Another pass at fixing up references

PHPSkills/FactorGraphs/Factor.php

@@ -50,7 +50,7 @@ abstract class Factor
     {
         Guard::argumentIsValidIndex($messageIndex, count($this->_messages), "messageIndex");
         $message = &$this->_messages[$messageIndex];
-        $variable = &$this->_messageToVariableBinding->getValue($this->_messages[$messageIndex]);
+        $variable = &$this->_messageToVariableBinding->getValue($message);
         return $this->updateMessageVariable($message, $variable);
     }
 
@@ -62,7 +62,8 @@ abstract class Factor
     /// Resets the marginal of the variables a factor is connected to
     public function resetMarginals()
     {
-        foreach ($this->_messageToVariableBinding->getAllValues() as $currentVariable)
+        $allValues = &$this->_messageToVariableBinding->getAllValues();
+        foreach ($allValues as $currentVariable)
         {
             $currentVariable->resetToPrior();
         }
@@ -73,21 +74,21 @@ abstract class Factor
     {
         Guard::argumentIsValidIndex($messageIndex, count($this->_messages), "messageIndex");
 
-        $message = $this->_messages[$messageIndex];
-        $variable = $this->_messageToVariableBinding->getValue($message);
+        $message = &$this->_messages[$messageIndex];
+        $variable = &$this->_messageToVariableBinding->getValue($message);
         return $this->sendMessageVariable($message, $variable);
     }
 
     protected abstract function sendMessageVariable(Message &$message, Variable &$variable);
 
-    public abstract function createVariableToMessageBinding(Variable &$variable);
+    public abstract function &createVariableToMessageBinding(Variable &$variable);
 
-    protected function createVariableToMessageBindingWithMessage(Variable &$variable, Message &$message)
+    protected function &createVariableToMessageBindingWithMessage(Variable &$variable, Message &$message)
     {
         $index = count($this->_messages);
-        $this->_messages[] = $message;        
+        $this->_messages[] = &$message;
         $this->_messageToVariableBinding->setValue($message, $variable);
-        $this->_variables[] = $variable;
+        $this->_variables[] = &$variable;
         return $message;
     }
 

PHPSkills/FactorGraphs/FactorGraph.php

@@ -1,16 +1,19 @@
 <?php
 namespace Moserware\Skills\FactorGraphs;
 
+require_once(dirname(__FILE__) . "/VariableFactory.php");
+
 class FactorGraph
 {
     private $_variableFactory;
 
     public function &getVariableFactory()
     {
-        return $this->_variableFactory;
+        $factory = &$this->_variableFactory;
+        return $factory;
     }
 
-    public function setVariableFactory(&$factory)
+    public function setVariableFactory(VariableFactory &$factory)
     {
         $this->_variableFactory = &$factory;
     }

PHPSkills/FactorGraphs/FactorGraphLayer.php

@@ -1,6 +1,7 @@
 <?php
 namespace Moserware\Skills\FactorGraphs;
 
+require_once(dirname(__FILE__) . "/Factor.php");
 require_once(dirname(__FILE__) . "/FactorGraph.php");
 require_once(dirname(__FILE__) . "/Schedule.php");
 
@@ -18,24 +19,28 @@ abstract class FactorGraphLayer
 
     protected function &getInputVariablesGroups()
     {
-        return $this->_inputVariablesGroups;        
+        $inputVariablesGroups = &$this->_inputVariablesGroups;
+        return $inputVariablesGroups;
     }
 
     // HACK
 
     public function &getParentFactorGraph()
     {
-        return $this->_parentFactorGraph;
+        $parentFactorGraph = &$this->_parentFactorGraph;
+        return $parentFactorGraph;
     }
 
     public function &getOutputVariablesGroups()
     {
-        return $this->_outputVariablesGroups;        
+        $outputVariablesGroups = &$this->_outputVariablesGroups;
+        return $outputVariablesGroups;
     }
 
     public function &getLocalFactors()
     {
-        return $this->_localFactors;        
+        $localFactors = &$this->_localFactors;
+        return $localFactors;
     }
 
     public function setInputVariablesGroups(&$value)
@@ -43,12 +48,12 @@ abstract class FactorGraphLayer
         $this->_inputVariablesGroups = $value;
     }
 
-    protected function scheduleSequence($itemsToSequence, $name)
+    protected function scheduleSequence(array $itemsToSequence, $name)
     {
         return new ScheduleSequence($name, $itemsToSequence);
     }
 
-    protected function addLayerFactor(&$factor)
+    protected function addLayerFactor(Factor &$factor)
     {
         $this->_localFactors[] = $factor;
     }

