Cleanup in src/, adding namespaces, removing php closing tag and general code cleanup

src/FactorGraphs/DefaultVariable.php

@@ -0,0 +1,21 @@
+<?php namespace Moserware\Skills\FactorGraphs;
+
+use Exception;
+
+class DefaultVariable extends Variable
+{
+    public function __construct()
+    {
+        parent::__construct("Default", null);
+    }
+
+    public function &getValue()
+    {
+        return null;
+    }
+
+    public function setValue(&$value)
+    {
+        throw new Exception();
+    }
+}

src/FactorGraphs/Factor.php

@@ -1,11 +1,6 @@
-<?php
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/../Guard.php");
-require_once(dirname(__FILE__) . "/../HashMap.php");
-require_once(dirname(__FILE__) . "/Message.php");
-require_once(dirname(__FILE__) . "/Variable.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
+use Exception;
 use Moserware\Skills\Guard;
 use Moserware\Skills\HashMap;
 
@@ -38,12 +33,12 @@ abstract class Factor
     {
         return count($this->_messages);
     }
-    
+
     protected function &getVariables()
     {
         return $this->_variables;
     }
-    
+
     protected function &getMessages()
     {
         return $this->_messages;
@@ -56,7 +51,7 @@ abstract class Factor
     {
         Guard::argumentIsValidIndex($messageIndex, count($this->_messages), "messageIndex");
         $message = &$this->_messages[$messageIndex];
-        $variable = &$this->_messageToVariableBinding->getValue($message);        
+        $variable = &$this->_messageToVariableBinding->getValue($message);
         return $this->updateMessageVariable($message, $variable);
     }
 
@@ -71,8 +66,7 @@ abstract class Factor
     public function resetMarginals()
     {
         $allValues = &$this->_messageToVariableBinding->getAllValues();
-        foreach ($allValues as &$currentVariable)
-        {
+        foreach ($allValues as &$currentVariable) {
             $currentVariable->resetToPrior();
         }
     }
@@ -108,6 +102,4 @@ abstract class Factor
     {
         return ($this->_name != null) ? $this->_name : base::__toString();
     }
-}
-
-?>
+}

src/FactorGraphs/FactorGraph.php

@@ -1,7 +1,4 @@
-<?php
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/VariableFactory.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
 class FactorGraph
 {
@@ -17,5 +14,4 @@ class FactorGraph
     {
         $this->_variableFactory = &$factory;
     }
-}
-?>
+}

src/FactorGraphs/FactorGraphLayer.php

@@ -1,9 +1,4 @@
-<?php
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/Factor.php");
-require_once(dirname(__FILE__) . "/FactorGraph.php");
-require_once(dirname(__FILE__) . "/Schedule.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
 abstract class FactorGraphLayer
 {
@@ -69,6 +64,4 @@ abstract class FactorGraphLayer
     {
         return null;
     }
-}
-
-?>
+}

src/FactorGraphs/FactorList.php

@@ -1,8 +1,4 @@
-<?php
-
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/Factor.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
 /**
  * Helper class for computing the factor graph's normalization constant.
@@ -14,8 +10,7 @@ class FactorList
     public function getLogNormalization()
     {
         $list = &$this->_list;
-        foreach($list as &$currentFactor)
-        {
+        foreach ($list as &$currentFactor) {
             $currentFactor->resetMarginals();
         }
 
@@ -23,22 +18,19 @@ class FactorList
 
         $listCount = count($this->_list);
 
-        for ($i = 0; $i < $listCount; $i++)
-        {
+        for ($i = 0; $i < $listCount; $i++) {
             $f = $this->_list[$i];
 
             $numberOfMessages = $f->getNumberOfMessages();
 
-            for ($j = 0; $j < $numberOfMessages; $j++)
-            {
+            for ($j = 0; $j < $numberOfMessages; $j++) {
                 $sumLogZ += $f->sendMessageIndex($j);
             }
         }
 
         $sumLogS = 0;
 
-        foreach($list as &$currentFactor)
-        {
+        foreach ($list as &$currentFactor) {
             $sumLogS = $sumLogS + $currentFactor->getLogNormalization();
         }
 
@@ -55,6 +47,4 @@ class FactorList
         $this->_list[] = $factor;
         return $factor;
     }
-}
-
-?>
+}

src/FactorGraphs/KeyedVariable.php

@@ -0,0 +1,18 @@
+<?php namespace Moserware\Skills\FactorGraphs;
+
+class KeyedVariable extends Variable
+{
+    private $_key;
+
+    public function __construct(&$key, $name, &$prior)
+    {
+        parent::__construct($name, $prior);
+        $this->_key = &$key;
+    }
+
+    public function &getKey()
+    {
+        $key = &$this->_key;
+        return $key;
+    }
+}

src/FactorGraphs/Message.php

@@ -1,14 +1,13 @@
-<?php
-namespace Moserware\Skills\FactorGraphs;
+<?php namespace Moserware\Skills\FactorGraphs;
 
 class Message
 {
-    private $_name;    
+    private $_name;
     private $_value;
 
     public function __construct(&$value = null, $name = null)
     {
-        $this->_name = $name;        
+        $this->_name = $name;
         $this->_value = $value;
     }
 
