Fix a lot of lint, mostly trailing whitespace.

This is lint reported by the new lint-checking functionality in beautify.py.
(We can change to a different lint checker if we have a better one, but it
would probably still flag these same problems.)

Lint checking can help a lot, but only if we get the lint under control.

16 files changed, 356 insertions, 356 deletions

diff --git a/scripts/ems/web/analysis.php b/scripts/ems/web/analysis.php
index 00bb9e15f..57776dd22 100644
--- a/scripts/ems/web/analysis.php
+++ b/scripts/ems/web/analysis.php
@@ -1,4 +1,4 @@
-<?php 
+<?php
 
 # main page frame, triggers the loading of parts
 function show_analysis() {
@@ -122,7 +122,7 @@ function precision_by_coverage() {
     $log_info[$log_count]["precision"] += $item[1];
     $log_info[$log_count]["delete"] += $item[2];
     $log_info[$log_count]["length"] += $item[3];
-    $log_info[$log_count]["total"] += $item[4];    
+    $log_info[$log_count]["total"] += $item[4];
   }
   print "<h4>By log<sub>2</sub>-count in the training corpus</h4>";
   precision_by_coverage_graph("byCoverage",$log_info,$total,$img_width,SORT_NUMERIC);
@@ -159,7 +159,7 @@ function precision_by_coverage_factored($img_width,$total,$file,$factor_id) {
     $log_info_factored[$factor][$log_count]["precision"] += $item[2];
     $log_info_factored[$factor][$log_count]["delete"] += $item[3];
     $log_info_factored[$factor][$log_count]["length"] += $item[4];
-    $log_info_factored[$factor][$log_count]["total"] += $item[5];    
+    $log_info_factored[$factor][$log_count]["total"] += $item[5];
   }
   print "<h4>By factor ".factor_name("input",$factor_id)."</h4>";
   precision_by_coverage_graph("byFactor",$info_factored_sum,$total,$img_width,SORT_STRING);
@@ -203,7 +203,7 @@ function precision_by_word($type) {
     if ($byCoverage != -2 && $byCoverage != $log_count) {
 	continue;
     }
-   
+
     //# filter for factor
     $word = $item[5];
     if ($byFactor != "false" && $byFactor != $item[6]) {
@@ -231,7 +231,7 @@ function precision_by_word($type) {
 function precision_by_coverage_latex($name,$log_info,$total,$img_width,$sort_type) {
   $keys = array_keys($log_info);
   sort($keys,$sort_type);
-  
+
   $img_width /= 100;
   print "<div id=\"LatexToggle$name\" onClick=\"document.getElementById('Latex$name').style.display = 'block'; this.style.display = 'none';\" style=\"display:none;\"><font size=-2>(show LaTeX)</font></div>\n";
   print "<div id=\"Latex$name\" style=\"display:none;\">\n";
@@ -242,7 +242,7 @@ function precision_by_coverage_latex($name,$log_info,$total,$img_width,$sort_typ
       $height = 1.8-$line/10*1.8;
       print "\\draw[thin,lightgray] (0.2,-$height) ";
       print "node[anchor=east,black] {".$line."0\\%} -- ";
-      print "($img_width,-$height) ;<br>\n"; 
+      print "($img_width,-$height) ;<br>\n";
   }
   print "% co-ordinates for deletion<br>\n";
   for($line=0;$line<=3;$line++) {
@@ -251,7 +251,7 @@ function precision_by_coverage_latex($name,$log_info,$total,$img_width,$sort_typ
       if ($line != 0) {
 	  print "node[anchor=east,black] {".$line."0\\%} ";
       }
-      print "-- ($img_width,-$height) ;<br>\n"; 
+      print "-- ($img_width,-$height) ;<br>\n";
   }
 
   print "% boxes<br>\n";
@@ -265,13 +265,13 @@ function precision_by_coverage_latex($name,$log_info,$total,$img_width,$sort_typ
 
     $width += $x;
     $height += $y;
-    
+
     print "\\filldraw[very thin,gray] ($x,-$y) rectangle($width,-$height) ;<br>";
     print "\\draw[very thin,black] ($x,-$y) rectangle($width,-$height);<br>";
     if ($width-$x>.1) {
 	print "\\draw (".(($x+$width)/2).",-1.8) node[anchor=north,black] {".$i."};<br>";
     }
- 
+
 
     $del_ratio = $log_info[$i]["delete"]/$log_info[$i]["total"];
     $height = $del_ratio*1.80;
@@ -281,10 +281,10 @@ function precision_by_coverage_latex($name,$log_info,$total,$img_width,$sort_typ
     print "\\filldraw[very thin,lightgray] ($x,-2) rectangle($width,-$height);<br>\n";
     print "\\draw[very thin,black] ($x,-2) rectangle($width,-$height);<br>\n";
 
-    $total_so_far += $log_info[$i]["total"];   
+    $total_so_far += $log_info[$i]["total"];
   }
   print "\\end{tikzpicture}</code>";
-  print "</div>"; 
+  print "</div>";
 }
 
 function precision_by_coverage_graph($name,$log_info,$total,$img_width,$sort_type) {
@@ -351,7 +351,7 @@ ctx.font = '9px serif';
     print "ctx.fillRect ($x, 200, $width, $height);";
 
     $total_so_far += $log_info[$i]["total"];
-   
+
     if ($width>3) {
       print "ctx.fillStyle = \"rgb(0,0,0)\";";
       // print "ctx.rotate(-1.5707);";
@@ -410,7 +410,7 @@ function ngram_summary() {
 	 $info["$type-1-correct"],
 	 $info["$type-2-correct"],
 	 $info["$type-3-correct"],
-	 $info["$type-4-correct"]);    
+	 $info["$type-4-correct"]);
   printf("<tr><td>&nbsp;</td><td>%.1f%s</td><td>%.1f%s</td><td>%.1f%s</td><td>%.1f%s</td></tr>\n",
 	 $info["$type-1-correct"]/$info["$type-1-total"]*100,'%',
 	 $info["$type-2-correct"]/$info["$type-2-total"]*100,'%',
@@ -483,7 +483,7 @@ function ngram_show($type) {
   $data = file(get_current_analysis_filename("basic","n-gram-$type.$order"));
   for($i=0;$i<count($data);$i++) {
      $item = split("\t",$data[$i]);
-     $line["total"] = $item[0]; 
+     $line["total"] = $item[0];
      $line["correct"] = $item[1];
      $line["ngram"] = $item[2];
      $ngram[] = $line;
@@ -496,7 +496,7 @@ function ngram_show($type) {
     $sort = 'ratio_worst';
     $smooth = 1;
   }
-  
+
   // sort index
   for($i=0;$i<count($ngram);$i++) {
     if ($sort == "abs_worst") {
@@ -806,7 +806,7 @@ function segmentation_summary() {
       if (array_key_exists($in,$count) &&
           array_key_exists($out,$count[$in])) {
 	  $c = $count[$in][$out];
-      } 
+      }
       else { $c = 0; }
       printf("<td align=right nowrap>%d (%.1f%s)</td>",$c,100*$c/$total,"%");
     }
@@ -885,8 +885,8 @@ function bleu_show() {
   $count = $_GET['count'];
   if ($count == 0) { $count = 5; }
 
-  $filter = ""; 
-  if (array_key_exists("filter",$_GET)) { 
+  $filter = "";
+  if (array_key_exists("filter",$_GET)) {
     $filter = base64_decode($_GET['filter']);
   }
 
@@ -924,7 +924,7 @@ function bleu_show() {
   if ($filter != "") {
     print "; filter: '$filter'";
   }
-  
+
   sentence_annotation($count,$filter);
   print "<p align=center><A HREF=\"javascript:show('bleu','" . $_GET['sort'] . "',5+$count,'".base64_encode($filter)."')\">5 more</A> | ";
   print "<A HREF=\"javascript:show('bleu','" . $_GET['sort'] . "',10+$count,'".base64_encode($filter)."')\">10 more</A> | ";
@@ -950,28 +950,28 @@ function sentence_annotation($count,$filter) {
 	$word = explode(" ",$item[0]);
 	$keep = 0;
 	for($j=0;$j<count($word);$j++) {
-	  if ($word[$j] == $filter) { 
-	    $keep = 1; 
+	  if ($word[$j] == $filter) {
+	    $keep = 1;
 	  }
 	}
-	if (!$keep) { $filtered[$i] = 1; }	
+	if (!$keep) { $filtered[$i] = 1; }
       }
-    }  
+    }
   }
-  
-  # load bleu scores 
+
+  # load bleu scores
   $data = file(get_current_analysis_filename("basic","bleu-annotation"));
   for($i=0;$i<count($data);$i++) {
     $item = split("\t",$data[$i]);
     if (! array_key_exists($item[1],$filtered)) {
-      $line["bleu"] = $item[0]; 
-      $line["id"] = $item[1]; 
+      $line["bleu"] = $item[0];
+      $line["id"] = $item[1];
       $line["system"] = $item[2];
-      $line["reference"] = ""; 
+      $line["reference"] = "";
       for($j=3;$j<count($item);$j++) {
         if ($j>3) { $line["reference"] .= "<br>"; };
         $line["reference"] .= $item[$j];
-      } 
+      }
       $bleu[] = $line;
     }
   }
@@ -987,7 +987,7 @@ function sentence_annotation($count,$filter) {
     else if ($sort == "worst" || $sort == "75") {
       $a_idx = $a["bleu"];
       $b_idx = $b["bleu"];
-      if ($a_idx == $b_idx) { 
+      if ($a_idx == $b_idx) {
         $a_idx = $b["id"];
         $b_idx = $a["id"];
       }
@@ -995,7 +995,7 @@ function sentence_annotation($count,$filter) {
     else if ($sort == "best" || $sort == "avg" || $sort == "25") {
       $a_idx = -$a["bleu"];
       $b_idx = -$b["bleu"];
-      if ($a_idx == $b_idx) { 
+      if ($a_idx == $b_idx) {
         $a_idx = $a["id"];
         $b_idx = $b["id"];
       }
@@ -1021,7 +1021,7 @@ function sentence_annotation($count,$filter) {
 
