
 @MISC{ApacheAnt,
@@ -698,23 +698,23 @@
   title = {The {Apache} {Ant} Project},
   howpublished = {Available on the World Wide Web at \url{http://ant.apache.org/}},
   url = {http://ant.apache.org/},
-  year = {2012},
+  year = {2015},
 }
 
 @MISC{JSBMLSVN,
   author = {{JSBML Team}},
   title = {The {JSBML} {SVN} repository},
-  howpublished = {Available on the World Wide Web at \url{http://sourceforge.net/scm/?type=svn&group_id=279608}},
-  url = {http://sourceforge.net/scm/?type=svn&group_id=279608},
-  year = {2012},
+  howpublished = {Available on the World Wide Web at \url{https://sourceforge.net/p/jsbml/code}},
+  url = {https://sourceforge.net/p/jsbml/code},
+  year = {2015},
 }
 
 @MISC{unitontology,
   author = {George Gkoutos},
   title = {{The Ontology of Units of Measurement}},
-  howpublished = {Available on the World Wide Web at \url{http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit}},
-  url = {http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit},
-  year = {2012}, 
+  howpublished = {Available on the World Wide Web at \url{http://www.obofoundry.org/ontology/uo.html}},
+  url = {http://www.obofoundry.org/ontology/uo.html},
+  year = {2015}, 
 }
 
 @MISC{log4j,
@@ -722,7 +722,7 @@
   title = {log4j},
   howpublished = {Available on the World Wide Web at \url{http://logging.apache.org/log4j/1.2/}},
   url = {http://logging.apache.org/log4j/1.2/},
-  year = {2010}, 
+  year = {2015}, 
 }
 
 @MISC{tomcat,
@@ -730,15 +730,15 @@
   title = {{Apache Tomcat}},
   howpublished = {Available on the World Wide Web at \url{http://tomcat.apache.org/}},
   url = {http://tomcat.apache.org/},
-  year = {2012}, 
+  year = {2015}, 
 }
 
 @MISC{logViewersWebpage,
   author = {{Wikipedia Foundation}},
-  title = {Log4j Log Viewers},
-  howpublished = {Available on the World Wide Web at \url{http://en.wikipedia.org/wiki/Log4j#Log_Viewers}},
-  url = {http://en.wikipedia.org/wiki/Log4j#Log_Viewers},
-  year = {2012}, 
+  title = {Chainsaw log viewer with some alternatives},
+  howpublished = {Available on the World Wide Web at \url{https://en.wikipedia.org/wiki/Chainsaw_(log_file_viewer)}},
+  url = {https://en.wikipedia.org/wiki/Chainsaw_(log_file_viewer)},
+  year = {2015}, 
 }
 
 @MISC{libSBMLwebsite,
@@ -746,7 +746,7 @@
   title = {{libSBML}},
   howpublished = {Available on the World Wide Web at \url{http://sbml.org/Software/libSBML}},
   url = {http://sbml.org/Software/libSBML},
-  year = {2012}, 
+  year = {2015}, 
 }
 
 @MISC{graphvizWebsite,
@@ -756,7 +756,7 @@
   title = {{Graphviz} -- Graph Visualization Software},
   howpublished = {Available on the World Wide Web at \url{http://www.graphviz.org/}},
   url = {http://www.graphviz.org/},
-  year = {2012}, 
+  year = {2015}, 
 }
 
 @MISC{junitWebsite,
@@ -764,5 +764,5 @@
   title = {{JUnit.org}},
   howpublished = {Available on the World Wide Web at \url{http://www.junit.org}},
   url = {http://www.junit.org},
-  year = {2012}, 
+  year = {2015}, 
 }

Modified: trunk/core/doc/user_guide/JSBML_getting_started.tex
===================================================================
--- trunk/core/doc/user_guide/JSBML_getting_started.tex	2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/JSBML_getting_started.tex	2015-11-26 16:32:15 UTC (rev 2407)
@@ -19,7 +19,10 @@
 you have installed the JAR file on your computer, it is sufficient to add
 it to your Java build and/or class path in order to use JSBML.
 
