[Jsbml-svn] SF.net SVN: jsbml:[2272] branches/astnode2-merging-alternate

[<nik...@us...>]

Revision: 2272
          http://sourceforge.net/p/jsbml/code/2272
Author:   niko-rodrigue
Date:     2015-05-01 10:16:48 +0000 (Fri, 01 May 2015)
Log Message:
-----------
merged from trunk until rev 2254

Revision Links:
--------------
    http://sourceforge.net/p/jsbml/code/2254

Modified Paths:
--------------
    branches/astnode2-merging-alternate/build.xml
    branches/astnode2-merging-alternate/core/build.xml
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java

Added Paths:
-----------
    branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml

Removed Paths:
-------------
    branches/astnode2-merging-alternate/core/resources/META-INF/

Property Changed:
----------------
    branches/astnode2-merging-alternate/

Index: branches/astnode2-merging-alternate
===================================================================
--- branches/astnode2-merging-alternate	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate	2015-05-01 10:16:48 UTC (rev 2272)

Property changes on: branches/astnode2-merging-alternate
___________________________________________________________________
Modified: svn:mergeinfo
## -1 +1 ##
-/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2232
+/trunk:2191,2194-2195,2197-2200,2202-2206,2209-2213,2216-2220,2222,2224-2244,2246-2248,2251-2254
\ No newline at end of property
Modified: branches/astnode2-merging-alternate/build.xml
===================================================================
--- branches/astnode2-merging-alternate/build.xml	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/build.xml	2015-05-01 10:16:48 UTC (rev 2272)
@@ -247,6 +247,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 
 		</jar>
@@ -316,6 +317,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 		</jar>
 	</target>

Modified: branches/astnode2-merging-alternate/core/build.xml
===================================================================
--- branches/astnode2-merging-alternate/core/build.xml	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/build.xml	2015-05-01 10:16:48 UTC (rev 2272)
@@ -368,6 +368,7 @@
 				<provider classname="org.sbml.jsbml.xml.parsers.RenderParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.ReqParser" />
 				<provider classname="org.sbml.jsbml.xml.parsers.SpatialParser" />
+				<provider classname="org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader" />
 			</service>
 		</jar>
 	</target>

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/ParserManager.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -21,8 +21,10 @@
  */
 package org.sbml.jsbml.xml.parsers;
 
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Map;
 import java.util.ServiceConfigurationError;
 import java.util.ServiceLoader;
@@ -66,6 +68,15 @@
    */
   private Logger logger = Logger.getLogger(ParserManager.class);
 
+  private String[] parserDefaults = 
+    {"org.sbml.jsbml.xml.parsers.UncertMLXMLNodeReader", "org.sbml.jsbml.xml.parsers.SBMLCoreParser", 
+    "org.sbml.jsbml.xml.parsers.MathMLStaxParser", "org.sbml.jsbml.xml.parsers.ArraysParser", "org.sbml.jsbml.xml.parsers.CompParser",
+    "org.sbml.jsbml.xml.parsers.DistribParser", "org.sbml.jsbml.xml.parsers.DynParser", "org.sbml.jsbml.xml.parsers.FBCParser",
+    "org.sbml.jsbml.xml.parsers.GroupsParser", "org.sbml.jsbml.xml.parsers.L3LayoutParser", "org.sbml.jsbml.xml.parsers.LayoutParser",
+    "org.sbml.jsbml.xml.parsers.MultiParser", "org.sbml.jsbml.xml.parsers.QualParser", "org.sbml.jsbml.xml.parsers.RenderParser",
+    "org.sbml.jsbml.xml.parsers.ReqParser", "org.sbml.jsbml.xml.parsers.SpatialParser", "org.sbml.jsbml.xml.parsers.XMLNodeReader"};
+
+
   /**
    * Private constructor to make sure that we have only one {@link ParserManager} per JVM.
    */
@@ -91,7 +102,8 @@
   private void init() {
     // loading the ReadingParsers
     Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
-
+    List<String> classNames = new ArrayList<String>();
+    
     // TODO - each time we add one HashMap entry, check that it was not defined already
     // so that we notice problems as early as possible if two packages declared to take care of the same namespace
 
@@ -102,7 +114,8 @@
         if (readingParser != null) {
 
           String packageName = "core";
-
+          classNames.add(readingParser.getClass().getName());
+          
           if (readingParser instanceof PackageParser) {
             packageName = ((PackageParser) readingParser).getPackageName();
             packageParsers.put(packageName, (PackageParser) readingParser);
@@ -133,6 +146,7 @@
         if (writingParser != null) {
 
           String packageName = "core";
+          classNames.add(writingParser.getClass().getName());
 
           if (writingParser instanceof PackageParser) {
             packageName = ((PackageParser) writingParser).getPackageName();
@@ -149,7 +163,78 @@
 
       }
     }
+    
+    // TODO - check the maps and add the parsers by hand if they are not present.
+    // prevent problems when developers are not setting properly eclipse, when jar 
+    // files are not generated with 
+ 
+    for (String parserClassName  : parserDefaults) {
+      if (! classNames.contains(parserClassName)) {
+        
+        try {
+          Object newInstance = Class.forName(parserClassName).newInstance();
+          
+          if (newInstance instanceof ReadingParser) {
+            ReadingParser readingParser = (ReadingParser) newInstance;
+            
+            String packageName = "core";
+            
+            if (readingParser instanceof PackageParser) {
+              packageName = ((PackageParser) readingParser).getPackageName();
+              packageParsers.put(packageName, (PackageParser) readingParser);
+            }
+            for (String namespaceURI : readingParser.getNamespaces()) {
+              readingParsers.put(namespaceURI, readingParser);
+              namespaceToNameMap.put(namespaceURI, packageName);
+            }
 