   $retained = array();
   for($i=$offset;$i<$count+$offset && $i<count($bleu);$i++) {
-    $line = $bleu[$i]; 
+    $line = $bleu[$i];
     $retained[$line["id"]] = 1;
   }
 
@@ -1056,7 +1056,7 @@ function sentence_annotation($count,$filter) {
       list($sentence,$brackets,$nt,$words) = split("\t",$data[$i]);
       if ($sentence != $last_sentence) { $span = 0; }
       $last_sentence = $sentence;
-      if (array_key_exists($sentence,$retained)) {      
+      if (array_key_exists($sentence,$retained)) {
 	$segmentation[$sentence][$span]["brackets"] = $brackets;
 #	  $segmentation[$sentence][$span]["nt"] = $nt;
 	$segmentation[$sentence][$span]["words"] = rtrim($words);
@@ -1083,7 +1083,7 @@ function sentence_annotation($count,$filter) {
       list($sentence,$brackets,$nt,$words) = split("\t",$data[$i]);
       if ($sentence != $last_sentence) { $span = 0; }
       $last_sentence = $sentence;
-      if (array_key_exists($sentence,$retained)) {      
+      if (array_key_exists($sentence,$retained)) {
 	$segmentation_out[$sentence][$span]["brackets"] = $brackets;
 	$segmentation_out[$sentence][$span]["nt"] = $nt;
 	$segmentation_out[$sentence][$span]["words"] = rtrim($words);
@@ -1109,7 +1109,7 @@ function sentence_annotation($count,$filter) {
       list($sentence,$depth,$start_div,$end_div,$start_div_in,$end_div_in,$children) = split(" ",$data[$i]);
       if ($sentence != $last_sentence) { $n = 0; }
       $last_sentence = $sentence;
-      if (array_key_exists($sentence,$retained)) {      
+      if (array_key_exists($sentence,$retained)) {
 	$node[$sentence][$n]['depth'] = $depth;
 	$node[$sentence][$n]['start_div'] = $start_div;
 	$node[$sentence][$n]['end_div'] = $end_div;
@@ -1119,10 +1119,10 @@ function sentence_annotation($count,$filter) {
 	$n++;
       }
     }
-  } 
+  }
 
   # display
-  if ($filter != "") { 
+  if ($filter != "") {
       print " (".(count($input)-count($filtered))." retaining)";
   }
   print "</font><BR>\n";
@@ -1130,7 +1130,7 @@ function sentence_annotation($count,$filter) {
   $biconcor = get_biconcor_version($dir,$set,$id);
   //print "<div id=\"debug\">$sort / $offset</div>";
   for($i=$offset;$i<$count+$offset && $i<count($bleu);$i++) {
-     $line = $bleu[$i]; 
+     $line = $bleu[$i];
      $search_graph_dir = get_current_analysis_filename("basic","search-graph");
      if (file_exists($search_graph_dir) && file_exists($search_graph_dir."/graph.".$line["id"])) {
        $state = return_state_for_link();
@@ -1279,7 +1279,7 @@ function input_annotation($sentence,$input,$segmentation,$filter) {
       print "<tr><td colspan=".($sep_end-$sep_start)."><div style=\"position:relative; z-index:1;\">";
       for($j=$sep_start;$j<$sep_end;$j++) {
         if ($segmentation && array_key_exists($j,$segmentation["input_start"])) {
-          $id = $segmentation["input_start"][$j];  
+          $id = $segmentation["input_start"][$j];
           print "<span id=\"input-$sentence-$id\" style=\"border-color:#000000; border-style:solid; border-width:1px;\" onmouseover=\"highlight_phrase($sentence,$id);\" onmouseout=\"lowlight_phrase($sentence,$id);\">";
         }
         if (array_key_exists($j,$coverage)) {
@@ -1413,7 +1413,7 @@ function annotation_hierarchical($sentence,$segmentation,$segmentation_out,$node
 	    print "<span style=\"opacity:0\">|</span>";
 	}
 
-	$span_word = array(); 
+	$span_word = array();
 	if ($words != "") { $span_word = split(" ",$words); }
 	for($w=0;$w<count($span_word);$w++) {
 	    if ($w > 0) { print " "; }
diff --git a/scripts/ems/web/analysis_diff.php b/scripts/ems/web/analysis_diff.php
index 2f0947e13..214ae1592 100644
--- a/scripts/ems/web/analysis_diff.php
+++ b/scripts/ems/web/analysis_diff.php
@@ -1,4 +1,4 @@
-<?php 
+<?php
 
 function diff_analysis() {
   global $task,$user,$setup,$id,$id2,$set;
@@ -15,7 +15,7 @@ function diff_analysis() {
       print "Run $id2 ($c2) vs $id ($c)";
   }
   print "</h4>";
-  
+
 ?><script language="javascript" src="javascripts/prototype.js"></script>
 <script language="javascript" src="javascripts/scriptaculous.js"></script>
 <script>
@@ -96,9 +96,9 @@ function precision_by_coverage_diff() {
     $log_info[$log_count]["precision"] += $item[1];
     $log_info[$log_count]["delete"] += $item[2];
     $log_info[$log_count]["length"] += $item[3];
-    $log_info[$log_count]["total"] += $item[4];    
+    $log_info[$log_count]["total"] += $item[4];
   }
-  $log_info_new = $log_info;  
+  $log_info_new = $log_info;
 
   // load base data
   $data = file(get_current_analysis_filename("precision","precision-by-corpus-coverage"));
@@ -154,7 +154,7 @@ function precision_by_coverage_diff_factored($img_width,$total,$file,$factor_id)
     $log_info_factored[$factor][$log_count]["precision"] += $item[2];
     $log_info_factored[$factor][$log_count]["delete"] += $item[3];
     $log_info_factored[$factor][$log_count]["length"] += $item[4];
-    $log_info_factored[$factor][$log_count]["total"] += $item[5];    
+    $log_info_factored[$factor][$log_count]["total"] += $item[5];
   }
   $info_factored_new = $info_factored;
   $info_factored_sum_new = $info_factored_sum;
@@ -225,7 +225,7 @@ function precision_by_word_diff($type) {
     if ($byCoverage != -2 && $byCoverage != $log_count) {
       continue;
     }
-   
+
     //# filter for factor
     $word = $item[5];
     if ($byFactor != "false" && $byFactor != $item[6]) {
@@ -258,7 +258,7 @@ function precision_by_word_diff($type) {
     if ($byCoverage != -2 && $byCoverage != $log_count) {
 	continue;
     }
-   
+
     //# filter for factor
     $word = $item[5];
     if ($byFactor != "false" && $byFactor != $item[6]) {
@@ -319,7 +319,7 @@ ctx.fillRect (0, 0, $size, $size);
     $surface = $item[5];
     $word[$surface] = array();
     $word[$surface]["precision"] = $item[0]; # number of precise translations
-    $word[$surface]["delete"] = $item[1];    # number of deleted 
+    $word[$surface]["delete"] = $item[1];    # number of deleted
     $word[$surface]["total"] = $item[2];     # number of all translations
     $word[$surface]["coverage"] = $item[4];  # count in training corpus
     if ($item[4] == 0) { $log_count = -1; }
@@ -369,7 +369,7 @@ ctx.fillRect (0, 0, $size, $size);
       $matrix[$base][$alt]["coverage2"] = 0;
     }
     # ignore mismatches in source words due to tokenization / casing
-    if (array_key_exists($surface,$word)) { 
+    if (array_key_exists($surface,$word)) {
       $matrix[$base][$alt]["precision1"] += $word[$surface]["precision"];
       $matrix[$base][$alt]["delete1"]    += $word[$surface]["delete"];
       $matrix[$base][$alt]["total1"]     += $word[$surface]["total"];
@@ -413,14 +413,14 @@ ctx.fillRect (0, 0, $size, $size);
 	    $prec_imp = (int)(sqrt($prec1-$prec2));
 	    $prec_color = "255,100,100";
 	  }
-	  else {	    
+	  else {
 	    $prec_base = (int)(sqrt($prec2));
 	    $prec_imp = (int)(sqrt($prec2-$prec1));
 	    $prec_color = "100,255,100";
 	  }
 	  $prec_base_top = (int)(($total-$prec_base)/2);
 	  $prec_imp_top = (int)(($total-$prec_imp)/2);
-	
+
 	  $del1 = $matrix[$base][$alt]["delete1"]*$scale;
 	  $del2 = $matrix[$base][$alt]["delete2"]*$scale;
 	  if ($del1 > $del2) {
@@ -428,7 +428,7 @@ ctx.fillRect (0, 0, $size, $size);
 	    $del_imp = $del1-$del2;
 	    $del_color = "150,100,255";
 	  }
-	  else {	    
+	  else {
 	    $del_base = $del2;
 	    $del_imp = $del2-$del1;
 	    $del_color = "100,200,200";
@@ -470,7 +470,7 @@ ctx.fillRect (0, ".($total+$del_base_height).", $total, $del_imp_height);
 function precision_by_coverage_diff_matrix_details() {
   $alt = $_GET["alt"];
   $base = $_GET["base"];
-    
+
   $impact_total = 0;
   $data = file(get_current_analysis_filename("precision","precision-by-input-word"));
   $word = array(); $class = array();
@@ -483,7 +483,7 @@ function precision_by_coverage_diff_matrix_details() {
       $surface = $item[5];
       $word[$surface] = array();
       $word[$surface]["precision"] = $item[0]; # number of precise translations
-      $word[$surface]["delete"] = $item[1];    # number of deleted 
+      $word[$surface]["delete"] = $item[1];    # number of deleted
       $word[$surface]["total"] = $item[2];     # number of all translations
       $word[$surface]["coverage"] = $item[4];  # count in training corpus
     }
@@ -502,7 +502,7 @@ function precision_by_coverage_diff_matrix_details() {
     $surface = $item[5];
     if ($log_count-$base == $alt && array_key_exists($surface,$word)) {
       $precision = $item[0]; # number of precise translations
-      $delete = $item[1];    # number of deleted 
+      $delete = $item[1];    # number of deleted
       $total = $item[3];     # number of all translations + deletions
       $coverage = $item[4];  # count in training corpus
       $surface = $item[5];
@@ -527,17 +527,17 @@ function precision_by_coverage_diff_matrix_details() {
     }
   }
   sort($all_out);
-  foreach($all_out as $out) { $o = explode("\t",$out); print $o[1]; }  
+  foreach($all_out as $out) { $o = explode("\t",$out); print $o[1]; }
   print "</table>";
 }
 