+\subsection{Maven dependencies}
 
+%% TODO
+
 \subsection{The JSBML archive without dependencies}
 
 \begin{table}[b]
@@ -32,9 +35,8 @@
     \toprule
     \textbf{\sffamily Library name} & \textbf{Purpose} & \textbf{Source URL} \\
     \midrule
-    biojava-1.7-ontology.jar
-    & A stripped-down version of biojava-1.7
-    containing mostly ontology-related classes~\citep{Holland2008}.
+    biojava3-ontology-3.1.0.jar
+    & biojava3 ontology-related classes~\citep{Holland2008}.
     \index{Ontology}
     & \href{http://biojava.org}{biojava.org} \\
 
@@ -43,19 +45,15 @@
     run the tests in the \code{tests} folder.
     & \href{http://www.junit.org}{www.junit.org} \\
 
-    stax2-api-3.0.3.jar
+    stax2-api-3.1.4.jar
     & Used for reading and writing XML.
     & \href{http://docs.codehaus.org/display/WSTX/StAX2}{docs.codehaus.org/display/WSTX/StAX2} \\
 
-    stax-api-1.0.1.jar
+    woodstox-core-5.0.1.jar
     & Used for reading and writing XML.
-    & \href{http://stax.codehaus.org}{stax.codehaus.org} \\
-
-    woodstox-core-lgpl-4.0.9.jar
-    & Used for reading and writing XML.
     & \href{http://woodstox.codehaus.org}{woodstox.codehaus.org} \\
     
-    staxmate-2.0.0.jar
+    staxmate-2.3.0.jar
     & Used for reading and writing XML. Provides a more user-friendly StAX
     interface.
     & \href{http://staxmate.codehaus.org}{staxmate.codehaus.org} \\
@@ -70,7 +68,7 @@
     Dec. 2010), containing classes for date manipulation. 
     & \href{http://jigsaw.w3.org}{jigsaw.w3.org} \\
 
-    log4j-1.2.8.jar
+    log4j-1.2.17.jar
     & Library for logging errors and other diagnostics.
     & \href{http://logging.apache.org/log4j}{logging.apache.org/log4j} \\
 
@@ -101,7 +99,7 @@
 Download whichever format is more convenient for you and unpack the archive
 on your computer somewhere.  The act of unpacking the archive will create a
 folder on your computer named after the distribution version; for
-example, this may be ``\code{jsbml-1.0}''.  Next, you will need to compile
+example, this may be ``\code{jsbml-}\jsbmlversion''.  Next, you will need to compile
 the Java source code.  JSBML comes with a \emph{build file} (i.e., scripted
 instructions in a specialized format) for Apache Ant~\citep{ApacheAnt};
 you can use other approaches for compiling the JSBML classes and
@@ -112,7 +110,7 @@
 
 \begin{example}[style=bash, title={Compiling JSBML with Ant; this example
     uses Bash shell syntax.}] 
-cd jsbml-1.0
+cd jsbml-|\jsbmlversion|
 ant compile
 \end{example}
 
@@ -137,13 +135,13 @@
 
 The fourth approach to obtaining a copy of JSBML is to retrieve it directly
 from the Subversion repository~\cite{JSBMLSVN}.  Here is an example of how
-to retrieve the latest version of the core JSBML sources:
+to retrieve the latest version of the JSBML sources:
 
 \newcommand{\dirname}{\code{\emph{\color{winered}jsbml}}\xspace}
 
 \begin{example}[style=bash, title={Downloading the latest JSBML 
     sources from the JSBML project's Subversion repository.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/core |\dirname|
+svn co https://svn.code.sf.net/p/jsbml/code/trunk |\dirname|
 cd |\dirname|
 \end{example}
 
@@ -170,7 +168,10 @@
 because the different parsers in JSBML are registered automatically using
 Java annotations.  To configure the annotation processor in Eclipse, follow
 the instructions found on the web page
-\url{https://code.google.com/p/spi/wiki/EclipseSettings}.
+\url{https://code.google.com/p/spi/wiki/EclipseSettings}. If you checkout 
+the full trunk (and not just the core), you can find a folder dev, which 
+contains a README.txt file that has also these instructions and further 
+important information.
 