+            if (readingParser instanceof WritingParser) {
+              for (String namespaceURI : readingParser.getNamespaces()) {
+                writingParsers.put(namespaceURI, (WritingParser) readingParser);
+              }
+            }
+          }
+          
+          if (newInstance instanceof WritingParser)
+          {
+            WritingParser writingParser = (WritingParser) newInstance;
+
+            String packageName = "core";
+
+            if (writingParser instanceof PackageParser) {
+              packageName = ((PackageParser) writingParser).getPackageName();
+              packageParsers.put(packageName, (PackageParser) writingParser);
+            }
+
+            for (String namespaceURI : writingParser.getNamespaces()) {
+              writingParsers.put(namespaceURI, writingParser);
+              namespaceToNameMap.put(namespaceURI, packageName);
+            }
+          }
+        } catch (ClassNotFoundException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+          }
+        }
+        catch (InstantiationException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+        catch (IllegalAccessException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+      }
+    }
+
+
   }
 
   // <br /><dependency><br />
@@ -225,6 +310,7 @@
   public Map<String, ReadingParser> getReadingParsers() {
 
     Map<String, ReadingParser> clonedMap = new HashMap<String, ReadingParser>();
+    List<String> classNames = new ArrayList<String>();
 
     Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
 
@@ -234,6 +320,8 @@
 
         if (readingParser != null) {
 
+          classNames.add(readingParser.getClass().getName());
+          
           for (String namespaceURI : readingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, readingParser);
           }
@@ -243,7 +331,44 @@
         // No need to print the message again, it is printed once in the init() method
       }
     }
+    
+    for (String parserClassName  : parserDefaults) {
+      if (! classNames.contains(parserClassName)) {
+        
+        try {
+          Object newInstance = Class.forName(parserClassName).newInstance();
+          
+          if (newInstance instanceof ReadingParser) {
+            ReadingParser readingParser = (ReadingParser) newInstance;
+            
+            for (String namespaceURI : readingParser.getNamespaces()) {
+              clonedMap.put(namespaceURI, readingParser);
+            }
+          }
+        } catch (ClassNotFoundException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+          }
+        }
+        catch (InstantiationException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+        catch (IllegalAccessException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+      }
+    }
 
+
     return clonedMap;
   }
 
@@ -255,6 +380,7 @@
   public Map<String, WritingParser> getWritingParsers() {
 
     Map<String, WritingParser> clonedMap = new HashMap<String, WritingParser>();
+    List<String> classNames = new ArrayList<String>();
 
     Iterator<ReadingParser> readingParserList = ServiceLoader.load(ReadingParser.class).iterator();
 
@@ -264,6 +390,8 @@
 
         if (readingParser != null && readingParser instanceof WritingParser) {
 
+          classNames.add(readingParser.getClass().getName());
+
           for (String namespaceURI : readingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, (WritingParser) readingParser);
           }
@@ -282,6 +410,8 @@
 
         if (writingParser != null) {
 
+          classNames.add(writingParser.getClass().getName());
+
           for (String namespaceURI : writingParser.getNamespaces()) {
             clonedMap.put(namespaceURI, writingParser);
           }
@@ -292,6 +422,41 @@
       }
     }
 
+    for (String parserClassName  : parserDefaults) {
+      if (! classNames.contains(parserClassName)) {
+        
+        try {
+          Object newInstance = Class.forName(parserClassName).newInstance();
+          
+          if (newInstance instanceof WritingParser) {
+            WritingParser readingParser = (WritingParser) newInstance;
+            
+            for (String namespaceURI : readingParser.getNamespaces()) {
+              clonedMap.put(namespaceURI, readingParser);
+            }
+          }
+        } catch (ClassNotFoundException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+          }
+        }
+        catch (InstantiationException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+        catch (IllegalAccessException e) 
+        {
+          if (logger.isDebugEnabled()) {
+            logger.debug("problem loading class '" + parserClassName + "': " + e.getMessage());
+            e.printStackTrace();
+          }
+        }
+      }
+    }
 
     return clonedMap;
   }

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/parsers/SBMLCoreParser.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -1249,8 +1249,7 @@
   @Override
   public void writeCharacters(SBMLObjectForXML xmlObject,
     Object sbmlElementToWrite) {
-    // The method should never be called !
-    log4jLogger.warn("The SBML core XML element should not have any content, everything should be stored as attribute.");
+    // The SBML core XML element should not have any content, everything should be stored as attribute.
   }
 
   /* (non-Javadoc)

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLReader.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -695,7 +695,7 @@
         if (!characters.isWhiteSpace()) {
           isText = true; // the characters are not only 'white spaces'
         }
-        if ((sbmlElements.peek() instanceof XMLNode) || isInsideNotes || isInsideAnnotation) {
+        if ((!sbmlElements.isEmpty() && (sbmlElements.peek() instanceof XMLNode)) || isInsideNotes || isInsideAnnotation) {
           isText = true; // We want to keep the whitespace/formatting when reading html block
         }
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/xml/stax/SBMLWriter.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -1025,6 +1025,7 @@
         childParser.writeElement(childXmlObject, nextObjectToWrite);
         childParser.writeNamespaces(childXmlObject, nextObjectToWrite);
         childParser.writeAttributes(childXmlObject, nextObjectToWrite);
+        childParser.writeCharacters(childXmlObject, nextObjectToWrite);
 
         if (!childXmlObject.isSetName()) {
           logger.error("XML name not set, element ignored!");
@@ -1062,6 +1063,11 @@
             indent + indentCount, false);
           elementIsNested = isClosedAnnotation = true;
         }
+        
+        if (childXmlObject.getCharacters() != null && childXmlObject.getCharacters().trim().length() != 0) {
+          newOutPutElement.addCharacters(childXmlObject.getCharacters());
+        }
+        
         if (s.getChildCount() > 0) {
           // make sure that we'll have line breaks if an element has any sub elements.
           elementIsNested = true;