 function precision_by_coverage_diff_graph($name,$log_info,$log_info_new,$total,$img_width,$sort_type) {
   $keys = array_keys($log_info);
   sort($keys,$sort_type);
-  
+
   print "<div id=\"Toggle$name\" onClick=\"document.getElementById('Table$name').style.display = 'none'; this.style.display = 'none';\" style=\"display:none;\"><font size=-2>(hide table)</font></div>\n";
   print "<div id=\"Table$name\" style=\"display:none;\">\n";
-  print "<table border=1><tr><td align=center>&nbsp;</td><td align=center colspan=3>Precision</td><td align=center colspan=2>Precision Impact</td><td align=center colspan=3>Delete</td><td align=center colspan=2>Delete Impact</td><td align=center>Length</td></tr>\n";  
+  print "<table border=1><tr><td align=center>&nbsp;</td><td align=center colspan=3>Precision</td><td align=center colspan=2>Precision Impact</td><td align=center colspan=3>Delete</td><td align=center colspan=2>Delete Impact</td><td align=center>Length</td></tr>\n";
   foreach ($keys as $i) {
     if (array_key_exists($i,$log_info)) {
       print "<tr><td align=center>$i</td>";
@@ -595,7 +595,7 @@ ctx.font = '9px serif';
     print "ctx.fillRect ($x, 250, $width, $height);";
 
     $total_so_far += $log_info[$i]["total"];
-   
+
     if ($width>3) {
       print "ctx.fillStyle = \"rgb(0,0,0)\";";
       // print "ctx.rotate(-1.5707);";
@@ -763,9 +763,9 @@ function bleu_diff_annotation() {
     $data = file(get_analysis_filename($dir,$set,$idx?$id2:$id,"basic","bleu-annotation"));
     for($i=0;$i<count($data);$i++) {
       $item = split("\t",$data[$i]);
-      $annotation[$item[1]]["bleu$idx"] = $item[0]; 
-      $annotation[$item[1]]["system$idx"] = $item[2]; 
-      $annotation[$item[1]]["reference"] = $item[3]; 
+      $annotation[$item[1]]["bleu$idx"] = $item[0];
+      $annotation[$item[1]]["system$idx"] = $item[2];
+      $annotation[$item[1]]["reference"] = $item[3];
       $annotation[$item[1]]["id"] = $item[1];
     }
   }
@@ -825,7 +825,7 @@ function bleu_diff_annotation() {
 
   // display
   for($i=0;$i<$count && $i<count($annotation);$i++) {
-     $line = $annotation[$i]; 
+     $line = $annotation[$i];
      print "<font size=-2>[src]</font> ".$input[$line["id"]]."<br>";
 
      $word_with_score1 = split(" ",$line["system1"]);
@@ -840,7 +840,7 @@ function bleu_diff_annotation() {
      $matched_with_score1 = preg_replace('/D/',"",$matched_with_score);
      bleu_line_diff( $word_with_score1, $matched1, $matched_with_score1 );
 
-     print "<font size=-2>[".$id."-".$line["id"].":".$line["bleu0"]."]</font> ";     
+     print "<font size=-2>[".$id."-".$line["id"].":".$line["bleu0"]."]</font> ";
      $matched0 = preg_replace('/I/',"",$matched);
      $matched_with_score0 = preg_replace('/I/',"",$matched_with_score);
      bleu_line_diff( $word_with_score0, $matched0, $matched_with_score0 );
@@ -875,14 +875,14 @@ function ngram_diff($type) {
 
   // load data
   $order = $_GET['order'];
-  
+
   for($idx=0;$idx<2;$idx++) {
     $data = file(get_analysis_filename($dir,$set,$idx?$id2:$id,"basic","n-gram-$type.$order"));
     for($i=0;$i<count($data);$i++) {
       $item = split("\t",$data[$i]);
-      $ngram_hash[$item[2]]["total$idx"] = $item[0]; 
+      $ngram_hash[$item[2]]["total$idx"] = $item[0];
       $ngram_hash[$item[2]]["correct$idx"] = $item[1];
-    }  
+    }
     unset($data);
   }
 
@@ -893,7 +893,7 @@ function ngram_diff($type) {
     $sort = 'ratio_worse';
     $smooth = 1;
   }
-  
+
   error_reporting(E_ERROR); // otherwise undefined counts trigger notices
 
   // sort index
@@ -914,12 +914,12 @@ function ngram_diff($type) {
         + (2*$item["correct0"] - $item["total0"]);
     }
     else if ($sort == "ratio_worse") {
-      $item["index"] = 
+      $item["index"] =
           ($item["correct1"] + $smooth) / ($item["total1"] + $smooth)
         - ($item["correct0"] + $smooth) / ($item["total0"] + $smooth);
     }
     else if ($sort == "ratio_better") {
-      $item["index"] = 
+      $item["index"] =
         - ($item["correct1"] + $smooth) / ($item["total1"] + $smooth)
         + ($item["correct0"] + $smooth) / ($item["total0"] + $smooth);
     }
@@ -1010,7 +1010,7 @@ function ngram_diff($type) {
     }
     else {
       printf("<td align=right>%+d</td><td>(%d)</td><td align=right>%+d</td><td>(%d)</td></tr>", $ok_diff,$ok,$wrong_diff,$wrong);
-    } 
+    }
   }
   print "</table>\n";
 }
diff --git a/scripts/ems/web/bilingual-concordance.css b/scripts/ems/web/bilingual-concordance.css
index 4648a21dd..f9941175e 100644
--- a/scripts/ems/web/bilingual-concordance.css
+++ b/scripts/ems/web/bilingual-concordance.css
@@ -17,57 +17,57 @@
   text-align: center;
 }
 
-table.biconcor { 
-  table-layout: fixed; 
-  padding: 0px; 
-  margin: 0px; 
+table.biconcor {
+  table-layout: fixed;
+  padding: 0px;
+  margin: 0px;
 }
 
-tr.biconcor { 
-  padding: 0px; 
-  margin: 0px; 
+tr.biconcor {
+  padding: 0px;
+  margin: 0px;
 }
 
-td.biconcor { 
-  white-space: nowrap; 
-  overflow: hidden; 
-  padding: 0px; 
-  margin: 0px; 
+td.biconcor {
+  white-space: nowrap;
+  overflow: hidden;
+  padding: 0px;
+  margin: 0px;
 }
 
-td.pp_source_left { 
+td.pp_source_left {
   font-size: 70%;
-  text-align: right; 
+  text-align: right;
 }
 
-td.pp_target_left { 
+td.pp_target_left {
   font-size: 70%;
-  text-align: right; 
+  text-align: right;
 }
 
-td.pp_source { 
+td.pp_source {
   font-size: 70%;
-  font-weight: bold; 
+  font-weight: bold;
 }
 
-td.pp_target { 
+td.pp_target {
   font-size: 70%;
-  font-weight: bold; 
+  font-weight: bold;
 }
 
-td.mismatch_target { 
+td.mismatch_target {
   font-size: 70%;
   text-align: center;
 }
 
-td.pp_source_right { 
+td.pp_source_right {
   font-size: 70%;
-  border-style:solid; 
-  border-width:0px 2px 0px 0px ; 
-  border-color: black; 
+  border-style:solid;
+  border-width:0px 2px 0px 0px ;
+  border-color: black;
 }
 