 Finally, you can run the \code{ParserManager} class to check that the list of
 parsers are not empty and that they contain the parsers you need.
@@ -208,7 +209,7 @@
 
 \begin{example}[style=bash, title={Downloading the latest JSBML extensions
     source folder from the project's Subversion repository.}] 
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/extensions extensions
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/extensions jsbml-extensions
 \end{example}
 
 Each of the extensions has its own Ant build script, located in a file
@@ -224,6 +225,7 @@
 
 \subsubsection{JSBML Modules}
 \label{sec:jsbml-modules}
+%% TODO - add few words about the tidy writer module
 
 JSBML currently provides five additional modules.  Each provides features
 for task-specific purposes. Binary versions of the modules can be found at
@@ -250,7 +252,7 @@
 listed in the first column of \tab{tab:jsbml-modules}:
 
 \begin{example}[style=bash, title={Obtaining a JSBML module.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/|\modulename| |\modulename|
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/modules/|\modulename| |\modulename|
 \end{example}
 
 (In other words, if you would like to obtain both the Android and libSBML
@@ -311,7 +313,7 @@
 
 \begin{example}[style=bash, title={Retrieving the \emph{SBML Bar Graph}
     example application.}] 
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/examples/sbmlbargraph sbmlbargraph
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/examples/sbmlbargraph sbmlbargraph
 \end{example}
 
 Finally, please read the ``\code{README.txt}'' file in the freshly-obtained

Modified: trunk/core/doc/user_guide/JSBMLdoc.cls
===================================================================
--- trunk/core/doc/user_guide/JSBMLdoc.cls	2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/JSBMLdoc.cls	2015-11-26 16:32:15 UTC (rev 2407)
@@ -28,7 +28,8 @@
 %% It would be so nice to be able to put the CVS/RCS 'Date' tag in the
 %% \filedate below.  Unfortunately, LaTeX will barf on the resulting string.
 
-\def\filedate{2012/04/06}
+\def\filedate{2015/12/01}
+\def\jsbmlversion{1.1}
 
 \NeedsTeXFormat{LaTeX2e}
 

Modified: trunk/core/doc/user_guide/User_Guide.tex
===================================================================
--- trunk/core/doc/user_guide/User_Guide.tex	2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/User_Guide.tex	2015-11-26 16:32:15 UTC (rev 2407)
@@ -36,7 +36,7 @@
 
 \title{\textls[20]{User Guide for JSBML}}
 
-\version{1.0 \\[0.5em]{\normalsize Document version: 24 October 2014}}
+\version{1.1 \\[0.5em]{\normalsize Document version: 01 December 2015}}
 
 \newcommand{\where}[1]{\,\textsuperscript{#1}}
 \newcommand{\divider}[1]{\multicolumn{3}{c}{\emph{#1}:}}
@@ -102,7 +102,7 @@
 Before you can use JSBML, you will need to obtain a copy of the library.
 \sec{sec:obtaining-jsbml} below describes different ways of doing
 this, and explains which additional libraries you may need. JSBML also
-requires the use of a Java Runtime Environment (JRE) version~1.5 or
+requires the use of a Java Runtime Environment (JRE) version~1.6 or
 later~\cite{JavaDownloadURL}. \index{Java Runtime Environment (JRE)} In the
 rest of this document, we assume that you have already installed a suitable
 JRE or Java Development Kit (JDK), and know how to configure the Java class

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[Jsbml-svn] SF.net SVN: jsbml:[2407] trunk/core/doc

The Java library for working with the SBML format.

[Jsbml-svn] SF.net SVN: jsbml:[2407] trunk/core/doc