General cleanup and removal of all unnecessary references

src/FactorGraphs/DefaultVariable.php

@@ -2,6 +2,7 @@
 
 use Exception;
 
+// XXX: This class is not used anywhere
 class DefaultVariable extends Variable
 {
     public function __construct()
@@ -9,12 +10,12 @@ 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();
     }

src/FactorGraphs/Factor.php

@@ -34,24 +34,26 @@ abstract class Factor
         return count($this->_messages);
     }
 
-    protected function &getVariables()
+    protected function getVariables()
     {
         return $this->_variables;
     }
 
-    protected function &getMessages()
+    protected function getMessages()
     {
         return $this->_messages;
     }
 
     /**
      * Update the message and marginal of the i-th variable that the factor is connected to
+     * @param $messageIndex
+     * @throws Exception
      */
     public function updateMessageIndex($messageIndex)
     {
         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 $this->updateMessageVariable($message, $variable);
     }
 
@@ -65,41 +67,41 @@ abstract class Factor
      */
     public function resetMarginals()
     {
-        $allValues = &$this->_messageToVariableBinding->getAllValues();
-        foreach ($allValues as &$currentVariable) {
+        $allValues = $this->_messageToVariableBinding->getAllValues();
+        foreach ($allValues as $currentVariable) {
             $currentVariable->resetToPrior();
         }
     }
 
     /**
      * Sends the ith message to the marginal and returns the log-normalization constant
+     * @param $messageIndex
+     * @return
+     * @throws Exception
      */
     public function sendMessageIndex($messageIndex)
     {
         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);
+    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);
-        $localMessages = &$this->_messages;
-        $localMessages[] = &$message;
         $this->_messageToVariableBinding->setValue($message, $variable);
-        $localVariables = &$this->_variables;
-        $localVariables[] = &$variable;
+        $this->_messages[] = $message;
+        $this->_variables[] = $variable;
         return $message;
     }
 
     public function __toString()
     {
-        return ($this->_name != null) ? $this->_name : base::__toString();
+        return ($this->_name != null) ? $this->_name : null;
     }
 }

src/FactorGraphs/FactorGraph.php

@@ -4,14 +4,13 @@ class FactorGraph
 {
     private $_variableFactory;
 
-    public function &getVariableFactory()
+    public function getVariableFactory()
     {
-        $factory = &$this->_variableFactory;
-        return $factory;
+        return $this->_variableFactory;
     }
 
-    public function setVariableFactory(VariableFactory &$factory)
+    public function setVariableFactory(VariableFactory $factory)
     {
-        $this->_variableFactory = &$factory;
+        $this->_variableFactory = $factory;
     }
 }

src/FactorGraphs/FactorGraphLayer.php

@@ -1,5 +1,5 @@
 <?php namespace Moserware\Skills\FactorGraphs;
-
+// edit this
 abstract class FactorGraphLayer
 {
     private $_localFactors = array();
@@ -7,38 +7,39 @@ abstract class FactorGraphLayer
     private $_inputVariablesGroups = array();
     private $_parentFactorGraph;
 
-    protected function __construct(FactorGraph &$parentGraph)
+    protected function __construct(FactorGraph $parentGraph)
     {
-        $this->_parentFactorGraph = &$parentGraph;
+        $this->_parentFactorGraph = $parentGraph;
     }
 
-    protected function &getInputVariablesGroups()
+    protected function getInputVariablesGroups()
     {
-        $inputVariablesGroups = &$this->_inputVariablesGroups;
-        return $inputVariablesGroups;
+        return $this->_inputVariablesGroups;
     }
 
     // HACK
 
-    public function &getParentFactorGraph()
+    public function getParentFactorGraph()
     {
-        $parentFactorGraph = &$this->_parentFactorGraph;
-        return $parentFactorGraph;
+        return $this->_parentFactorGraph;
     }
 
+    /**
+     * This reference is still needed
+     *
+     * @return array
+     */
     public function &getOutputVariablesGroups()
     {
-        $outputVariablesGroups = &$this->_outputVariablesGroups;
-        return $outputVariablesGroups;
+        return $this->_outputVariablesGroups;
     }
 