-td.pp_target_right { 
+td.pp_target_right {
   font-size: 70%;
 }
 
@@ -88,11 +88,11 @@ span.mismatch_misaligned {
 }
 
 span.mismatch_aligned {
-  font-weight: bold; 
+  font-weight: bold;
 }
 
 td.pp_more {
   font-size: 70%;
   color: navy;
-  text-align: center; 
+  text-align: center;
 }
diff --git a/scripts/ems/web/comment.php b/scripts/ems/web/comment.php
index 04628ea4f..dcd51ab00 100644
--- a/scripts/ems/web/comment.php
+++ b/scripts/ems/web/comment.php
@@ -1,4 +1,4 @@
-<?php 
+<?php
   $fp = fopen("comment","a");
   fwrite($fp,$_GET{'run'} . ";" . $_GET{'text'} . "\n");
   fclose($fp);
diff --git a/scripts/ems/web/diff.php b/scripts/ems/web/diff.php
index 71e732af1..f440d3240 100644
--- a/scripts/ems/web/diff.php
+++ b/scripts/ems/web/diff.php
@@ -37,7 +37,7 @@ function compute_diff($base,$change) {
   foreach ($all_parameters as $parameter) {
     if (!array_key_exists($parameter,$parameter_base)) {
       $parameter_base[$parameter] = "";
-    } 
+    }
     if (!array_key_exists($parameter,$parameter_change)) {
       $parameter_change[$parameter] = "";
     }
diff --git a/scripts/ems/web/hierarchical-segmentation.css b/scripts/ems/web/hierarchical-segmentation.css
index 47f2c2693..e66555070 100644
--- a/scripts/ems/web/hierarchical-segmentation.css
+++ b/scripts/ems/web/hierarchical-segmentation.css
@@ -10,7 +10,7 @@ div.leaf {
 	border:1px solid black;
 	margin:2px;
 	padding:0px;
-	font-weight: normal; 
+	font-weight: normal;
 	background-color: white;	
 }
 div.empty {
@@ -34,7 +34,7 @@ div.continued {
 	margin-right: 0px;
 	padding: 0px;
 	padding-top: 0px;
-	font-weight: normal; 
+	font-weight: normal;
 	background-color: white;		
 }
 div.opening {
@@ -44,7 +44,7 @@ div.opening {
 	margin:2px;
 	margin-right: 0px;
 	padding: 0px;
-	font-weight: normal; 
+	font-weight: normal;
 	background-color: white;		
 }
 div.closing {
@@ -54,6 +54,6 @@ div.closing {
 	margin:2px;
 	margin-left: 0px;
 	padding: 0px;
-	font-weight: normal; 
+	font-weight: normal;
 	background-color: white;		
 }
diff --git a/scripts/ems/web/hierarchical-segmentation.js b/scripts/ems/web/hierarchical-segmentation.js
index b4eb206ce..819ed121e 100644
--- a/scripts/ems/web/hierarchical-segmentation.js
+++ b/scripts/ems/web/hierarchical-segmentation.js
@@ -1,6 +1,6 @@
-var nodeIn = []; 
+var nodeIn = [];
 var nodeOut = [];
-var nodeChildren = []; 
+var nodeChildren = [];
 var max_depth = [];
 var span_count_in = [];
 var span_count_out = [];
diff --git a/scripts/ems/web/index.php b/scripts/ems/web/index.php
index d216b114a..9c918a96a 100644
--- a/scripts/ems/web/index.php
+++ b/scripts/ems/web/index.php
@@ -29,7 +29,7 @@ else if (array_key_exists("setup",$_POST) || array_key_exists("setup",$_GET)) {
 
   if (array_key_exists("show",$_GET)) { show(); }
   else if (array_key_exists("diff",$_GET)) { diff(); }
-  else if (array_key_exists("analysis",$_GET)) { 
+  else if (array_key_exists("analysis",$_GET)) {
     $action = $_GET["analysis"];
     $set = $_GET["set"];
     $id = $_GET["id"];
@@ -60,7 +60,7 @@ else if (array_key_exists("setup",$_POST) || array_key_exists("setup",$_GET)) {
         if ($match[2] == $set) {
           $id_array[] = $match[1];
         }
-      }      
+      }
     }
     if (count($id_array) != 2) {
       print "ERROR: comp 2!";
diff --git a/scripts/ems/web/javascripts/scriptaculous-js-1.8.3/src/unittest.js b/scripts/ems/web/javascripts/scriptaculous-js-1.8.3/src/unittest.js
index 33a0c7157..cd3d19b39 100644
--- a/scripts/ems/web/javascripts/scriptaculous-js-1.8.3/src/unittest.js
+++ b/scripts/ems/web/javascripts/scriptaculous-js-1.8.3/src/unittest.js
@@ -19,10 +19,10 @@ Event.simulateMouse = function(element, eventName) {
     metaKey:  false
   }, arguments[2] || {});
   var oEvent = document.createEvent("MouseEvents");
-  oEvent.initMouseEvent(eventName, true, true, document.defaultView, 
-    options.buttons, options.pointerX, options.pointerY, options.pointerX, options.pointerY, 
+  oEvent.initMouseEvent(eventName, true, true, document.defaultView,
+    options.buttons, options.pointerX, options.pointerY, options.pointerX, options.pointerY,
     options.ctrlKey, options.altKey, options.shiftKey, options.metaKey, 0, $(element));
-  
+
   if(this.mark) Element.remove(this.mark);
   this.mark = document.createElement('div');
   this.mark.appendChild(document.createTextNode(" "));
@@ -34,10 +34,10 @@ Event.simulateMouse = function(element, eventName) {
   this.mark.style.height = "5px;";
   this.mark.style.borderTop = "1px solid red;";
   this.mark.style.borderLeft = "1px solid red;";
-  
+
   if(this.step)
     alert('['+new Date().getTime().toString()+'] '+eventName+'/'+Test.Unit.inspect(options));
-  
+
   $(element).dispatchEvent(oEvent);
 };
 
@@ -55,7 +55,7 @@ Event.simulateKey = function(element, eventName) {
   }, arguments[2] || {});
 