@@ -19,14 +18,12 @@ class Message
     }
 
     public function setValue(&$value)
-    {        
+    {
         $this->_value = &$value;
     }
 
     public function __toString()
     {
-        return $this->_name; 
+        return (string)$this->_name;
     }
-}
-
-?>
+}

src/FactorGraphs/Schedule.php

@@ -1,7 +1,4 @@
-<?php
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/Factor.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
 abstract class Schedule
 {
@@ -18,77 +15,4 @@ abstract class Schedule
     {
         return $this->_name;
     }
-}
-
-class ScheduleStep extends Schedule
-{
-    private $_factor;
-    private $_index;
-
-    public function __construct($name, Factor &$factor, $index)
-    {
-        parent::__construct($name);
-        $this->_factor = $factor;
-        $this->_index = $index;
-    }
-
-    public function visit($depth = -1, $maxDepth = 0)
-    {
-        $currentFactor = &$this->_factor;        
-        $delta = $currentFactor->updateMessageIndex($this->_index);
-        return $delta;
-    }
-}
-
-class ScheduleSequence extends Schedule
-{
-    private $_schedules;
-
-    public function __construct($name, array $schedules)
-    {
-        parent::__construct($name);
-        $this->_schedules = $schedules;
-    }
-
-    public function visit($depth = -1, $maxDepth = 0)
-    {
-        $maxDelta = 0;
-
-        $schedules = &$this->_schedules;
-        foreach ($schedules as &$currentSchedule)
-        {
-            $currentVisit = $currentSchedule->visit($depth + 1, $maxDepth);
-            $maxDelta = max($currentVisit, $maxDelta);
-        }
-
-        return $maxDelta;
-    }
-}
-
-class ScheduleLoop extends Schedule
-{
-    private $_maxDelta;
-    private $_scheduleToLoop;
-
-    public function __construct($name, Schedule &$scheduleToLoop, $maxDelta)
-    {
-        parent::__construct($name);
-        $this->_scheduleToLoop = $scheduleToLoop;
-        $this->_maxDelta = $maxDelta;
-    }
-
-    public function visit($depth = -1, $maxDepth = 0)
-    {
-        $totalIterations = 1;
-        $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
-        while ($delta > $this->_maxDelta)
-        {
-            $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
-            $totalIterations++;
-        }
-
-        return $delta;
-    }
-}
-
-?>
+}

src/FactorGraphs/ScheduleLoop.php

@@ -0,0 +1,26 @@
+<?php namespace Moserware\Skills\FactorGraphs;
+
+class ScheduleLoop extends Schedule
+{
+    private $_maxDelta;
+    private $_scheduleToLoop;
+
+    public function __construct($name, Schedule &$scheduleToLoop, $maxDelta)
+    {
+        parent::__construct($name);
+        $this->_scheduleToLoop = $scheduleToLoop;
+        $this->_maxDelta = $maxDelta;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $totalIterations = 1;
+        $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
+        while ($delta > $this->_maxDelta) {
+            $delta = $this->_scheduleToLoop->visit($depth + 1, $maxDepth);
+            $totalIterations++;
+        }
+
+        return $delta;
+    }
+}

src/FactorGraphs/ScheduleSequence.php

@@ -0,0 +1,25 @@
+<?php namespace Moserware\Skills\FactorGraphs;
+
+class ScheduleSequence extends Schedule
+{
+    private $_schedules;
+
+    public function __construct($name, array $schedules)
+    {
+        parent::__construct($name);
+        $this->_schedules = $schedules;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $maxDelta = 0;
+
+        $schedules = &$this->_schedules;
+        foreach ($schedules as &$currentSchedule) {
+            $currentVisit = $currentSchedule->visit($depth + 1, $maxDepth);
+            $maxDelta = max($currentVisit, $maxDelta);
+        }
+
+        return $maxDelta;
+    }
+}

src/FactorGraphs/ScheduleStep.php

@@ -0,0 +1,21 @@
+<?php namespace Moserware\Skills\FactorGraphs;
+
+class ScheduleStep extends Schedule
+{
+    private $_factor;
+    private $_index;
+
+    public function __construct($name, Factor &$factor, $index)
+    {
+        parent::__construct($name);
+        $this->_factor = $factor;
+        $this->_index = $index;
+    }
+
+    public function visit($depth = -1, $maxDepth = 0)
+    {
+        $currentFactor = &$this->_factor;
+        $delta = $currentFactor->updateMessageIndex($this->_index);
+        return $delta;
+    }
+}

src/FactorGraphs/Variable.php

@@ -16,12 +16,12 @@ class Variable
 
     public function &getValue()
     {
-        $value = &$this->_value;        
+        $value = &$this->_value;
         return $value;
     }
 
     public function setValue(&$value)
-    {        
+    {
         $this->_value = &$value;
     }
 
@@ -34,40 +34,4 @@ class Variable
     {
         return $this->_name;
     }
-}
-
-class DefaultVariable extends Variable
-{
-    public function __construct()
-    {
-        parent::__construct("Default", null);
-    }
-
-    public function &getValue()
-    {
-        return null;
-    }
-
-    public function setValue(&$value)
-    {
-        throw new Exception();
-    }
-}
-
-class KeyedVariable extends Variable
-{
-    private $_key;
-    public function __construct(&$key, $name, &$prior)
-    {
-        parent::__construct($name, $prior);
-        $this->_key = &$key;
-    }
-
-    public function &getKey()
-    {
-        $key = &$this->_key;
-        return $key;
-    }
-}
-
-?>
+}

src/FactorGraphs/VariableFactory.php

@@ -1,8 +1,4 @@
-<?php
-
-namespace Moserware\Skills\FactorGraphs;
-
-require_once(dirname(__FILE__) . "/Variable.php");
+<?php namespace Moserware\Skills\FactorGraphs;
 
 class VariableFactory
 {
@@ -28,5 +24,3 @@ class VariableFactory
         return $newVar;
     }
 }
-
-?>