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -231,7 +231,7 @@
 
   @Override
   public boolean readAttribute(String attributeName, String prefix, String value) {
-    boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value)) && (SpatialConstants.shortLabel == prefix);
+    boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
     if (!isAttributeRead) {
       isAttributeRead = true;
       if (attributeName.equals(SpatialConstants.spatialId)) {

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/BoundaryCondition.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -329,6 +329,7 @@
     if (!isAttributeRead) {
       isAttributeRead = true;
       if (attributeName.equals(SpatialConstants.type)) {
+        // TODO: In the specs v0.90, the type name begins with capital letter.
         if (!Pattern.matches("[a-z]*", value)) {
           throw new SBMLException("The value is not all lower-case.");
         }

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CompartmentMapping.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -269,8 +269,7 @@
 
   @Override
   public boolean readAttribute(String attributeName, String prefix, String value) {
-    boolean isAttributeRead = (super.readAttribute(attributeName, prefix, value))
-        && (SpatialConstants.shortLabel == prefix);
+    boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
     if (!isAttributeRead) {
       isAttributeRead = true;
       if (attributeName.equals(SpatialConstants.domainType)) {

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -23,8 +23,10 @@
 
 import java.text.MessageFormat;
 import java.util.Map;
+import java.util.regex.Pattern;
 
 import org.sbml.jsbml.AbstractSBase;
+import org.sbml.jsbml.SBMLException;
 
 
 
@@ -111,6 +113,15 @@
     return coordinate != null;
   }
 
+  /**
+   * @param coordinate
+   */
+  public void setCoordinate(String coordinate) {
+    if (!Pattern.matches("[a-z]*", coordinate)) {
+      throw new SBMLException("The value is not all lower-case.");
+    }
+    setCoordinate(CoordinateKind.valueOf(coordinate.toUpperCase()));
+  }
 
   /**
    * @param coordinate the coordinate to set
@@ -151,7 +162,7 @@
       isAttributeRead = true;
       if (attributeName.equals(SpatialConstants.coordinate)) {
         try {
-          setCoordinate(CoordinateKind.valueOf(value));
+          setCoordinate(value);          
         } catch (Exception e) {
           MessageFormat.format(
             SpatialConstants.bundle.getString("COULD_NOT_READ"), value,

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricObject.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -52,6 +52,10 @@
   /**
    * 
    */
+  private String pointIndex;  
+  /**
+   * 
+   */
   private Integer pointIndexLength;
   /**
    * 
@@ -85,6 +89,9 @@
     if (po.isSetCompression()) {
       setCompression(po.getCompression());
     }
+    if (po.isSetPointIndex()) {
+      setPointIndex(po.getPointIndex());
+    }    
     if (po.isSetPointIndexLength()) {
       setPointIndexLength(po.getPointIndexLength());
     }
@@ -138,6 +145,10 @@
       if (equal && isSetCompression()) {
         equal &= po.getCompression().equals(getCompression());
       }
+      equal &= po.isSetPointIndex() == isSetPointIndex();
+      if (equal && isSetPointIndex()) {
+        equal &= po.getPointIndex() == getPointIndex();
+      }
       equal &= po.isSetPointIndexLength() == isSetPointIndexLength();
       if (equal && isSetPointIndexLength()) {
         equal &= po.getPointIndexLength() == getPointIndexLength();
@@ -323,13 +334,81 @@
   