   var oEvent = document.createEvent("KeyEvents");
-  oEvent.initKeyEvent(eventName, true, true, window, 
+  oEvent.initKeyEvent(eventName, true, true, window,
     options.ctrlKey, options.altKey, options.shiftKey, options.metaKey,
     options.keyCode, options.charCode );
   $(element).dispatchEvent(oEvent);
@@ -123,7 +123,7 @@ Test.Unit.Logger.prototype = {
   _toHTML: function(txt) {
     return txt.escapeHTML().replace(/\n/g,"<br/>");
   },
-  addLinksToResults: function(){ 
+  addLinksToResults: function(){
     $$("tr.failed .nameCell").each( function(td){ // todo: limit to children of this.log
       td.title = "Run only this test";
       Event.observe(td, 'click', function(){ window.location.search = "?tests=" + td.innerHTML;});
@@ -162,7 +162,7 @@ Test.Unit.Runner.prototype = {
           if(/^test/.test(testcase)) {
             this.tests.push(
                new Test.Unit.Testcase(
-                 this.options.context ? ' -> ' + this.options.titles[testcase] : testcase, 
+                 this.options.context ? ' -> ' + this.options.titles[testcase] : testcase,
                  testcases[testcase], testcases["setup"], testcases["teardown"]
                ));
           }
@@ -203,7 +203,7 @@ Test.Unit.Runner.prototype = {
   },
   postResults: function() {
     if (this.options.resultsURL) {
-      new Ajax.Request(this.options.resultsURL, 
+      new Ajax.Request(this.options.resultsURL,
         { method: 'get', parameters: 'result=' + this.getResult(), asynchronous: false });
     }
   },
@@ -240,9 +240,9 @@ Test.Unit.Runner.prototype = {
       errors     +=   this.tests[i].errors;
     }
     return (
-      (this.options.context ? this.options.context + ': ': '') + 
-      this.tests.length + " tests, " + 
-      assertions + " assertions, " + 
+      (this.options.context ? this.options.context + ': ': '') +
+      this.tests.length + " tests, " +
+      assertions + " assertions, " +
       failures   + " failures, " +
       errors     + " errors");
   }
@@ -258,7 +258,7 @@ Test.Unit.Assertions.prototype = {
   },
   summary: function() {
     return (
-      this.assertions + " assertions, " + 
+      this.assertions + " assertions, " +
       this.failures   + " failures, " +
       this.errors     + " errors" + "\n" +
       this.messages.join("\n"));
@@ -284,55 +284,55 @@ Test.Unit.Assertions.prototype = {
   },
   assert: function(expression) {
     var message = arguments[1] || 'assert: got "' + Test.Unit.inspect(expression) + '"';
-    try { expression ? this.pass() : 
+    try { expression ? this.pass() :
       this.fail(message); }
     catch(e) { this.error(e); }
   },
   assertEqual: function(expected, actual) {
     var message = arguments[2] || "assertEqual";
     try { (expected == actual) ? this.pass() :
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) + 
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
   assertInspect: function(expected, actual) {
     var message = arguments[2] || "assertInspect";
     try { (expected == actual.inspect()) ? this.pass() :
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) + 
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
   assertEnumEqual: function(expected, actual) {
     var message = arguments[2] || "assertEnumEqual";
-    try { $A(expected).length == $A(actual).length && 
+    try { $A(expected).length == $A(actual).length &&
       expected.zip(actual).all(function(pair) { return pair[0] == pair[1] }) ?
-        this.pass() : this.fail(message + ': expected ' + Test.Unit.inspect(expected) + 
+        this.pass() : this.fail(message + ': expected ' + Test.Unit.inspect(expected) +
           ', actual ' + Test.Unit.inspect(actual)); }
     catch(e) { this.error(e); }
   },
   assertNotEqual: function(expected, actual) {
     var message = arguments[2] || "assertNotEqual";
-    try { (expected != actual) ? this.pass() : 
+    try { (expected != actual) ? this.pass() :
       this.fail(message + ': got "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
-  assertIdentical: function(expected, actual) { 
-    var message = arguments[2] || "assertIdentical"; 
-    try { (expected === actual) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
-        '", actual "' + Test.Unit.inspect(actual) + '"'); } 
-    catch(e) { this.error(e); } 
+  assertIdentical: function(expected, actual) {
+    var message = arguments[2] || "assertIdentical";
+    try { (expected === actual) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
+        '", actual "' + Test.Unit.inspect(actual) + '"'); }
+    catch(e) { this.error(e); }
   },
-  assertNotIdentical: function(expected, actual) { 
-    var message = arguments[2] || "assertNotIdentical"; 
-    try { !(expected === actual) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
-        '", actual "' + Test.Unit.inspect(actual) + '"'); } 
-    catch(e) { this.error(e); } 
+  assertNotIdentical: function(expected, actual) {
+    var message = arguments[2] || "assertNotIdentical";
+    try { !(expected === actual) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
+        '", actual "' + Test.Unit.inspect(actual) + '"'); }
+    catch(e) { this.error(e); }
   },
   assertNull: function(obj) {
     var message = arguments[1] || 'assertNull';
-    try { (obj==null) ? this.pass() : 
+    try { (obj==null) ? this.pass() :
       this.fail(message + ': got "' + Test.Unit.inspect(obj) + '"'); }
     catch(e) { this.error(e); }
   },
@@ -353,38 +353,38 @@ Test.Unit.Assertions.prototype = {
   },
   assertType: function(expected, actual) {
     var message = arguments[2] || 'assertType';
-    try { 
-      (actual.constructor == expected) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
+    try {
+      (actual.constructor == expected) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + (actual.constructor) + '"'); }
     catch(e) { this.error(e); }
   },
   assertNotOfType: function(expected, actual) {
     var message = arguments[2] || 'assertNotOfType';
-    try { 
-      (actual.constructor != expected) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
+    try {
+      (actual.constructor != expected) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + (actual.constructor) + '"'); }
     catch(e) { this.error(e); }
   },
   assertInstanceOf: function(expected, actual) {
     var message = arguments[2] || 'assertInstanceOf';
-    try { 
-      (actual instanceof expected) ? this.pass() : 
+    try {
+      (actual instanceof expected) ? this.pass() :
       this.fail(message + ": object was not an instance of the expected type"); }
-    catch(e) { this.error(e); } 
+    catch(e) { this.error(e); }
   },
   assertNotInstanceOf: function(expected, actual) {
     var message = arguments[2] || 'assertNotInstanceOf';
-    try { 
-      !(actual instanceof expected) ? this.pass() : 
+    try {
+      !(actual instanceof expected) ? this.pass() :
       this.fail(message + ": object was an instance of the not expected type"); }
-    catch(e) { this.error(e); } 
+    catch(e) { this.error(e); }
   },
   assertRespondsTo: function(method, obj) {
     var message = arguments[2] || 'assertRespondsTo';
     try {
-      (obj[method] && typeof obj[method] == 'function') ? this.pass() : 
+      (obj[method] && typeof obj[method] == 'function') ? this.pass() :
       this.fail(message + ": object doesn't respond to [" + method + "]"); }
     catch(e) { this.error(e); }
   },
@@ -393,7 +393,7 @@ Test.Unit.Assertions.prototype = {
     try {
       var m = obj[method];
       if(!m) m = obj['is'+method.charAt(0).toUpperCase()+method.slice(1)];
-      m() ? this.pass() : 
+      m() ? this.pass() :
       this.fail(message + ": method returned false"); }
     catch(e) { this.error(e); }
   },
@@ -402,17 +402,17 @@ Test.Unit.Assertions.prototype = {
     try {
       var m = obj[method];
       if(!m) m = obj['is'+method.charAt(0).toUpperCase()+method.slice(1)];
-      !m() ? this.pass() : 
+      !m() ? this.pass() :
       this.fail(message + ": method returned true"); }
     catch(e) { this.error(e); }
   },
   assertRaise: function(exceptionName, method) {
     var message = arguments[2] || 'assertRaise';
-    try { 
+    try {
       method();
       this.fail(message + ": exception expected but none was raised"); }
     catch(e) {
-      ((exceptionName == null) || (e.name==exceptionName)) ? this.pass() : this.error(e); 
+      ((exceptionName == null) || (e.name==exceptionName)) ? this.pass() : this.error(e);
     }
   },
   assertElementsMatch: function() {
@@ -434,7 +434,7 @@ Test.Unit.Assertions.prototype = {
     var startAt = new Date();
     (iterations || 1).times(operation);
     var timeTaken = ((new Date())-startAt);
-    this.info((arguments[2] || 'Operation') + ' finished ' + 
+    this.info((arguments[2] || 'Operation') + ' finished ' +
        iterations + ' iterations in ' + (timeTaken/1000)+'s' );
     return timeTaken;
   },
@@ -444,7 +444,7 @@ Test.Unit.Assertions.prototype = {
     this.assertNotNull(element);
     if(element.style && Element.getStyle(element, 'display') == 'none')
       return false;
-    
+
     return this._isVisible(element.parentNode);
   },
   assertNotVisible: function(element) {
@@ -457,7 +457,7 @@ Test.Unit.Assertions.prototype = {
     var startAt = new Date();
     (iterations || 1).times(operation);
     var timeTaken = ((new Date())-startAt);
-    this.info((arguments[2] || 'Operation') + ' finished ' + 
+    this.info((arguments[2] || 'Operation') + ' finished ' +
        iterations + ' iterations in ' + (timeTaken/1000)+'s' );
     return timeTaken;
   }
@@ -468,7 +468,7 @@ Object.extend(Object.extend(Test.Unit.Testcase.prototype, Test.Unit.Assertions.p
   initialize: function(name, test, setup, teardown) {
     Test.Unit.Assertions.prototype.initialize.bind(this)();
     this.name           = name;
-    
+
     if(typeof test == 'string') {
       test = test.gsub(/(\.should[^\(]+\()/,'#{0}this,');
       test = test.gsub(/(\.should[^\(]+)\(this,\)/,'#{1}(this)');
@@ -478,7 +478,7 @@ Object.extend(Object.extend(Test.Unit.Testcase.prototype, Test.Unit.Assertions.p
     } else {
       this.test = test || function() {};
     }
-    
+
     this.setup          = setup || function() {};
     this.teardown       = teardown || function() {};
     this.isWaiting      = false;
@@ -519,23 +519,23 @@ Test.setupBDDExtensionMethods = function(){
     shouldNotBeAn:   'assertNotOfType',
     shouldBeNull:    'assertNull',
     shouldNotBeNull: 'assertNotNull',
-    
+
     shouldBe:        'assertReturnsTrue',
     shouldNotBe:     'assertReturnsFalse',
     shouldRespondTo: 'assertRespondsTo'
   };
-  var makeAssertion = function(assertion, args, object) { 
+  var makeAssertion = function(assertion, args, object) {
    	this[assertion].apply(this,(args || []).concat([object]));
   };
-  
-  Test.BDDMethods = {};   
-  $H(METHODMAP).each(function(pair) { 
-    Test.BDDMethods[pair.key] = function() { 
-       var args = $A(arguments); 
-       var scope = args.shift(); 
-       makeAssertion.apply(scope, [pair.value, args, this]); }; 
+
+  Test.BDDMethods = {};
+  $H(METHODMAP).each(function(pair) {
+    Test.BDDMethods[pair.key] = function() {
+       var args = $A(arguments);
+       var scope = args.shift();
+       makeAssertion.apply(scope, [pair.value, args, this]); };
   });
-  
+
   [Array.prototype, String.prototype, Number.prototype, Boolean.prototype].each(
     function(p){ Object.extend(p, Test.BDDMethods) }
   );
@@ -543,7 +543,7 @@ Test.setupBDDExtensionMethods = function(){
 
 Test.context = function(name, spec, log){
   Test.setupBDDExtensionMethods();
-  
+
   var compiledSpec = {};
   var titles = {};
   for(specName in spec) {
@@ -557,7 +557,7 @@ Test.context = function(name, spec, log){
         var body = spec[specName].toString().split('\n').slice(1);
         if(/^\{/.test(body[0])) body = body.slice(1);
         body.pop();
-        body = body.map(function(statement){ 
+        body = body.map(function(statement){
           return statement.strip()
         });
         compiledSpec[testName] = body.join('\n');
diff --git a/scripts/ems/web/javascripts/sound.js b/scripts/ems/web/javascripts/sound.js
index a286eb98e..0a63379fb 100644
--- a/scripts/ems/web/javascripts/sound.js
+++ b/scripts/ems/web/javascripts/sound.js
@@ -56,4 +56,4 @@ if(Prototype.Browser.Gecko && navigator.userAgent.indexOf("Win") > 0){
     Sound.template = new Template('<embed type="audio/x-pn-realaudio-plugin" style="height:0" id="sound_#{track}_#{id}" src="#{url}" loop="false" autostart="true" hidden="true"/>');
   else
     Sound.play = function(){};
-} 
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/scripts/ems/web/javascripts/unittest.js b/scripts/ems/web/javascripts/unittest.js
index 33a0c7157..cd3d19b39 100644
--- a/scripts/ems/web/javascripts/unittest.js
+++ b/scripts/ems/web/javascripts/unittest.js
@@ -19,10 +19,10 @@ Event.simulateMouse = function(element, eventName) {
     metaKey:  false
   }, arguments[2] || {});
   var oEvent = document.createEvent("MouseEvents");
-  oEvent.initMouseEvent(eventName, true, true, document.defaultView, 
-    options.buttons, options.pointerX, options.pointerY, options.pointerX, options.pointerY, 
+  oEvent.initMouseEvent(eventName, true, true, document.defaultView,
+    options.buttons, options.pointerX, options.pointerY, options.pointerX, options.pointerY,
     options.ctrlKey, options.altKey, options.shiftKey, options.metaKey, 0, $(element));
-  
+
   if(this.mark) Element.remove(this.mark);
   this.mark = document.createElement('div');
   this.mark.appendChild(document.createTextNode(" "));
@@ -34,10 +34,10 @@ Event.simulateMouse = function(element, eventName) {
   this.mark.style.height = "5px;";
   this.mark.style.borderTop = "1px solid red;";
   this.mark.style.borderLeft = "1px solid red;";
-  
+
   if(this.step)
     alert('['+new Date().getTime().toString()+'] '+eventName+'/'+Test.Unit.inspect(options));
-  
+
   $(element).dispatchEvent(oEvent);
 };
 
