updated formatting. Rearranged toc. Renamed index-all to reference-all.

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXAnalysis.md

@@ -31,7 +31,7 @@ If you also want to support Athena, you should extend `IPHXAthenaAnalysis` inste
 ### execute
 ```java
 void execute()
-    throws java.lang.Exception
+      throws java.lang.Exception
 ```
 Executes the analysis. If the analysis does not run successfully, e.g. the solution does not converge, then an exception should be thrown.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXComponent.md

@@ -40,7 +40,7 @@ The above functions are used by the "describe" command in ModelCenter Remote Exe
 ### end
 ```java
 void end()
-    throws java.lang.Exception
+         throws java.lang.Exception
 ```
 Notifies the driver that it has ended. The driver should perform any necessary shutdown functions.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXDriver.md

@@ -32,7 +32,7 @@ This is the interface that drivers managed by ModelCenter Remote Execution must
 ### initializeIterations
 ```java
 void initializeIterations()
-    throws java.lang.Exception
+                   throws java.lang.Exception
 ```
 Initializes the driver to a starting state. This function will be called once before a series of step() calls will be made. The function should reset things like iteration counts to initial values.
 
@@ -42,7 +42,7 @@ Initializes the driver to a starting state. This function will be called once be
 ### startIteration
 ```java
 void startIteration()
-    throws java.lang.Exception
+             throws java.lang.Exception
 ```
 Performs the first step for an iteration of a driver. The driver should set values for all output reference variables. The client application will load these values and compute new values for the input references.
 
@@ -52,7 +52,7 @@ Performs the first step for an iteration of a driver. The driver should set valu
 ### endIteration
 ```java
 boolean endIteration()
-    throws java.lang.Exception
+              throws java.lang.Exception
 ```
 Performs the second step for an iteration of a driver. Prior to calling this function, the client application will have set values for all input reference variables. The driver should use these values to determine the next iteration, if any.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXHaltableComponent.md

@@ -23,7 +23,7 @@ This is a specialized interface for ModelCenter Remote Execution. If a component
 ### halt
 ```java
 void halt()
-    throws java.lang.Exception
+   throws java.lang.Exception
 ```
 Notifies the component to stop doing whatever it is currently doing.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXMonitorable.md

@@ -28,7 +28,7 @@ This is the interface that analyses which provide information about running proc
 ### listProcesses
 ```java
 PHXProcessInfo[] listProcesses()
-    throws java.io.IOException
+                        throws java.io.IOException
 ```
 Lists all the running processes associated with a component.
 
@@ -38,7 +38,7 @@ Lists all the running processes associated with a component.
 ### listMonitorableFiles
 ```java
 java.lang.String[] listMonitorableFiles()
-    throws java.io.IOException
+                                 throws java.io.IOException
 ```
 Lists all items that may be monitored for output as a component is running. Note that this is normally in addition to any PHXRawFile output variables that your component exposes. Because of this, these names must not conflict with any variable names.
 
@@ -48,7 +48,7 @@ Lists all items that may be monitored for output as a component is running. Note
 ### getMonitor
 ```java
 java.lang.Object getMonitor(java.lang.String monitorName)
-    throws PHXNoSuchObjectException
+                     throws PHXNoSuchObjectException
 ```
 Gets a specified monitor. This method can return PHXRawFile objects to publish files for monitoring that don't appear as a regular variable, or PHXMonitorableStream objects to publish random streams of monitor data.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXRunQueue.md

@@ -17,8 +17,9 @@ public interface IPHXRunQueue
 
 ### setRunQueue
 ```java
-void setRunQueue(java.lang.String connector, java.lang.String queue)
-    throws java.lang.Exception
+void setRunQueue(java.lang.String connector, 
+                 java.lang.String queue)
+          throws java.lang.Exception
 ```
 Sets the run queue for a component. It is important that this class throws [PHXNoSuchCategoryException](library/PHXNoSuchCategoryException.md) and [ClassNotFoundException](../util/PHXClassNotFoundException.md) in the appropriate cases as they are handled in special ways by the [PHXLibrarianMounter](library/PHXLibrarianMounter.md) and [PHXLibrarianCombiner](library/PHXLibrarianCombiner.md).
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXSelfManager.md

@@ -33,7 +33,8 @@ This interface is for components that determine their properties at runtime. The
 ### getValue
 ```java
 java.lang.String getValue(java.lang.String name)
-    throws PHXNoSuchObjectException, java.lang.Exception
+                   throws PHXNoSuchObjectException, 
+                          java.lang.Exception
 ```
 Function for retrieving a specified value.
 
@@ -49,8 +50,11 @@ Function for retrieving a specified value.
 