PHPSkills/FactorGraphs/FactorList.php

@@ -13,7 +13,8 @@ class FactorList
 
     public function getLogNormalization()
     {
-        foreach($this->_list as $currentFactor)
+        $list = &$this->_list;
+        foreach($list as &$currentFactor)
         {
             $currentFactor->resetMarginals();
         }
@@ -36,7 +37,7 @@ class FactorList
 
         $sumLogS = 0;
 
-        foreach($this->_list as $currentFactor)
+        foreach($list as &$currentFactor)
         {
             $sumLogS = $sumLogS + $currentFactor->getLogNormalization();
         }
@@ -49,7 +50,7 @@ class FactorList
         return count($this->_list);
     }
 
-    public function addFactor(Factor &$factor)
+    public function &addFactor(Factor &$factor)
     {
         $this->_list[] = $factor;
         return $factor;

PHPSkills/FactorGraphs/Message.php

@@ -6,7 +6,7 @@ class Message
     private $_name;    
     private $_value;
 
-    public function __construct($value = null, $name = null)
+    public function __construct(&$value = null, $name = null)
     {
         $this->_name = $name;        
         $this->_value = $value;
@@ -14,7 +14,8 @@ class Message
 
     public function& getValue()
     {
-        return $this->_value;
+        $value = &$this->_value;
+        return $value;
     }
 
     public function setValue(&$value)

PHPSkills/FactorGraphs/Schedule.php

@@ -1,6 +1,8 @@
 <?php
 namespace Moserware\Skills\FactorGraphs;
 
+require_once(dirname(__FILE__) . "/Factor.php");
+
 abstract class Schedule
 {
     private $_name;
@@ -23,7 +25,7 @@ class ScheduleStep extends Schedule
     private $_factor;
     private $_index;
 
-    public function __construct($name, $factor, $index)
+    public function __construct($name, Factor &$factor, $index)
     {
         parent::__construct($name);
         $this->_factor = $factor;
@@ -41,7 +43,7 @@ class ScheduleSequence extends Schedule
 {
     private $_schedules;
 
-    public function __construct($name, $schedules)
+    public function __construct($name, array $schedules)
     {
         parent::__construct($name);
         $this->_schedules = $schedules;
@@ -51,7 +53,8 @@ class ScheduleSequence extends Schedule
     {
         $maxDelta = 0;
 
-        foreach ($this->_schedules as $currentSchedule)
+        $schedules = &$this->_schedules;
+        foreach ($schedules as &$currentSchedule)
         {
             $maxDelta = max($currentSchedule->visit($depth + 1, $maxDepth), $maxDelta);
         }
@@ -65,7 +68,7 @@ class ScheduleLoop extends Schedule
     private $_maxDelta;
     private $_scheduleToLoop;
 
-    public function __construct($name, Schedule $scheduleToLoop, $maxDelta)
+    public function __construct($name, Schedule &$scheduleToLoop, $maxDelta)
     {
         parent::__construct($name);
         $this->_scheduleToLoop = $scheduleToLoop;

PHPSkills/FactorGraphs/Variable.php

@@ -7,7 +7,7 @@ class Variable
     private $_prior;
     private $_value;
 
-    public function __construct($name, $prior)
+    public function __construct($name, &$prior)
     {
         $this->_name = "Variable[" . $name . "]";
         $this->_prior = $prior;
@@ -16,7 +16,8 @@ class Variable
 
     public function &getValue()
     {
-        return $this->_value;
+        $value = &$this->_value;
+        return $value;
     }
 
     public function setValue(&$value)
@@ -42,12 +43,12 @@ class DefaultVariable extends Variable
         parent::__construct("Default", null);
     }
 
-    public function getValue()
+    public function &getValue()
     {
         return null;
     }
 
-    public function setValue($value)
+    public function setValue(&$value)
     {
         throw new Exception();
     }
@@ -56,7 +57,7 @@ class DefaultVariable extends Variable
 class KeyedVariable extends Variable
 {
     private $_key;
-    public function __construct($key, $name, $prior)
+    public function __construct($key, $name, &$prior)
     {
         parent::__construct($name, $prior);
         $this->_key = $key;

PHPSkills/FactorGraphs/VariableFactory.php

@@ -14,14 +14,14 @@ class VariableFactory
         $this->_variablePriorInitializer = &$variablePriorInitializer;
     }
 
-    public function createBasicVariable($name)
+    public function &createBasicVariable($name)
     {
         $initializer = $this->_variablePriorInitializer;
         $newVar = new Variable($name, $initializer());
         return $newVar;
     }
 
-    public function createKeyedVariable($key, $name)
+    public function &createKeyedVariable(&$key, $name)
     {
         $initializer = $this->_variablePriorInitializer;
         $newVar = new KeyedVariable($key, $name, $initializer());