@@ -55,7 +55,7 @@ Event.simulateKey = function(element, eventName) {
   }, arguments[2] || {});
 
   var oEvent = document.createEvent("KeyEvents");
-  oEvent.initKeyEvent(eventName, true, true, window, 
+  oEvent.initKeyEvent(eventName, true, true, window,
     options.ctrlKey, options.altKey, options.shiftKey, options.metaKey,
     options.keyCode, options.charCode );
   $(element).dispatchEvent(oEvent);
@@ -123,7 +123,7 @@ Test.Unit.Logger.prototype = {
   _toHTML: function(txt) {
     return txt.escapeHTML().replace(/\n/g,"<br/>");
   },
-  addLinksToResults: function(){ 
+  addLinksToResults: function(){
     $$("tr.failed .nameCell").each( function(td){ // todo: limit to children of this.log
       td.title = "Run only this test";
       Event.observe(td, 'click', function(){ window.location.search = "?tests=" + td.innerHTML;});
@@ -162,7 +162,7 @@ Test.Unit.Runner.prototype = {
           if(/^test/.test(testcase)) {
             this.tests.push(
                new Test.Unit.Testcase(
-                 this.options.context ? ' -> ' + this.options.titles[testcase] : testcase, 
+                 this.options.context ? ' -> ' + this.options.titles[testcase] : testcase,
                  testcases[testcase], testcases["setup"], testcases["teardown"]
                ));
           }
@@ -203,7 +203,7 @@ Test.Unit.Runner.prototype = {
   },
   postResults: function() {
     if (this.options.resultsURL) {
-      new Ajax.Request(this.options.resultsURL, 
+      new Ajax.Request(this.options.resultsURL,
         { method: 'get', parameters: 'result=' + this.getResult(), asynchronous: false });
     }
   },
@@ -240,9 +240,9 @@ Test.Unit.Runner.prototype = {
       errors     +=   this.tests[i].errors;
     }
     return (
-      (this.options.context ? this.options.context + ': ': '') + 
-      this.tests.length + " tests, " + 
-      assertions + " assertions, " + 
+      (this.options.context ? this.options.context + ': ': '') +
+      this.tests.length + " tests, " +
+      assertions + " assertions, " +
       failures   + " failures, " +
       errors     + " errors");
   }
@@ -258,7 +258,7 @@ Test.Unit.Assertions.prototype = {
   },
   summary: function() {
     return (
-      this.assertions + " assertions, " + 
+      this.assertions + " assertions, " +
       this.failures   + " failures, " +
       this.errors     + " errors" + "\n" +
       this.messages.join("\n"));
@@ -284,55 +284,55 @@ Test.Unit.Assertions.prototype = {
   },
   assert: function(expression) {
     var message = arguments[1] || 'assert: got "' + Test.Unit.inspect(expression) + '"';
-    try { expression ? this.pass() : 
+    try { expression ? this.pass() :
       this.fail(message); }
     catch(e) { this.error(e); }
   },
   assertEqual: function(expected, actual) {
     var message = arguments[2] || "assertEqual";
     try { (expected == actual) ? this.pass() :
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) + 
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
   assertInspect: function(expected, actual) {
     var message = arguments[2] || "assertInspect";
     try { (expected == actual.inspect()) ? this.pass() :
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) + 
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
   assertEnumEqual: function(expected, actual) {
     var message = arguments[2] || "assertEnumEqual";
-    try { $A(expected).length == $A(actual).length && 
+    try { $A(expected).length == $A(actual).length &&
       expected.zip(actual).all(function(pair) { return pair[0] == pair[1] }) ?
-        this.pass() : this.fail(message + ': expected ' + Test.Unit.inspect(expected) + 
+        this.pass() : this.fail(message + ': expected ' + Test.Unit.inspect(expected) +
           ', actual ' + Test.Unit.inspect(actual)); }
     catch(e) { this.error(e); }
   },
   assertNotEqual: function(expected, actual) {
     var message = arguments[2] || "assertNotEqual";
-    try { (expected != actual) ? this.pass() : 
+    try { (expected != actual) ? this.pass() :
       this.fail(message + ': got "' + Test.Unit.inspect(actual) + '"'); }
     catch(e) { this.error(e); }
   },
-  assertIdentical: function(expected, actual) { 
-    var message = arguments[2] || "assertIdentical"; 
-    try { (expected === actual) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
-        '", actual "' + Test.Unit.inspect(actual) + '"'); } 
-    catch(e) { this.error(e); } 
+  assertIdentical: function(expected, actual) {
+    var message = arguments[2] || "assertIdentical";
+    try { (expected === actual) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
+        '", actual "' + Test.Unit.inspect(actual) + '"'); }
+    catch(e) { this.error(e); }
   },
-  assertNotIdentical: function(expected, actual) { 
-    var message = arguments[2] || "assertNotIdentical"; 
-    try { !(expected === actual) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
-        '", actual "' + Test.Unit.inspect(actual) + '"'); } 
-    catch(e) { this.error(e); } 
+  assertNotIdentical: function(expected, actual) {
+    var message = arguments[2] || "assertNotIdentical";
+    try { !(expected === actual) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
+        '", actual "' + Test.Unit.inspect(actual) + '"'); }
+    catch(e) { this.error(e); }
   },
   assertNull: function(obj) {
     var message = arguments[1] || 'assertNull';
-    try { (obj==null) ? this.pass() : 
+    try { (obj==null) ? this.pass() :
       this.fail(message + ': got "' + Test.Unit.inspect(obj) + '"'); }
     catch(e) { this.error(e); }
   },
@@ -353,38 +353,38 @@ Test.Unit.Assertions.prototype = {
   },
   assertType: function(expected, actual) {
     var message = arguments[2] || 'assertType';
-    try { 
-      (actual.constructor == expected) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
+    try {
+      (actual.constructor == expected) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + (actual.constructor) + '"'); }
     catch(e) { this.error(e); }
   },
   assertNotOfType: function(expected, actual) {
     var message = arguments[2] || 'assertNotOfType';
-    try { 
-      (actual.constructor != expected) ? this.pass() : 
-      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +  
+    try {
+      (actual.constructor != expected) ? this.pass() :
+      this.fail(message + ': expected "' + Test.Unit.inspect(expected) +
         '", actual "' + (actual.constructor) + '"'); }
     catch(e) { this.error(e); }
   },
   assertInstanceOf: function(expected, actual) {
     var message = arguments[2] || 'assertInstanceOf';
-    try { 
-      (actual instanceof expected) ? this.pass() : 
+    try {
+      (actual instanceof expected) ? this.pass() :
       this.fail(message + ": object was not an instance of the expected type"); }
-    catch(e) { this.error(e); } 
+    catch(e) { this.error(e); }
   },
   assertNotInstanceOf: function(expected, actual) {
     var message = arguments[2] || 'assertNotInstanceOf';
-    try { 
-      !(actual instanceof expected) ? this.pass() : 
+    try {
+      !(actual instanceof expected) ? this.pass() :
       this.fail(message + ": object was an instance of the not expected type"); }
-    catch(e) { this.error(e); } 
+    catch(e) { this.error(e); }
   },
   assertRespondsTo: function(method, obj) {
     var message = arguments[2] || 'assertRespondsTo';
     try {
-      (obj[method] && typeof obj[method] == 'function') ? this.pass() : 
+      (obj[method] && typeof obj[method] == 'function') ? this.pass() :
       this.fail(message + ": object doesn't respond to [" + method + "]"); }
     catch(e) { this.error(e); }
   },
@@ -393,7 +393,7 @@ Test.Unit.Assertions.prototype = {
     try {
       var m = obj[method];
       if(!m) m = obj['is'+method.charAt(0).toUpperCase()+method.slice(1)];
-      m() ? this.pass() : 
+      m() ? this.pass() :
       this.fail(message + ": method returned false"); }
     catch(e) { this.error(e); }
   },
@@ -402,17 +402,17 @@ Test.Unit.Assertions.prototype = {
     try {
       var m = obj[method];
       if(!m) m = obj['is'+method.charAt(0).toUpperCase()+method.slice(1)];
-      !m() ? this.pass() : 
+      !m() ? this.pass() :
       this.fail(message + ": method returned true"); }
     catch(e) { this.error(e); }
   },
   assertRaise: function(exceptionName, method) {
     var message = arguments[2] || 'assertRaise';
-    try { 
+    try {
       method();
       this.fail(message + ": exception expected but none was raised"); }
     catch(e) {
-      ((exceptionName == null) || (e.name==exceptionName)) ? this.pass() : this.error(e); 
+      ((exceptionName == null) || (e.name==exceptionName)) ? this.pass() : this.error(e);
     }
   },
   assertElementsMatch: function() {
@@ -434,7 +434,7 @@ Test.Unit.Assertions.prototype = {
     var startAt = new Date();
     (iterations || 1).times(operation);
     var timeTaken = ((new Date())-startAt);
-    this.info((arguments[2] || 'Operation') + ' finished ' + 
+    this.info((arguments[2] || 'Operation') + ' finished ' +
        iterations + ' iterations in ' + (timeTaken/1000)+'s' );
     return timeTaken;
   },
@@ -444,7 +444,7 @@ Test.Unit.Assertions.prototype = {
     this.assertNotNull(element);
     if(element.style && Element.getStyle(element, 'display') == 'none')
       return false;
-    
+
     return this._isVisible(element.parentNode);
   },
   assertNotVisible: function(element) {
@@ -457,7 +457,7 @@ Test.Unit.Assertions.prototype = {
     var startAt = new Date();
     (iterations || 1).times(operation);
     var timeTaken = ((new Date())-startAt);
-    this.info((arguments[2] || 'Operation') + ' finished ' + 
+    this.info((arguments[2] || 'Operation') + ' finished ' +
        iterations + ' iterations in ' + (timeTaken/1000)+'s' );
     return timeTaken;
   }
@@ -468,7 +468,7 @@ Object.extend(Object.extend(Test.Unit.Testcase.prototype, Test.Unit.Assertions.p
   initialize: function(name, test, setup, teardown) {
     Test.Unit.Assertions.prototype.initialize.bind(this)();
     this.name           = name;
-    
+
     if(typeof test == 'string') {
       test = test.gsub(/(\.should[^\(]+\()/,'#{0}this,');
       test = test.gsub(/(\.should[^\(]+)\(this,\)/,'#{1}(this)');
@@ -478,7 +478,7 @@ Object.extend(Object.extend(Test.Unit.Testcase.prototype, Test.Unit.Assertions.p
     } else {
       this.test = test || function() {};
     }
-    
+
     this.setup          = setup || function() {};
     this.teardown       = teardown || function() {};
     this.isWaiting      = false;
@@ -519,23 +519,23 @@ Test.setupBDDExtensionMethods = function(){
     shouldNotBeAn:   'assertNotOfType',
     shouldBeNull:    'assertNull',
     shouldNotBeNull: 'assertNotNull',
-    
+
     shouldBe:        'assertReturnsTrue',
     shouldNotBe:     'assertReturnsFalse',
     shouldRespondTo: 'assertRespondsTo'
   };
-  var makeAssertion = function(assertion, args, object) { 
+  var makeAssertion = function(assertion, args, object) {
    	this[assertion].apply(this,(args || []).concat([object]));
   };
-  
-  Test.BDDMethods = {};   
-  $H(METHODMAP).each(function(pair) { 
-    Test.BDDMethods[pair.key] = function() { 
-       var args = $A(arguments); 
-       var scope = args.shift(); 
-       makeAssertion.apply(scope, [pair.value, args, this]); }; 
+
+  Test.BDDMethods = {};
+  $H(METHODMAP).each(function(pair) {
+    Test.BDDMethods[pair.key] = function() {
+       var args = $A(arguments);
+       var scope = args.shift();
+       makeAssertion.apply(scope, [pair.value, args, this]); };
   });
-  
+
   [Array.prototype, String.prototype, Number.prototype, Boolean.prototype].each(
     function(p){ Object.extend(p, Test.BDDMethods) }
   );
@@ -543,7 +543,7 @@ Test.setupBDDExtensionMethods = function(){
 