 ### setValue
 ```java
-void setValue(java.lang.String name, java.lang.String value)
-    throws PHXNoSuchObjectException, PHXNoSuchWriteableObjectException, java.lang.Exception
+void setValue(java.lang.String name, 
+              java.lang.String value)
+       throws PHXNoSuchObjectException, 
+              PHXNoSuchWriteableObjectException, 
+              java.lang.Exception
 ```
 Function for setting a specified value.
 
@@ -66,7 +70,8 @@ Function for setting a specified value.
 ### getPropertyDescriptors
 ```java
 PHXPropertyDescriptor[] getPropertyDescriptors(java.lang.String name)
-    throws PHXNoSuchObjectException, java.lang.Exception
+                                        throws PHXNoSuchObjectException, 
+                                               java.lang.Exception
 ```
 Function for retrieving the properties of an object.
 
@@ -96,7 +101,7 @@ Function for retrieving the methods of an object.
 ### invoke
 ```java
 java.lang.String invoke(java.lang.String methodName)
-    throws java.lang.Exception
+                 throws java.lang.Exception
 ```
 Invokes the named method.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXSelfManager2.md

@@ -37,7 +37,8 @@ This interface extends [`IPHXSelfManager`](IPHXSelfManager.md) and provides new
 ### getValue2
 ```java
 java.lang.Object getValue2(java.lang.String name)
-    throws PHXNoSuchObjectException, java.lang.Exception
+                    throws PHXNoSuchObjectException, 
+                           java.lang.Exception
 ```
 Function for retrieving a specified value.
 
@@ -48,13 +49,16 @@ Function for retrieving a specified value.
 - The value to be returned as any type of java Object.
 
 **Throws:**
-- `PHXNoSuchObjectException` - thrown if the specified name does not exist
+- [`PHXNoSuchObjectException`](PHXNoSuchObjectException.md) - thrown if the specified name does not exist
 - `java.lang.Exception` - an exception that may occur
 
 ### setValue2
 ```java
-void setValue2(java.lang.String name, PHXStringBuffer value)
-    throws PHXNoSuchObjectException, PHXNoSuchWriteableObjectException, java.lang.Exception
+void setValue2(java.lang.String name, 
+               PHXStringBuffer value)
+        throws PHXNoSuchObjectException, 
+               PHXNoSuchWriteableObjectException, 
+               java.lang.Exception
 ```
 Function for setting a specified value.
 
@@ -63,6 +67,6 @@ Function for setting a specified value.
 - `value` - the String representation of the value to set
 
 **Throws:**
-- `PHXNoSuchObjectException` - thrown if the specified name does not exist
-- `PHXNoSuchWriteableObjectException` - thrown if the specified name cannot be modified
+- [`PHXNoSuchObjectException`](PHXNoSuchObjectException.md) - thrown if the specified name does not exist
+- [`PHXNoSuchWriteableObjectException`](PHXNoSuchWriteableObjectException.md) - thrown if the specified name cannot be modified
 - `java.lang.Exception` - an exception that may occur

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXSelfManager3.md

@@ -36,7 +36,7 @@ This interface extends [`IPHXSelfManager2`](IPHXSelfManager2.md) and provides a
 ### invoke2
 ```java
 PHXInvokeReturn invoke2(java.lang.String methodName)
-    throws java.lang.Exception
+                 throws java.lang.Exception
 ```
 Invokes the named method.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/IPHXSetupFromFile.md

@@ -26,7 +26,7 @@ This interface defines the contract for components that can be set up or initial
 ## Method Detail
 