   
   /**
+   * Returns the value of {@link #pointIndex}.
+   *
+   * @return the value of {@link #pointIndex}.
+   */
+  public String getPointIndex() {
+    if (isSetPointIndex()) {
+      return pointIndex;
+    }
+    // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+    throw new PropertyUndefinedError(SpatialConstants.pointIndex, this);
+  }
+
+
+  /**
+   * Returns whether {@link #pointIndex} is set.
+   *
+   * @return whether {@link #pointIndex} is set.
+   */
+  public boolean isSetPointIndex() {
+    return this.pointIndex != null;
+  }
+
+
+  /**
+   * Sets the value of pointIndex
+   *
+   * @param pointIndex the value of pointIndex to be set.
+   */
+  public void setPointIndex(String pointIndex) {
+    String oldPointIndex = this.pointIndex;
+    this.pointIndex = pointIndex;
+    firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+  }
+
+
+  /**
+   * Unsets the variable pointIndex.
+   *
+   * @return {@code true} if pointIndex was set before, otherwise {@code false}.
+   */
+  public boolean unsetPointIndex() {
+    if (isSetPointIndex()) {
+      String oldPointIndex = this.pointIndex;
+      this.pointIndex = null;
+      this.pointIndexLength = null;
+      firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+      return true;
+    }
+    return false;
+  }
+  
+  /**
+   * Appends the variable data to pointIndex.
+   * @return {@code true} if data was appended to pointIndex, otherwise {@code false}.
+   */
+  public boolean append(String data) {
+    if (data == null) { return false; }
+    if (isSetPointIndex()) {
+      String oldPointIndex = this.pointIndex;
+      this.pointIndex = this.pointIndex + data;
+      firePropertyChange(SpatialConstants.pointIndex, oldPointIndex, this.pointIndex);
+    } else {
+      setPointIndex(data);
+    }
+    return true;
+  }
+  
+  /**
    * Returns the value of pointIndexLength.
    *
    * @return the value of pointIndexLength.
    */
   public int getPointIndexLength() {
     if (isSetPointIndexLength()) {
-      return pointIndexLength.intValue();
+      return pointIndexLength;
     }
     // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
     throw new PropertyUndefinedError(SpatialConstants.pointIndexLength, this);
@@ -447,6 +526,9 @@
     if (isSetCompression()) {
       hashCode += prime * getCompression().hashCode();
     }
+    if (isSetPointIndex()) {
+      hashCode += prime * getPointIndex().hashCode();
+    }
     if (isSetPointIndexLength()) {
       hashCode += prime * getPointIndexLength();
     }
@@ -514,21 +596,21 @@
         try {
           setCompression(value);
         } catch (Exception e) {
-          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
         }
       }
       else if (attributeName.equals(SpatialConstants.pointIndexLength)) {
         try {
           setPointIndexLength(StringTools.parseSBMLInt(value));
         } catch (Exception e) {
-          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.pointIndexLength);
         }
       }
       else if (attributeName.equals(SpatialConstants.dataType)) {
         try {
           setDataType(value);
         } catch (Exception e) {
-          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+          MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
         }
       }      
       else {
@@ -551,6 +633,8 @@
     builder.append(domainType);
     builder.append(", compression=");
     builder.append(compression);
+    builder.append(", pointIndex=");
+    builder.append(pointIndex);
     builder.append(", pointIndexLength=");
     builder.append(pointIndexLength);
     builder.append(", dataType=");

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -69,6 +69,10 @@
   /**
    * 
    */
+  private String samples;
+  /**
+   * 
+   */
   private Integer samplesLength;
   /**
    * 
@@ -106,14 +110,15 @@
     if (sf.isSetCompression()) {
       setCompression(sf.getCompression());
     }
+    if (sf.isSetSamples()) {
+      setSamples(sf.getSamples());
+    }        
     if (sf.isSetSamplesLength()) {
       setSamplesLength(sf.getSamplesLength());
     }    
     if (sf.isSetInterpolation()) {
       setInterpolation(sf.getInterpolation());
     }
-
-    // TODO - data ?
   }
 
   /**
@@ -172,6 +177,10 @@
       if (equal && isSetSamplesLength()) {
         equal &= sf.getSamplesLength() == getSamplesLength();
       }      
+      equal &= sf.isSetSamples() == isSetSamples();
+      if (equal && isSetSamples()) {
+        equal &= sf.getSamples() == getSamples();
+      }
       equal &= sf.isSetDataType() == isSetDataType();
       if (equal && isSetDataType()) {
         equal &= sf.getDataType().equals(getDataType());
@@ -491,7 +500,75 @@
     return false;
   }
 
+  
+  /**
+   * Returns the value of {@link #samples}.
+   *
+   * @return the value of {@link #samples}.
+   */
+  public String getSamples() {
+    if (isSetSamples()) {
+      return samples;
+    }
+    // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+    throw new PropertyUndefinedError(SpatialConstants.samples, this);
+  }
 
+
+  /**
+   * Returns whether {@link #samples} is set.
+   *
+   * @return whether {@link #samples} is set.
+   */
+  public boolean isSetSamples() {
+    return this.samples != null;
+  }
+
+
+  /**
+   * Sets the value of samples
+   *
+   * @param samples the value of samples to be set.
+   */
+  public void setSamples(String samples) {
+    String oldSamples = this.samples;
+    this.samples = samples;
+    firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+  }
+
+
+  /**
+   * Unsets the variable samples.
+   *
+   * @return {@code true} if samples was set before, otherwise {@code false}.
+   */
+  public boolean unsetSamples() {
+    if (isSetSamples()) {
+      String oldSamples = this.samples;
+      this.samples = null;
+      this.samplesLength = null;
+      firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Appends the variable data to samples.
+   * @return {@code true} if data was appended to samples, otherwise {@code false}.
+   */
+  public boolean append(String data) {
+    if (data == null) { return false; }
+    if (isSetSamples()) {
+      String oldSamples = this.samples;
+      this.samples = this.samples + data;
+      firePropertyChange(SpatialConstants.samples, oldSamples, this.samples);
+    } else {
+      setSamples(data);
+    }
+    return true;
+  }
+  
 /**
  * Returns the value of {@link #samplesLength}.
  *
@@ -689,6 +766,10 @@
       hashCode += prime * getCompression().hashCode();
     }
     
+    if (isSetSamples()) {
+      hashCode += prime * getSamples().hashCode();
+    }
+    
     if (isSetSamplesLength()) {
       hashCode += prime * getSamplesLength();
     }
@@ -733,6 +814,11 @@
       attributes.put(SpatialConstants.shortLabel + ":interpolation",
         getInterpolation().toString());
     }
+    if (isSetSamplesLength()) {
+      attributes.remove("samplesLength");
+      attributes.put(SpatialConstants.shortLabel + ":samplesLength",
+        String.valueOf(getSamplesLength()));
+    }    
     return attributes;
   }
 