-    public function &getLocalFactors()
+    public function getLocalFactors()
     {
-        $localFactors = &$this->_localFactors;
-        return $localFactors;
+        return $this->_localFactors;
     }
 
-    public function setInputVariablesGroups(&$value)
+    public function setInputVariablesGroups($value)
     {
         $this->_inputVariablesGroups = $value;
     }
@@ -48,7 +49,7 @@ abstract class FactorGraphLayer
         return new ScheduleSequence($name, $itemsToSequence);
     }
 
-    protected function addLayerFactor(Factor &$factor)
+    protected function addLayerFactor(Factor $factor)
     {
         $this->_localFactors[] = $factor;
     }

src/FactorGraphs/FactorList.php

@@ -9,7 +9,7 @@ class FactorList
 
     public function getLogNormalization()
     {
-        $list = &$this->_list;
+        $list = $this->_list;
         foreach ($list as &$currentFactor) {
             $currentFactor->resetMarginals();
         }
@@ -42,7 +42,7 @@ class FactorList
         return count($this->_list);
     }
 
-    public function &addFactor(Factor &$factor)
+    public function addFactor(Factor $factor)
     {
         $this->_list[] = $factor;
         return $factor;

src/FactorGraphs/KeyedVariable.php

@@ -4,15 +4,14 @@ 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;
+        $this->_key = $key;
     }
 
-    public function &getKey()
+    public function getKey()
     {
-        $key = &$this->_key;
-        return $key;
+        return $this->_key;
     }
 }

src/FactorGraphs/Message.php

@@ -5,21 +5,20 @@ 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;
     }
 
-    public function& getValue()
+    public function getValue()
     {
-        $value = &$this->_value;
-        return $value;
+        return $this->_value;
     }
 
-    public function setValue(&$value)
+    public function setValue($value)
     {
-        $this->_value = &$value;
+        $this->_value = $value;
     }
 
     public function __toString()

src/FactorGraphs/ScheduleLoop.php

@@ -5,7 +5,7 @@ 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;

src/FactorGraphs/ScheduleSequence.php

@@ -14,8 +14,8 @@ class ScheduleSequence extends Schedule
     {
         $maxDelta = 0;
 
-        $schedules = &$this->_schedules;
-        foreach ($schedules as &$currentSchedule) {
+        $schedules = $this->_schedules;
+        foreach ($schedules as $currentSchedule) {
             $currentVisit = $currentSchedule->visit($depth + 1, $maxDepth);
             $maxDelta = max($currentVisit, $maxDelta);
         }

src/FactorGraphs/ScheduleStep.php

@@ -5,7 +5,7 @@ class ScheduleStep extends Schedule
     private $_factor;
     private $_index;
 
-    public function __construct($name, Factor &$factor, $index)
+    public function __construct($name, Factor $factor, $index)
     {
         parent::__construct($name);
         $this->_factor = $factor;
@@ -14,7 +14,7 @@ class ScheduleStep extends Schedule
 
     public function visit($depth = -1, $maxDepth = 0)
     {
-        $currentFactor = &$this->_factor;
+        $currentFactor = $this->_factor;
         $delta = $currentFactor->updateMessageIndex($this->_index);
         return $delta;
     }

src/FactorGraphs/Variable.php

@@ -7,22 +7,21 @@ class Variable
     private $_prior;
     private $_value;
 
-    public function __construct($name, &$prior)
+    public function __construct($name, $prior)
     {
         $this->_name = "Variable[" . $name . "]";
         $this->_prior = $prior;
         $this->resetToPrior();
     }
 
-    public function &getValue()
+    public function getValue()
     {
-        $value = &$this->_value;
-        return $value;
+        return $this->_value;
     }
 
-    public function setValue(&$value)
+    public function setValue($value)
     {
-        $this->_value = &$value;
+        $this->_value = $value;
     }
 
     public function resetToPrior()

src/FactorGraphs/VariableFactory.php

@@ -7,17 +7,17 @@ class VariableFactory
 
     public function __construct($variablePriorInitializer)
     {
-        $this->_variablePriorInitializer = &$variablePriorInitializer;
+        $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());