 ### setupFromFile
-```
+```java
 public void setupFromFile(java.lang.String fileName)
                    throws java.io.IOException
 ```

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXComponentBranch.md

@@ -59,7 +59,7 @@ Constructs an empty named branch
 ### PHXComponentBranch
 ```java
 public PHXComponentBranch(org.w3c.dom.Element branchElement)
-        throws java.io.IOException
+                   throws java.io.IOException
 ```
 Constructs a branch based on an XML branch node
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXComponentVersion.md

@@ -53,7 +53,10 @@ Constructs a version with a given name
 
 ### PHXComponentVersion
 ```java
-public PHXComponentVersion(java.lang.String name, java.lang.String author, java.lang.String description, java.util.Date date)
+public PHXComponentVersion(java.lang.String name, 
+                          java.lang.String author, 
+                          java.lang.String description, 
+                          java.util.Date date)
 ```
 Constructs a version with the specified meta data
 
@@ -66,7 +69,7 @@ Constructs a version with the specified meta data
 ### PHXComponentVersion
 ```java
 public PHXComponentVersion(org.w3c.dom.Element versionNode)
-        throws java.io.IOException
+                    throws java.io.IOException
 ```
 Constructs a version based on information in an XML Element
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXGroup.md

@@ -57,7 +57,7 @@ A utility class for holding sub-variables. Internally used to manage groups of v
 ### PHXGroup
 ```java
 public PHXGroup(java.lang.String name)
-        throws PHXInvalidNameException
+         throws PHXInvalidNameException
 ```
 
 **Parameters:**
@@ -80,8 +80,8 @@ retrieves the name of the group
 ### addGroup
 ```java
 public void addGroup(PHXGroup group)
-          throws PHXNameAlreadyInUseException,
-                 PHXInvalidNameException
+              throws PHXNameAlreadyInUseException,
+                     PHXInvalidNameException
 ```
 adds a child group to the group
 
@@ -95,7 +95,7 @@ adds a child group to the group
 ### getGroup
 ```java
 public PHXGroup getGroup(java.lang.String childName)
-              throws PHXNoSuchObjectException
+                  throws PHXNoSuchObjectException
 ```
 retrieves a child group.
 
@@ -123,8 +123,8 @@ retrieves a child group. Does not throw an exception on failure.
 ### makeGroup
 ```java
 public PHXGroup makeGroup(java.lang.String childName)
-                 throws PHXNameAlreadyInUseException,
-                        PHXInvalidNameException
+                   throws PHXNameAlreadyInUseException,
+                          PHXInvalidNameException
 ```
 creates a child group. If the group already exists, it is retrieved
 
@@ -141,7 +141,7 @@ creates a child group. If the group already exists, it is retrieved
 ### removeGroup
 ```java
 public void removeGroup(java.lang.String childName)
-               throws java.lang.Exception
+                 throws java.lang.Exception
 ```
 remove a child group. If the group doesn't exist, it just returns
 
@@ -181,8 +181,8 @@ retrieves all the subgroups in the group
 ### addVariable
 ```java
 public void addVariable(PHXVariableInfo varInfo)
-               throws PHXNameAlreadyInUseException,
-                      PHXInvalidNameException
+                 throws PHXNameAlreadyInUseException,
+                        PHXInvalidNameException
 ```
 stores a variable in the group.
 
@@ -196,7 +196,7 @@ stores a variable in the group.
 ### getVariableInfo
 ```java
 public PHXVariableInfo getVariableInfo(java.lang.String varName)
-                            throws PHXNoSuchObjectException
+                                throws PHXNoSuchObjectException
 ```
 retrieves a variable from the group.
 

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXInvalidNameException.md

@@ -54,11 +54,6 @@ public PHXInvalidNameException(java.lang.String name)
 ### checkName
 ```java
 public static void checkName(java.lang.String name)
-    throws PHXInvalidNameException
+                      throws PHXInvalidNameException
 ```
 Checks a name to see if it's valid.
-
-### See Also
-- [`PHXNameAlreadyInUseException`](PHXNameAlreadyInUseException.md)
-- [`PHXGroup`](PHXGroup.md)
-- [`PHXSimpleSelfManager`](PHXSimpleSelfManager.md)

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXMethodDescriptor.md

@@ -57,12 +57,15 @@ public PHXMethodDescriptor(java.lang.String name)
 
 ### PHXMethodDescriptor
 ```java
-public PHXMethodDescriptor(java.lang.String name, java.lang.String fullName)
+public PHXMethodDescriptor(java.lang.String name, 
+                           java.lang.String fullName)
 ```
 
 ### PHXMethodDescriptor
 ```java
-public PHXMethodDescriptor(java.lang.String name, java.lang.String fullName, boolean downloadInputs)
+public PHXMethodDescriptor(java.lang.String name, 
+                           java.lang.String fullName, 
+                           boolean downloadInputs)
 ```
 
 ## Method Detail
@@ -118,11 +121,3 @@ public java.lang.String toString()
 ```java
 public static PHXMethodDescriptor fromString(java.lang.String str)
 ```
-
-### See Also
-- [`PHXSelfManager`](PHXSelfManager.md)
-- [`PHXSimpleSelfManager`](PHXSimpleSelfManager.md)
-- [`PHXSimpleSelfManager2`](PHXSimpleSelfManager2.md)
-- [`PHXSimpleSelfManager3`](PHXSimpleSelfManager3.md)
-- [`PHXInvokeReturn`](PHXInvokeReturn.md)
-- [`PHXGroup`](PHXGroup.md)

2025R2/modelCenter_java_api/com/phoenix_int/aserver/PHXRunShare.RunInfo.md

@@ -56,5 +56,6 @@ public java.io.File runFolder
 public RunInfo(java.lang.String cmd, java.lang.String runFolder)
 ```
 
-See also: [PHXRunShare](PHXRunShare.md)
+**See also:** 
+- [PHXRunShare](PHXRunShare.md)