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[sbml-svn] SF.net SVN: sbml:[18350] trunk/libsbml/docs/src
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From: <mh...@us...> - 2013-08-30 03:16:05
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Revision: 18350
http://sourceforge.net/p/sbml/code/18350
Author: mhucka
Date: 2013-08-30 03:16:01 +0000 (Fri, 30 Aug 2013)
Log Message:
-----------
Added more text snippets.
Modified Paths:
--------------
trunk/libsbml/docs/src/Makefile.in
Added Paths:
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trunk/libsbml/docs/src/common-text/what-are-plugins.html
trunk/libsbml/docs/src/common-text/what-is-metaid.html
trunk/libsbml/docs/src/common-text/what-is-metaidref.html
trunk/libsbml/docs/src/common-text/what-is-sidref.html
trunk/libsbml/docs/src/common-text/what-is-unitsidref.html
trunk/libsbml/docs/src/common-text/what-is-user-data.html
Modified: trunk/libsbml/docs/src/Makefile.in
===================================================================
--- trunk/libsbml/docs/src/Makefile.in 2013-08-30 03:15:01 UTC (rev 18349)
+++ trunk/libsbml/docs/src/Makefile.in 2013-08-30 03:16:01 UTC (rev 18350)
@@ -169,6 +169,12 @@
common-text/unitkind-table.txt \
common-text/warn-default-args-in-docs.html \
common-text/xmlid-syntax.html \
+ common-text/what-are-plugins.html \
+ common-text/what-is-metaid.html \
+ common-text/what-is-metaidref.html \
+ common-text/what-is-sidref.html \
+ common-text/what-is-unitsidref.html \
+ common-text/what-is-user-data.html \
csdocfilter.py \
doxygen-base-stylesheet.css \
doxygen-config-c.txt.cmake \
Added: trunk/libsbml/docs/src/common-text/what-are-plugins.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-are-plugins.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-are-plugins.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,13 @@
+SBML Level 3 consists of a <em>Core</em> definition that can be extended
+via optional SBML Level 3 <em>packages</em>. A given model may indicate
+that it uses one or more SBML packages, and likewise, a software tool may be
+able to support one or more packages. LibSBML does not come preconfigured
+with all possible packages included and enabled, in part because not all
+package specifications have been finalized. To support the ability for
+software systems to enable support for the Level 3 packages they choose,
+libSBML features a <em>plug-in</em> mechanism. Each SBML Level 3
+package is implemented in a separate code plug-in that can be enabled by the
+application to support working with that SBML package. A given SBML model
+may thus contain not only objects defined by SBML Level 3 Core, but also
+objects created by libSBML plug-ins supporting additional Level 3
+packages.
Added: trunk/libsbml/docs/src/common-text/what-is-metaid.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-metaid.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-metaid.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,16 @@
+The optional attribute named "metaid", present on every major SBML component
+type, is for supporting metadata annotations using RDF (<a
+ href="http://www.w3.org/RDF/">Resource Description Format</a>). The
+attribute value has the data type <a
+ href="http://www.w3.org/TR/REC-xml/#id">XML <code>ID</code></a>, the XML
+identifier type, which means each "metaid" value must be globally unique
+within an SBML file. The latter point is important, because the uniqueness
+criterion applies across <em>any</em> attribute with type <code>ID</code>
+anywhere in the file, not just the "metaid" attribute used by
+SBML—something to be aware of if your application-specific XML content
+inside the "annotation" subelement happens to use the XML <code>ID</code>
+type. Although SBML only uses <a href="http://www.w3.org/TR/REC-xml/#id">XML
+<code>ID</code></a> for the "metaid" attribute, callers should be careful if
+they use XML <code>ID</code>'s in XML portions of a model that are not
+defined by SBML, such as in the application-specific content of the
+"annotation" subelement.
Added: trunk/libsbml/docs/src/common-text/what-is-metaidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-metaidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-metaidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,6 @@
+In SBML, object "meta" identifiers are of the XML data type <code>ID</code>;
+the SBML object attribute itself is typically named <code>metaid</code>. All
+attributes that hold values <em>referring</em> to values of type
+<code>ID</code> are of the XML data type <code>IDREF</code>. They are also
+sometimes informally referred to as "metaid refs", in analogy to the
+SBML-defined type <code>SIdRef</code>.
Added: trunk/libsbml/docs/src/common-text/what-is-sidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-sidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-sidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,8 @@
+In SBML, object identifiers are of a type called <code>SId</code>. In SBML
+Level 3, an explicit data type called <code>SIdRef</code> was introduced
+for attribute values that refer to <code>SId</code> values; in previous
+Levels of SBML, this data type did not exist and attributes were simply
+described to as "referring to an identifier", but the effective data type was
+the same as Level 3's <code>SIdRef</code>. These and other methods of
+libSBML refer to the type <code>SIdRef</code> for all Levels of SBML, even if
+the corresponding SBML specification did not explicitly name the data type.
Added: trunk/libsbml/docs/src/common-text/what-is-unitsidref.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-unitsidref.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-unitsidref.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,9 @@
+In SBML, unit definitions have identifiers of type <code>UnitSId</code>. In
+SBML Level 3, an explicit data type called <code>UnitSIdRef</code> was
+introduced for attribute values that refer to <code>UnitSId</code> values; in
+previous Levels of SBML, this data type did not exist and attributes were
+simply described to as "referring to a unit identifier", but the effective
+data type was the same as Level 3's <code>UnitSIdRef</code>. These and
+other methods of libSBML refer to the type <code>UnitSIdRef</code> for all
+Levels of SBML, even if the corresponding SBML specification did not
+explicitly name the data type.
Added: trunk/libsbml/docs/src/common-text/what-is-user-data.html
===================================================================
--- trunk/libsbml/docs/src/common-text/what-is-user-data.html (rev 0)
+++ trunk/libsbml/docs/src/common-text/what-is-user-data.html 2013-08-30 03:16:01 UTC (rev 18350)
@@ -0,0 +1,4 @@
+The user data associated with an SBML object can be used by an application
+developer to attach custom information to that object in the model. In case
+of a deep copy, this attribute will passed as it is. The attribute will be
+never interpreted by libSBML.
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