@@ -823,6 +909,8 @@
     builder.append(compression);
     builder.append(", samplesLength=");
     builder.append(samplesLength);    
+    builder.append(", samples=");
+    builder.append(samples);        
     builder.append(", data=");
     builder.append(data);
     builder.append("]");

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialConstants.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -151,7 +151,7 @@
   /**
    * 
    */
-  public static final String spatialId = "spatialId";
+  public static final String spatialId = "id";
   /**
    * 
    */
@@ -515,9 +515,19 @@
   /**
    * 
    */
+  public static final String arrayData = "arrayData";
+  
+  /**
+   * 
+   */
   public static final String arrayDataLength = "arrayDataLength";
 
   /**
+   * 
+   */
+  public static final String spatialRef = "spatialRef";
+
+  /**
    * @param level
    * @param version
    * @return

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -54,7 +54,10 @@
    * 
    */
   private DataKind dataType;
-
+  /**
+   * 
+   */
+  private String arrayData;
   
   
   
@@ -91,6 +94,9 @@
     if (sp.isSetDataType()) {
       setDataType(sp.getDataType());
     }    
+    if (sp.isSetArrayData()) {
+      setArrayData(sp.getArrayData());
+    }    
   }
 
 
@@ -111,6 +117,10 @@
       if (equal && isSetCompression()) {
         equal &= sp.getCompression().equals(getCompression());
       }
+      equal &= sp.isSetArrayData() == isSetArrayData();
+      if (equal && isSetArrayData()) {
+        equal &= sp.getArrayData() == getArrayData();
+      }      
       equal &= sp.isSetArrayDataLength() == isSetArrayDataLength();
       if (equal && isSetArrayDataLength()) {
         equal &= sp.getArrayDataLength() == getArrayDataLength();
@@ -192,13 +202,81 @@
   
   
   /**
+   * Returns the value of {@link #arrayData}.
+   *
+   * @return the value of {@link #arrayData}.
+   */
+  public String getArrayData() {
+    if (isSetArrayData()) {
+      return arrayData;
+    }
+    // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+    throw new PropertyUndefinedError(SpatialConstants.arrayData, this);
+  }
+
+
+  /**
+   * Returns whether {@link #arrayData} is set.
+   *
+   * @return whether {@link #arrayData} is set.
+   */
+  public boolean isSetArrayData() {
+    return this.arrayData != null;
+  }
+
+
+  /**
+   * Sets the value of arrayData
+   *
+   * @param arrayData the value of arrayData to be set.
+   */
+  public void setArrayData(String arrayData) {
+    String oldArrayData = this.arrayData;
+    this.arrayData = arrayData;
+    firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+  }
+
+
+  /**
+   * Unsets the variable arrayData.
+   *
+   * @return {@code true} if arrayData was set before, otherwise {@code false}.
+   */
+  public boolean unsetArrayData() {
+    if (isSetArrayData()) {
+      String oldArrayData = this.arrayData;
+      this.arrayData = null;
+      this.arrayDataLength = null;
+      firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+      return true;
+    }
+    return false;
+  }
+  
+  /**
+   * Appends the variable data to arrayData.
+   * @return {@code true} if data was appended to arrayData, otherwise {@code false}.
+   */
+  public boolean append(String data) {
+    if (data == null) { return false; }
+    if (isSetArrayData()) {
+      String oldArrayData = this.arrayData;
+      this.arrayData = this.arrayData + data;
+      firePropertyChange(SpatialConstants.arrayData, oldArrayData, this.arrayData);
+    } else {
+      setArrayData(data);
+    }
+    return true;
+  }
+  
+  /**
    * Returns the value of arrayDataLength.
    *
    * @return the value of arrayDataLength.
    */
   public int getArrayDataLength() {
     if (isSetArrayDataLength()) {
-      return arrayDataLength.intValue();
+      return arrayDataLength;
     }
     // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
     throw new PropertyUndefinedError(SpatialConstants.arrayDataLength, this);
@@ -313,6 +391,9 @@
     if (isSetArrayDataLength()) {
       hashCode += prime * getArrayDataLength();
     }
+    if (isSetArrayData()) {
+      hashCode += prime * getArrayData().hashCode();
+    }
     if (isSetDataType()) {
       hashCode += prime * getDataType().hashCode();
     }
@@ -350,21 +431,21 @@
       try {
         setCompression(value);
       } catch (Exception e) {
-        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.compression);
       }
     }
     else if (attributeName.equals(SpatialConstants.arrayDataLength)) {
       try {
         setArrayDataLength(StringTools.parseSBMLInt(value));
       } catch (Exception e) {
-        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.arrayDataLength);
       }
     }
     else if (attributeName.equals(SpatialConstants.dataType)) {
       try {
         setDataType(value);
       } catch (Exception e) {
-        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.polygonType);
+        MessageFormat.format(SpatialConstants.bundle.getString("COULD_NOT_READ"), value, SpatialConstants.dataType);
       }
     }      
     else {
@@ -382,6 +463,8 @@
     StringBuilder builder = new StringBuilder();
     builder.append("ParametricObject [compression=");
     builder.append(compression);
+    builder.append(", arrayData=");
+    builder.append(arrayData);    
     builder.append(", arrayDataLength=");
     builder.append(arrayDataLength);
     builder.append(", dataType=");

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSymbolReference.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -21,6 +21,10 @@
  */
 package org.sbml.jsbml.ext.spatial;
 
