made changes for preparations to push to master; still need to finish...

made changes for preparations to push to master; still need to finish documentation changes and line length changes

CMakeLists.txt

@@ -225,6 +225,7 @@ if(NOT XDMF_BUILD_CORE_ONLY)
     XdmfAttributeType
     XdmfCurvilinearGrid
     XdmfDomain
+    XdmfFunction
     XdmfGeometry
     XdmfGeometryType
     XdmfGraph

XdmfAttribute.hpp

@@ -53,12 +53,14 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline New
+   * @skipline //#initialization
+   * @until //#initialization
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline New
+   * @skipline #//initialization
+   * @until #//initialization
    *
    * @return constructed XdmfAttribute.
    */
@@ -77,14 +79,22 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline Assuming
-   * @skipline getCenter
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setCenter
+   * @until //#setCenter
+   * @skipline //#getCenter
+   * @until //#getCenter
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline Assuming
-   * @skipline getCenter
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setCenter
+   * @until #//setCenter
+   * @skipline #//getCenter
+   * @until #//getCenter
    *
    * @return XdmfAttributeCenter of the attribute.
    */
@@ -102,14 +112,22 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline Assuming
-   * @skipline getName
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setName
+   * @until //#setName
+   * @skipline //#getName
+   * @until //#getName
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline Assuming
-   * @skipline getName
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setName
+   * @until #//setName
+   * @skipline #//getName
+   * @until #//getName
    *
    * @return a string containing the name of the attribute.
    */
@@ -123,14 +141,22 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline Assuming
-   * @skipline getType
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setType
+   * @until //#setType
+   * @skipline //#getType
+   * @until //#getType
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline Assuming
-   * @skipline getType
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setType
+   * @until #//setType
+   * @skipline #//getType
+   * @until #//getType
    *
    * @return XdmfAttributeType of the attribute.
    */
@@ -144,14 +170,18 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline New
-   * @skipline setCenter
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setCenter
+   * @until //#setCenter
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline New
-   * @skipline setCenter
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setCenter
+   * @until #//setCenter
    *
    * @param center the XdmfAttributeCenter to set.
    */
@@ -165,16 +195,18 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline New
-   * @skipline newName
-   * @skipline setName
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setName
+   * @until //#setName
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline New
-   * @skipline newName
-   * @skipline setName
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setName
+   * @until #//setName
    *
    * @param name a string containing the name to set.
    */
@@ -188,14 +220,18 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfAttribute.cpp
-   * @skipline New
-   * @skipline setType
+   * @skipline //#initialization
+   * @until //#initialization
+   * @skipline //#setType
+   * @until //#setType
    *
    * Python
    *
    * @dontinclude XdmfExampleAttribute.py
-   * @skipline New
-   * @skipline setType
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//setType
+   * @until #//setType
    *
    * @param type XdmfAttributeType to set.
    */

XdmfAttributeCenter.hpp

@@ -42,14 +42,22 @@
  * C++
  *
  * @dontinclude ExampleXdmfAttribute.cpp
- * @skipline exampleCenter
- * @until }
+ * @skipline //#initialization
+ * @until //#initialization
+ * @skipline //#setCenter
+ * @until //#setCenter
+ * @skipline //#getCenter
+ * @until //#getCenter
  *
  * Python
  *
  * @dontinclude XdmfExampleAttribute.py
- * @skipline exampleCenter
- * @until do
+ * @skipline #//initialization
+ * @until #//initialization
+ * @skipline #//setCenter
+ * @until #//setCenter
+ * @skipline #//getCenter
+ * @until #//getCenter
  *
  *   Grid
  *   Cell

XdmfAttributeType.hpp

@@ -42,14 +42,22 @@
  * C++
  *
  * @dontinclude ExampleXdmfAttribute.cpp
- * @skipline exampleType
- * @until }
+ * @skipline //#initialization
+ * @until //#initialization
+ * @skipline //#setType
+ * @until //#setType
+ * @skipline //#getType
+ * @until //#getType
  *
  * Python
  *
  * @dontinclude XdmfExampleAttribute.py
- * @skipline exampleType
- * @until do
+ * @skipline #//initialization
+ * @until #//initialization
+ * @skipline #//setType
+ * @until #//setType
+ * @skipline #//getType
+ * @until #//getType
  *
  * Xdmf supports the following attribute types:
  *   NoAttributeType

XdmfCurvilinearGrid.cpp

@@ -182,7 +182,7 @@ public:
   private:
 
     XdmfTopologyTypeCurvilinear(const XdmfCurvilinearGrid * const curvilinearGrid) :
-      XdmfTopologyType(0, 0, 0, "foo", XdmfTopologyType::Structured, 0x1110),
+      XdmfTopologyType(0, 0, std::vector<shared_ptr<const XdmfTopologyType> >(), 0, "foo", XdmfTopologyType::Structured, 0x1110),
       mCurvilinearGrid(curvilinearGrid)
     {
     }