 Test.context = function(name, spec, log){
   Test.setupBDDExtensionMethods();
-  
+
   var compiledSpec = {};
   var titles = {};
   for(specName in spec) {
@@ -557,7 +557,7 @@ Test.context = function(name, spec, log){
         var body = spec[specName].toString().split('\n').slice(1);
         if(/^\{/.test(body[0])) body = body.slice(1);
         body.pop();
-        body = body.map(function(statement){ 
+        body = body.map(function(statement){
           return statement.strip()
         });
         compiledSpec[testName] = body.join('\n');
diff --git a/scripts/ems/web/lib.php b/scripts/ems/web/lib.php
index 6d936ddf4..68c58860b 100644
--- a/scripts/ems/web/lib.php
+++ b/scripts/ems/web/lib.php
@@ -21,7 +21,7 @@ function load_experiment_info() {
       file_exists($dir."/steps/1")) {
     $topd = dir($dir."/steps");
     while (false !== ($run = $topd->read())) {
-      if (preg_match('/^([0-9]+)$/',$run,$match) 
+      if (preg_match('/^([0-9]+)$/',$run,$match)
           && $run>0
           && !file_exists("$dir/steps/$run/deleted.$run")) {
         $d = dir($dir."/steps/$run");
@@ -49,7 +49,7 @@ function load_experiment_info() {
     }
     $experiment[$id]->start = $stat[9];
   }
-  
+
   reset($experiment);
   while (list($id,$info) = each($experiment)) {
     if (file_exists("$dir/evaluation/report.$id")) {
@@ -57,15 +57,15 @@ function load_experiment_info() {
       foreach ($f as $line_num => $line) {
 	if (preg_match('/^(.+): (.+)/',$line,$match)) {
 	  $experiment[$id]->result[$match[1]] = $match[2];
-          if (!$evalset || !array_key_exists($match[1],$evalset)) { 
-            $evalset[$match[1]] = 0; 
+          if (!$evalset || !array_key_exists($match[1],$evalset)) {
+            $evalset[$match[1]] = 0;
           }
 	  $evalset[$match[1]]++;
 	}
       }
     }
   }
-  
+
   krsort($experiment);
   uksort($evalset,"evalsetsort");
 }
@@ -81,7 +81,7 @@ function load_parameter($run) {
   if (file_exists($dir."/steps/new") ||
       file_exists($dir."/steps/$run")) {
     $file = file("$dir/steps/$run/parameter.$run");
-  } 
+  }
   else {
   $file = file("$dir/steps/parameter.$run");
   }
@@ -121,7 +121,7 @@ function process_file_entry($dir,$entry) {
 	if (file_exists($file.".STDOUT")) { $stat2 = stat($file.".STDOUT"); }
 	if ($stat2[9] > $stat[9]) { $stat = $stat2; }
 	$time = $stat[9];
-	
+
 	if (!$experiment || !array_key_exists($run,$experiment) ||
             !property_exists($experiment[$run],"last_step_time") ||
 	    $time > $experiment[$run]->last_step_time) {
@@ -142,7 +142,7 @@ function get_analysis_version($dir,$set,$id) {
     #while(list($type,$i) = each($analysis_version[$id][$set])) {
     #  print "$type=$i ";
     #}
-    #print ") FROM CACHE<br>"; 
+    #print ") FROM CACHE<br>";
     return $analysis_version[$id][$set];
   }
   $analysis_version[$id][$set]["basic"] = 0;
@@ -188,7 +188,7 @@ function get_analysis_version($dir,$set,$id) {
         file_exists("$dir/model/biconcor.$match[1]")) {
 	$analysis_version[$id][$set]["biconcor"] = $match[1];
       }
-    } 
+    }
   }
 
   # legacy stuff below...
@@ -225,7 +225,7 @@ function get_analysis_version($dir,$set,$id) {
   #while(list($type,$i) = each($analysis_version[$id][$set])) {
   #    print "$type=$i ";
   #}
-  #print ") ZZ<br>"; 
+  #print ") ZZ<br>";
   return $analysis_version[$id][$set];
 }
 