+import java.util.Map;
+
+import org.sbml.jsbml.PropertyUndefinedError;
+
 /**
  * @author Alex Thomas
  * @author Andreas Dr&auml;ger
@@ -37,15 +41,23 @@
   /**
    * 
    */
+  private String spatialRef;
+  
+  /**
+   * 
+   */
   public SpatialSymbolReference() {
     super();
   }
 
   /**
-   * @param classvar
+   * @param ssr
    */
-  public SpatialSymbolReference(SpatialSymbolReference classvar) {
-    super(classvar);
+  public SpatialSymbolReference(SpatialSymbolReference ssr) {
+    super(ssr);
+    if (ssr.isSetSpatialRef()) {
+      setSpatialRef(ssr.getSpatialRef());
+    }    
   }
 
   /**
@@ -71,5 +83,84 @@
   public boolean equals(Object object) {
     return super.equals(object);
   }
-
+
+  
+  /**
+   * Returns the value of {@link #spatialRef}.
+   *
+   * @return the value of {@link #spatialRef}.
+   */
+  public String getSpatialRef() {
+    //TODO: if variable is boolean, create an additional "isVar"
+    //TODO: return primitive data type if possible (e.g., int instead of Integer)
+    if (isSetSpatialRef()) {
+      return spatialRef;
+    }
+    // This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
+    throw new PropertyUndefinedError(SpatialConstants.spatialRef, this);
+  }
+
+
+  /**
+   * Returns whether {@link #spatialRef} is set.
+   *
+   * @return whether {@link #spatialRef} is set.
+   */
+  public boolean isSetSpatialRef() {
+    return this.spatialRef != null;
+  }
+
+
+  /**
+   * Sets the value of spatialRef
+   *
+   * @param spatialRef the value of spatialRef to be set.
+   */
+  public void setSpatialRef(String spatialRef) {
+    String oldSpatialRef = this.spatialRef;
+    this.spatialRef = spatialRef;
+    firePropertyChange(SpatialConstants.spatialRef, oldSpatialRef, this.spatialRef);
+  }
+
+
+  /**
+   * Unsets the variable spatialRef.
+   *
+   * @return {@code true} if spatialRef was set before, otherwise {@code false}.
+   */
+  public boolean unsetSpatialRef() {
+    if (isSetSpatialRef()) {
+      String oldSpatialRef = this.spatialRef;
+      this.spatialRef = null;
+      firePropertyChange(SpatialConstants.spatialRef, oldSpatialRef, this.spatialRef);
+      return true;
+    }
+    return false;
+  }
+  
+  
+  public Map<String, String> writeXMLAttributes() {
+    Map<String, String> attributes = super.writeXMLAttributes();
+    if (isSetSpatialRef()) {
+      attributes.remove(SpatialConstants.spatialRef);
+      attributes.put(SpatialConstants.shortLabel + ":" + SpatialConstants.spatialRef, getSpatialRef());
+    }
+    return attributes;
+  }
+
+
+  public boolean readAttribute(String attributeName, String prefix, String value) {
+    boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
+    if (!isAttributeRead) {
+      isAttributeRead = true;
+      System.out.println("SpatialSymbolReference: debug attribute name: " + attributeName);
+      if (attributeName.equals(SpatialConstants.spatialRef)) {
+        setSpatialRef(value);
+      }
+      else {
+        isAttributeRead = false;
+      }
+    }
+    return isAttributeRead;
+  }
 }

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java	2015-05-01 10:01:31 UTC (rev 2271)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/xml/parsers/SpatialParser.java	2015-05-01 10:16:48 UTC (rev 2272)
@@ -84,7 +84,7 @@
 @ProviderFor(ReadingParser.class)
 public class SpatialParser extends AbstractReaderWriter implements PackageParser {
 
-  // TODO - check that it is properly updated to the 0.88 draft specs
+  // TODO - check that it is properly updated to the 0.90 draft specs
 
   /**
    * A {@link Logger} for this class.
@@ -96,6 +96,28 @@
    */
   public static final String namespaceURIrequired = "http://www.sbml.org/sbml/level3/version1/req/version1";
 
+  
+  
+  @Override
+  public void processCharactersOf(String elementName, String characters,
+    Object contextObject) {
+    if (contextObject instanceof SpatialPoints) {
+      SpatialPoints spatialPoints = (SpatialPoints) contextObject;
+      spatialPoints.append(characters);
+    }
+    if (contextObject instanceof ParametricObject) {
+      ParametricObject parametricObject = (ParametricObject) contextObject;
+      parametricObject.append(characters);
+    }
+  }
+
+  @Override
+  public void writeCharacters(SBMLObjectForXML xmlObject,
+    Object sbmlElementToWrite) {
+    // TODO Auto-generated method stub
+    super.writeCharacters(xmlObject, sbmlElementToWrite);
+  }
+  
   /* (non-Javadoc)
    * @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getShortLabel()
    */
@@ -245,6 +267,7 @@
         param.addExtension(SpatialConstants.namespaceURI, spatialParam);
       }
 