XdmfCurvilinearGrid.hpp

@@ -54,15 +54,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline newPointsX
-   * @until New
+   * @skipline //#initializationdim2
+   * @until //#initializationdim2
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline newPointsX
-   * @until newPointsY
-   * @skipline newPointsX
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructor2
+   * @until #//constructor2
    *
    * @param xNumPoints the number of points in the x direction.
    * @param yNumPoints the number of points in the y direction.
@@ -81,16 +82,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skip 3
-   * @skipline newPointsX
-   * @until New
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline newPointsX
-   * @until newPointsZ
-   * @skipline newPointsZ
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructor3
+   * @until #//constructor3
    *
    * @param xNumPoints the number of points in the x direction.
    * @param yNumPoints the number of points in the y direction.
@@ -111,15 +112,16 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skip via
-   * @skipline newPoints
-   * @until XdmfCurvilinearGrid
+   * @skipline //#initializationvector
+   * @until //#initializationvector
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline newPoints
-   * @until exampleGrid
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructorvector
+   * @until #//constructorvector
    *
    * @param numPoints the number of points in each direction.
    *
@@ -142,14 +144,24 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline Assuming
-   * @skipline getDimensions
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
+   * @skipline //#setDimensions
+   * @until //#setDimensions
+   * @skipline //#getDimensions
+   * @until //#getDimensions
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline Assuming
-   * @skipline getDimensions
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructorvector
+   * @until #//constructorvector
+   * @skipline #//setDimensions
+   * @until #//setDimensions
+   * @skipline #//getDimensions
+   * @until #//getDimensions
    *
    * @return XdmfArray containing dimensions of this grid.
    */
@@ -164,8 +176,12 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline Assuming
-   * @skipline const
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
+   * @skipline //#setDimensions
+   * @until //#setDimensions
+   * @skipline //#getDimensionsconst
+   * @until //#getDimensionsconst
    *
    * Python: Python doesn't have a constant version
    *
@@ -181,14 +197,24 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline Assuming
-   * @skipline getGeometry
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
+   * @skipline //#setGeometry
+   * @until //#setGeometry
+   * @skipline //#getGeometry
+   * @until //#getGeometry
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline Assuming
-   * @skipline getGeometry
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructorvector
+   * @until #//constructorvector
+   * @skipline #//setGeometry
+   * @until #//setGeometry
+   * @skipline #//getGeometry
+   * @until #//getGeometry
    *
    * @return the geometry associated with this grid.
    */
@@ -203,18 +229,20 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline Assuming
-   * @skipline XdmfArray::New
-   * @until setDimensions
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
+   * @skipline //#setDimensions
+   * @until //#setDimensions
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skipline Assuming
-   * @skip setDimensions
-   * @skipline newPoints
-   * @until setDimensions
-   * Assuming that exampleGrid is a sharedPointer to an XdmfCurvilinearGrid object
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructorvector
+   * @until #//constructorvector
+   * @skipline #//setDimensions
+   * @until #//setDimensions
    *
    * @param dimensions the dimension of the grid.
    */
@@ -228,17 +256,20 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfCurvilinearGrid.cpp
-   * @skipline newData
-   * @until setGeometry
+   * @skipline //#initializationdim3
+   * @until //#initializationdim3
+   * @skipline //#setGeometry
+   * @until //#setGeometry
    *
    * Python
    *
    * @dontinclude XdmfExampleCurvilinearGrid.py
-   * @skip setGeometry
-   * @skipline newPoints
-   * @until insert
-   * Assuming that exampleGrid is a sharedPointer to an XdmfCurvilinearGrid object
-   * @skipline setGeometry
+   * @skipline #//initialization
+   * @until #//initialization
+   * @skipline #//constructorvector
+   * @until #//constructorvector
+   * @skipline #//setGeometry
+   * @until #//setGeometry
    *
    * @param geometry an XdmfGeometry to associate with this grid.
    */

XdmfDomain.hpp

@@ -55,12 +55,14 @@ public:
    * C++
    *
    * @dontinclude ExampleXdmfDomain.cpp
-   * @skipline New
+   * @skipline //#initialization
+   * @until //#initialization
    *
    * Python
    *
    * @dontinclude XdmfExampleDomain.py
-   * @skipline New
+   * @skipline #//initialization
+   * @until #//initialization
    *
    * @return constructed XdmfDomain.
    */