+      // TODO: CHECK create method. this might be the source of the problem.
       if (elementName.equals(SpatialConstants.spatialSymbolReference)) {
         SpatialSymbolReference ssr = new SpatialSymbolReference();
         spatialParam.setParamType(ssr);
@@ -314,14 +337,15 @@
         //        sfg.setSampledField(sf);
         //        return sf;
       }
-    } else if (contextObject instanceof SampledField) {
+      // NOTE: This has been moved in the listOf section below.
+//    } else if (contextObject instanceof SampledField) {
       //      SampledField sf = (SampledField) contextObject; // No more child in 0.88
       //      if (elementName.equals(SpatialConstants.imageData)){
       //        ImageData im = new ImageData();
       //        sf.setImageData(im);
       //        // sf.set
       //        return im;
-      //      }
+      //      } 
     } else if (contextObject instanceof CSGeometry) {
       CSGeometry csg = (CSGeometry) contextObject;
       if (elementName.equals(SpatialConstants.listOfCSGObjects)){
@@ -379,24 +403,14 @@
     } else if (contextObject instanceof ParametricGeometry) {
       ParametricGeometry pg = (ParametricGeometry) contextObject;
       if (elementName.equals(SpatialConstants.spatialPoints)){
-        SpatialPoints spatialPoints = pg.getSpatialPoints();
-        return spatialPoints;
+        SpatialPoints sp = new SpatialPoints();
+        pg.setSpatialPoints(sp);
+        return sp;
       } else if (elementName.equals(SpatialConstants.listOfParametricObjects)){
         ListOf<ParametricObject> listOfParametricObjects = pg.getListOfParametricObjects();
         return listOfParametricObjects;
       }
-    } else if (contextObject instanceof ParametricObject) {
-      ParametricObject po = (ParametricObject) contextObject;
-      if (elementName.equals(SpatialConstants.imageData)){
-        // TODO: THIS NEEDS to be updated with the details provided in the spatial package v0.90,
-        // See ArrayData text child and PointIndex text child
-        //PolygonObject polygonObject = new PolygonObject();
-        //po.setPolygonObject(polygonObject);
-        //return polygonObject;
-      }
-    }
-
-    else if (contextObject instanceof ListOf<?>) {
+    } else if (contextObject instanceof ListOf<?>) {
       ListOf<SBase> listOf = (ListOf<SBase>) contextObject;
 
       if (elementName.equals(SpatialConstants.coordinateComponent)) {
@@ -459,6 +473,11 @@
         SampledVolume elem = new SampledVolume();
         sfg.addSampledVolume(elem);
         return elem;
+      } else if (elementName.equals(SpatialConstants.sampledField)) {
+        Geometry g = (Geometry) listOf.getParentSBMLObject();
+        SampledField elem = new SampledField();
+        g.addSampledField(elem);
+        return elem;        
       } else if (elementName.equals(SpatialConstants.csgPrimitive)) {
         CSGSetOperator csgso = (CSGSetOperator) listOf.getParentSBMLObject();
         CSGPrimitive elem = new CSGPrimitive();

Copied: branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml (from rev 2240, trunk/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml)
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml	                        (rev 0)
+++ branches/astnode2-merging-alternate/extensions/spatial/test/org/sbml/jsbml/xml/test/data/spatial/sampled_field.xml	2015-05-01 10:16:48 UTC (rev 2272)
@@ -0,0 +1,311 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:req="http://www.sbml.org/sbml/level3/version1/req/version1" xmlns:spatial="http://www.sbml.org/sbml/level3/version1/spatial/version1" level="3" version="1" req:required="true" spatial:required="true">
+  <model>
+      <listOfUnitDefinitions>
+          <unitDefinition id="substance">
+              <listOfUnits>
+                  <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="volume">
+              <listOfUnits>
+                  <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="area">
+              <listOfUnits>
+                  <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="molecules">
+              <listOfUnits>
+                  <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="umol_um3_litre_1">
+              <listOfUnits>
+                  <unit kind="mole" exponent="1" scale="0" multiplier="1e-21"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="um3">
+              <listOfUnits>
+                  <unit kind="metre" exponent="3" scale="0" multiplier="1e-06"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="um2">
+              <listOfUnits>
+                  <unit kind="metre" exponent="2" scale="0" multiplier="1e-06"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="uM_um3_molecules_1">
+              <listOfUnits>
+                  <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-21"/>
+                  <unit kind="item" exponent="-1" scale="0" multiplier="1"/>
+                  <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="molecules_um_2_s_1">
+              <listOfUnits>
+                  <unit kind="dimensionless" exponent="1" scale="0" multiplier="1000000000000"/>
+                  <unit kind="item" exponent="1" scale="0" multiplier="1"/>
+                  <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+                  <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="pA_um_2">
+              <listOfUnits>
+                  <unit kind="dimensionless" exponent="1" scale="0" multiplier="1"/>
+                  <unit kind="ampere" exponent="1" scale="0" multiplier="1"/>
+                  <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+          <unitDefinition id="uM_um_s_1">
+              <listOfUnits>
+                  <unit kind="dimensionless" exponent="1" scale="0" multiplier="1e-09"/>
+                  <unit kind="metre" exponent="-2" scale="0" multiplier="1"/>
+                  <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+                  <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+              </listOfUnits>
+          </unitDefinition>
+      </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="Extracellular" name="Extracellular" spatialDimensions="3" constant="true">
+        <spatial:compartmentMapping spatial:id="ExtracellularExtracellular" spatial:domainType="Extracellular" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Cytosol_Extracellular_membrane" name="Cytosol_Extracellular_membrane" spatialDimensions="2" constant="true">
+        <spatial:compartmentMapping spatial:id="Cytosol_Extracellular_membraneCytosol_Extracellular_membrane" spatial:domainType="Cytosol_Extracellular_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Cytosol" name="Cytosol" spatialDimensions="3" constant="true">
+        <spatial:compartmentMapping spatial:id="CytosolCytosol" spatial:domainType="Cytosol" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Nucleus_Cytosol_membrane" name="Nucleus_Cytosol_membrane" spatialDimensions="2" constant="true">
+        <spatial:compartmentMapping spatial:id="Nucleus_Cytosol_membraneNucleus_Cytosol_membrane" spatial:domainType="Nucleus_Cytosol_membrane" spatial:unitSize="1"/>
+      </compartment>
+      <compartment id="Nucleus" name="Nucleus" spatialDimensions="3" constant="true">
+        <spatial:compartmentMapping spatial:id="NucleusNucleus" spatial:domainType="Nucleus" spatial:unitSize="1"/>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+        <species id="s1_nuc" compartment="Nucleus" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+            <annotation>
+                <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+                    <vcell:VCMLSpecific>
+                        <vcell:Compound Name="s1_2"/>
+                    </vcell:VCMLSpecific>
+                </vcell:VCellInfo>
+            </annotation>
+            <req:listOfChangedMaths>
+                <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+            </req:listOfChangedMaths>
+            <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+        </species>
+        <species id="s1_cyt" compartment="Cytosol" initialConcentration="10" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+            <annotation>
+                <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+                    <vcell:VCMLSpecific>
+                        <vcell:Compound Name="s1_2"/>
+                    </vcell:VCMLSpecific>
+                </vcell:VCellInfo>
+            </annotation>
+            <req:listOfChangedMaths>
+                <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+            </req:listOfChangedMaths>
+            <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+        </species>
+        <species id="s2_nuc" compartment="Nucleus" initialConcentration="5" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+            <annotation>
+                <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+                    <vcell:VCMLSpecific>
+                        <vcell:Compound Name="s2_2"/>
+                    </vcell:VCMLSpecific>
+                </vcell:VCellInfo>
+            </annotation>
+            <req:listOfChangedMaths>
+                <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+            </req:listOfChangedMaths>
+            <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+        </species>
+        <species id="s1_EC" compartment="Extracellular" initialConcentration="0" substanceUnits="molecules" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" spatial:isSpatial="true">
+            <annotation>
+                <vcell:VCellInfo xmlns:vcell="http://sourceforge.net/projects/vcell">
+                    <vcell:VCMLSpecific>
+                        <vcell:Compound Name="s1_2"/>
+                    </vcell:VCMLSpecific>
+                </vcell:VCellInfo>
+            </annotation>
+            <req:listOfChangedMaths>
+                <req:changedMath req:changedBy="spatial" req:viableWithoutChange="true"/>
+            </req:listOfChangedMaths>
+            <spatial:spatialSymbolReference spatial:spatialRef="spatial"/>
+        </species>
+    </listOfSpecies>
+    <listOfParameters>
+        <parameter id="x" value="0">
+            <spatial:spatialSymbolReference spatial:id="x"/>
+        </parameter>
+        <parameter id="y" value="0">
+            <spatial:spatialSymbolReference spatial:id="y"/>
+        </parameter>
+        <parameter id="s1_nuc_diff" value="10" constant="true">
+            <spatial:diffusionCoefficient spatial:variable="s1_nuc" spatial:type="isotropic"/>
+            <spatial:listOfCoordinateReferences>
+                <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+                <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+            </spatial:listOfCoordinateReferences>
+        </parameter>
+        <parameter id="s1_nuc_BC_Xm" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+        </parameter>
+        <parameter id="s1_nuc_BC_Xp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+        </parameter>
+        <parameter id="s1_nuc_BC_Ym" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+        </parameter>
+        <parameter id="s1_nuc_BC_Yp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_nuc" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Nucleus"/>
+        </parameter>
+        <parameter id="s1_cyt_diff" value="10" constant="true">
+            <spatial:diffusionCoefficient spatial:variable="s1_cyt" spatial:type="isotropic"/>
+            <spatial:listOfCoordinateReferences>
+                <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+                <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+            </spatial:listOfCoordinateReferences>
+        </parameter>
+        <parameter id="s1_cyt_BC_Xm" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+        </parameter>
+        <parameter id="s1_cyt_BC_Xp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+        </parameter>
+        <parameter id="s1_cyt_BC_Ym" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Cytosol"/>
+        </parameter>
+        <parameter id="s1_cyt_BC_Yp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_cyt" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet"/>
+        </parameter>
+        <parameter id="s1_EC_diff" value="10" constant="true">
+            <spatial:diffusionCoefficient spatial:variable="s1_EC" spatial:type="isotropic"/>
+            <spatial:listOfCoordinateReferences>
+                <spatial:coordinateReference spatial:coordinate="cartesianX"/>
+                <spatial:coordinateReference spatial:coordinate="cartesianY"/>
+            </spatial:listOfCoordinateReferences>
+        </parameter>
+        <parameter id="s1_EC_BC_Xm" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+        </parameter>
+        <parameter id="s1_EC_BC_Xp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Xmax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+        </parameter>
+        <parameter id="s1_EC_BC_Ym" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymin" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+        </parameter>
+        <parameter id="s1_EC_BC_Yp" value="0" constant="true">
+            <spatial:boundaryCondition spatial:variable="s1_EC" spatial:coordinateBoundary="Ymax" spatial:type="Dirichlet" spatial:boundaryDomainType="Extracellular"/>
+        </parameter>
+        <parameter id="KMOLE" value="0.00166112956810631" units="uM_um3_molecules_1" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+        <reaction id="flux1" name="flux1" reversible="true" fast="false" spatial:isLocal="true">
+            <listOfReactants>
+                <speciesReference species="s1_cyt" stoichiometry="1"/>
+            </listOfReactants>
+            <listOfProducts>
+                <speciesReference species="s1_nuc" stoichiometry="1"/>
+    ...
 
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