XdmfFunction.hpp

+/*****************************************************************************/
+/*                                    XDMF                                   */
+/*                       eXtensible Data Model and Format                    */
+/*                                                                           */
+/*  Id : XdmfFunction.hpp                                                    */
+/*                                                                           */
+/*  Author:                                                                  */
+/*     Kenneth Leiter                                                        */
+/*     kenneth.leiter@arl.army.mil                                           */
+/*     US Army Research Laboratory                                           */
+/*     Aberdeen Proving Ground, MD                                           */
+/*                                                                           */
+/*     Copyright @ 2011 US Army Research Laboratory                          */
+/*     All Rights Reserved                                                   */
+/*     See Copyright.txt for details                                         */
+/*                                                                           */
+/*     This software is distributed WITHOUT ANY WARRANTY; without            */
+/*     even the implied warranty of MERCHANTABILITY or FITNESS               */
+/*     FOR A PARTICULAR PURPOSE.  See the above copyright notice             */
+/*     for more information.                                                 */
+/*                                                                           */
+/*****************************************************************************/
+
+#ifndef XDMFFUNCTION_HPP_
+#define XDMFFUNCTION_HPP_
+
+// Includes
+#include "Xdmf.hpp"
+#include "XdmfArray.hpp"
+
+/**
+ * @brief 
+ *
+ * 
+ */
+class XDMF_EXPORT XdmfFunction : public XdmfItem {
+
+public:
+
+  /**
+   * Create a new XdmfFunction
+   *
+   * @return constructed XdmfFunction.
+   */
+  static shared_ptr<XdmfFunction> New();
+
+  virtual ~XdmfFunction();
+
+  LOKI_DEFINE_VISITABLE(XdmfFunction, XdmfItem);
+
+  static const std::string ItemTag;
+
+  /**
+   * Adds an operation to the list of viable operators.
+   *
+   * Example of Use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfArray.cpp
+   * @dontinclude ExampleXdmfArray.cpp
+   * @skipline //#declareoperation
+   * @until //#declareoperation
+   * @skipline //#programstart
+   * @until //#programstart
+   * @skipline //#addOperation
+   * @until //#addOperation
+   * @skipline //#programend
+   * @until //#programend
+   * @skipline //#defineoperation
+   * @until //#defineoperation
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleArray.py
+   * @skipline #//defineoperation
+   * @until #//defineoperation
+   * @skipline #//programstart
+   * @until #//programstart
+   * @skipline #//addOperation
+   * @until #//addOperation
+   *
+   * @param     newoperator     the character to be associated with the provided binary operation
+   * @param     functionref     a pointer to the function to be associated with the provided operator
+   * @param     priority        used to determine order of operations the higher the value the earlier it is evaluated
+   */
+  static int addOperation(char newoperator, shared_ptr<XdmfArray>(*functionref)(shared_ptr<XdmfArray>, shared_ptr<XdmfArray>), int priority);
+
+  /*
+   * adds a specified function to the list of functions used while evaluating strings
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfArray.cpp
+   * @skipline //#declarefunction
+   * @until //#declarefunction
+   * @skipline //#programstart
+   * @until //#programstart
+   * @skipline //#addFunction
+   * @until //#addFunction
+   * @skipline //#programend
+   * @until //#programend
+   * @skipline //#definefunction
+   * @until //#definefunction
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleArray.py
+   * @skipline #//definefunction
+   * @until #//definefunction
+   * @skipline #//programstart
+   * @until #//programstart
+   * @skipline #//addFunction
+   * @until #//addFunction
+   *
+   * @param     name            A string to be associated with the provided function during string evaluation
+   * @param     functionref     A pointer to the function to be associated with the given string
+   * @return                    The total number of functions currently associated
+   */
+  static int addFunction(std::string name, shared_ptr<XdmfArray>(*functionref)(std::vector<shared_ptr<XdmfArray> >));
+
+  /**
+   * Averages the values contained in all the provided arrays.
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfArray.cpp
+   * @skipline //#valueinit
+   * @until //#valueinit
+   * @skipline //#average
+   * @until //#average
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleArray.py
+   * @skipline #//valueinit
+   * @until #//valueinit
+   * @skipline #//average
+   * @until #//average
+   *
+   * @param     values  a vector containing the arrays to be used
+   * @return            an XdmfArray containing  one value which is the average of all values contained within the provided arrays
+   */
+  static shared_ptr<XdmfArray> average(std::vector<shared_ptr<XdmfArray> > values);
+
+  /**
+   * Joins the two provided arrays together end to end.
+   *
+   * Example of Use:
+   *
+   * C++
+   *
+   * @dontinclude ExampleXdmfArray.cpp
+   * @skipline //#valueinit
+   * @until //#valueinit
+   * @skipline //#chunk
+   * @until //#chunk
+   *
+   * Python
+   *
+   * @dontinclude XdmfExampleArray.py
+   * @skipline #//valueinit
+   * @until #//valueinit
+   * @skipline #//chunk
+   * @until #//chunk
+   *
+   * @param     val1            the first array being evaluated
+   * @param     val2            the second array being evaluated
+   * @return                    the arrays joined end to end
+   */
+  static shared_ptr<XdmfArray> chunk(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2);