diff --git a/scripts/ems/web/overview.php b/scripts/ems/web/overview.php
index ce0434bb8..534c7d8c0 100644
--- a/scripts/ems/web/overview.php
+++ b/scripts/ems/web/overview.php
@@ -39,7 +39,7 @@ function overview() {
       $report_info = "$dir/steps/$id/REPORTING_report.$id.INFO";
       // does the analysis file exist?
       if (file_exists($analysis)) {
-	if (!array_key_exists($set,$has_analysis)) { 
+	if (!array_key_exists($set,$has_analysis)) {
 	  $has_analysis[$set] = 0;
         }
         $has_analysis[$set]++;
@@ -138,7 +138,7 @@ new Ajax.Updater("<?php print "$module_step[0]-$module_step[1]-$id"; ?>", '?setS
 		}
 	      }
 	  }
-	  else { $score = ""; }  
+	  else { $score = ""; }
       }
   }
   print "var best_score = [];\n";
@@ -158,9 +158,9 @@ function getHTTPObject(){
     alert("Your browser does not support AJAX.");
     return null;
   }
-} 
+}
 function createCommentBox( runID ) {
-  document.getElementById("run-" + runID).innerHTML = "<form onsubmit=\"return false;\"><input id=\"comment-" + runID + "\" name=\"comment-" + runID + "\" size=30><br><input type=submit onClick=\"addComment('" + runID + "');\" value=\"Add Comment\"></form>"; 
+  document.getElementById("run-" + runID).innerHTML = "<form onsubmit=\"return false;\"><input id=\"comment-" + runID + "\" name=\"comment-" + runID + "\" size=30><br><input type=submit onClick=\"addComment('" + runID + "');\" value=\"Add Comment\"></form>";
   if (currentComment[runID]) {
     document.getElementById("comment-" + runID).value = currentComment[runID];
   }
@@ -196,7 +196,7 @@ function highlightBest() {
 	for (run in score) {
 	    var column = "score-"+run+"-"+set;
 	    if ($(column)) {
-	        if (score[run][set] == best_score[set]) {		
+	        if (score[run][set] == best_score[set]) {
 		   $(column).setStyle({ backgroundColor: '#a0ffa0'});
 		}
 	        else if (score[run][set]+1 >= best_score[set]) {
@@ -219,7 +219,7 @@ function highlightLine( id ) {
           $(column).setStyle({ backgroundColor: '#ffffff'});
         }
         else {
-	  if (score[run][set] < score[id][set]-1) {		
+	  if (score[run][set] < score[id][set]-1) {
 	    $(column).setStyle({ backgroundColor: '#ffa0a0'});
 	  }
 	  else if (score[run][set] < score[id][set]) {
@@ -234,7 +234,7 @@ function highlightLine( id ) {
 	}
       }
     }
-  }   
+  }
 }
 function lowlightAll() {
   for (run in score) {
@@ -298,13 +298,13 @@ function output_score($id,$info) {
           preg_match('/([\d\(\)\.\s]+) (METEOR[\-c]*)/',$each_score[$i],$match)) {
         if ($i>0) { print "<BR>"; }
 	$opened_a_tag = 0;
-        if ($set != "avg") { 
+        if ($set != "avg") {
 	  if (file_exists("$dir/evaluation/$set.cleaned.$id")) {
-	    print "<a href=\"?$state&show=evaluation/$set.cleaned.$id\">"; 
+	    print "<a href=\"?$state&show=evaluation/$set.cleaned.$id\">";
             $opened_a_tag = 1;
 	  }
           else if (file_exists("$dir/evaluation/$set.output.$id")) {
-            print "<a href=\"?$state&show=evaluation/$set.output.$id\">"; 
+            print "<a href=\"?$state&show=evaluation/$set.output.$id\">";
 	    $opened_a_tag = 1;
           }
         }
@@ -336,7 +336,7 @@ function tune_status($id) {
   if (! file_exists($dir."/tuning/tmp.".$id)) { return ""; }
   $d = dir($dir."/tuning/tmp.".$id);
   while (false !== ($entry = $d->read())) {
-    if (preg_match('/run(\d+).moses.ini/',$entry,$match) 
+    if (preg_match('/run(\d+).moses.ini/',$entry,$match)
         && $match[1] > $max_iteration) {
       $max_iteration = $match[1];
     }
@@ -383,7 +383,7 @@ function show() {
   }
 
   $fullname = $dir."/steps/".$extra.$_GET["show"];
-  if (preg_match("/\//",$_GET["show"])) { 
+  if (preg_match("/\//",$_GET["show"])) {
     $fullname = $dir."/".$_GET["show"];
   }
   if (preg_match("/graph/",$fullname)) {
diff --git a/scripts/ems/web/progress.perl b/scripts/ems/web/progress.perl
index fd742e410..fa2ce9e8f 100755
--- a/scripts/ems/web/progress.perl
+++ b/scripts/ems/web/progress.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl 
+#!/usr/bin/env perl
 
 use warnings;
 use strict;
diff --git a/scripts/ems/web/sgviz.js b/scripts/ems/web/sgviz.js
index 03ad4741a..3e63260ee 100644
--- a/scripts/ems/web/sgviz.js
+++ b/scripts/ems/web/sgviz.js
@@ -54,7 +54,7 @@ function process_hypotheses() {
 
 //
 // INITIALIZATION
-// 
+//
 
 function index_hypotheses_by_cell() {
   // init edge_lists
@@ -93,7 +93,7 @@ function find_reachable_hypotheses_recursive( id ) {
     find_reachable_hypotheses_recursive( children[c] );
   }
 }
-  
+
 function compute_best_derivation_scores() {
   for(var from=0; from<length; from++ ) {
     cell_derivation_score[from] = Array();
@@ -147,7 +147,7 @@ function click_menu( id, force_flag ) {
     return;
   }
   menu_processing = 1;
-  
+
   if (current_menu_selection == 1) { best_derivation(0); }
   if (current_menu_selection == 2) { unannotate_cells(); }
   if (current_menu_selection == 3) { unannotate_cells(); }
@@ -155,7 +155,7 @@ function click_menu( id, force_flag ) {
   if (current_menu_selection == 5) { remove_non_terminal_treemap(0); }
   if (current_menu_selection == 6 && SORT_OPTION != 3) { remove_hypothesis_overview(); }
   if (current_menu_selection == 6 && SORT_OPTION == 3) { remove_hypothesis_overview(); remove_non_terminal_treemap(); }
-  if (current_menu_selection > 0) { 
+  if (current_menu_selection > 0) {
     highlight_menu_button( current_menu_selection, 0 );
   }
 
@@ -196,8 +196,8 @@ function draw_menu_button( id, label ) {
   var content = document.createTextNode( label );
   button_label.appendChild( content );
   button_label.setAttribute("onclick","click_menu(" + id + ",0);")
-  
-  chart.appendChild( button_label );  
+
+  chart.appendChild( button_label );
 }
 
 function highlight_menu_button( id, on_off ) {
@@ -251,8 +251,8 @@ function draw_option_button( rule_option, id, label ) {
   button_label.setAttribute("pointer-events", "none");
   var content = document.createTextNode( label );
   button_label.appendChild( content );
-  
-  chart.appendChild( button_label );  
+
+  chart.appendChild( button_label );
 }
 
 function draw_sort_button( id, label ) {
@@ -294,8 +294,8 @@ function draw_sort_button( id, label ) {
   button_label.setAttribute("pointer-events", "none");
   var content = document.createTextNode( label );
   button_label.appendChild( content );
-  
-  chart.appendChild( button_label );  
+
+  chart.appendChild( button_label );
 }
 
 function click_sort( id ) {
@@ -319,17 +319,17 @@ var show_scores = 0;
 var show_id = 0;
 var show_derivation = 0;
 function click_option( id ) {
-  if (id == 1) { 
-    show_scores = !show_scores; 
+  if (id == 1) {
+    show_scores = !show_scores;
     highlight_option_button( 0, 1, show_scores );
   }
-  if (id == 2) { 
-    show_derivation = !show_derivation; 
+  if (id == 2) {
+    show_derivation = !show_derivation;
     color_cells();
     highlight_option_button( 0, 2, show_derivation );
   }
-  if (id == 3) { 
-    show_id = !show_id; 
+  if (id == 3) {
+    show_id = !show_id;
     highlight_option_button( 0, 3, show_id );
   }
   if (current_menu_selection > 0) {
@@ -340,15 +340,15 @@ function click_option( id ) {
 var show_hyp_score = 0;
 var show_derivation_score = 0;
 function click_rule_option( id ) {
-  if (id == 1) { 
-    show_hyp_score = !show_hyp_score; 
+  if (id == 1) {
+    show_hyp_score = !show_hyp_score;
     highlight_option_button( 1, 1, show_hyp_score );
   }
-  if (id == 2) { 
-    show_derivation_score = !show_derivation_score; 
+  if (id == 2) {
+    show_derivation_score = !show_derivation_score;
     highlight_option_button( 1, 2, show_derivation_score );
   }
-  if (id == 3) { 
+  if (id == 3) {
     if (ZOOM > 0) {
       ZOOM = 0;
     }
@@ -377,7 +377,7 @@ function draw_chart() {
   for (var from=0;from<length;from++) {
     for(var width=1; width<=length-from; width++) {
       var to = from + width - 1;
-      
+
       // logical container
       var container = document.createElementNS(xmlns,"svg");
       container.setAttribute("id", "cell-container-" + from + "-" + to);
@@ -385,7 +385,7 @@ function draw_chart() {
       var transform = document.createElementNS(xmlns,"g");
       transform.setAttribute("id", "cell-" + from + "-" + to);
       container.appendChild( transform );
-    
+
       // yellow box for the cell
 	    var cell = document.createElementNS(xmlns,"rect");
 	    cell.setAttribute("id", "cellbox-" + from + "-" + to);
@@ -403,7 +403,7 @@ function draw_chart() {
 		  cell.setAttribute("onclick","click_cell(" + from + "," + to + ");")
 		  transform.appendChild( cell );
     }
-    
+
     // box for the input word
     var input_box = document.createElementNS(xmlns,"rect");
     input_box.setAttribute("id", "inputbox-" + from);
@@ -415,8 +415,8 @@ function draw_chart() {
 	  input_box.setAttribute("height", CELL_HEIGHT/2);
 	  //cell.setAttribute("opacity", .75);
 	  input_box.setAttribute("fill", INPUT_REGULAR_COLOR);
-    chart.appendChild( input_box ); 
-    
+    chart.appendChild( input_box );
+
     // input word
     input_word = document.createElementNS(xmlns,"text");
     input_word.setAttribute("id", "input-" + from);
@@ -426,7 +426,7 @@ function draw_chart() {
     input_word.setAttribute("text-anchor", "middle");
     var content = document.createTextNode( input[from] );
     input_word.appendChild( content );
-    chart.appendChild( input_word );  
+    chart.appendChild( input_word );
 	}
   assign_chart_coordinates();
 }
@@ -435,7 +435,7 @@ function assign_chart_coordinates() {
   for (var from=0;from<length;from++) {
     for(var width=1; width<=length-from; width++) {
       var to = from + width - 1;
-      
+
 	    var x = from*CELL_WIDTH + (width-1)*CELL_WIDTH/2;
       var y = (length-width)*CELL_HEIGHT*(1-ZOOM);
       //alert("(x,y) = (" + length + "," + width + "), width = " + ZOOM + ", height = " + (1-ZOOM));
@@ -505,7 +505,7 @@ var current_from = -1;
 var current_to;
 function hover_cell( from, to ) {
   if (current_from >= 0) {
-    highlight_input( current_from, current_to, 0)    
+    highlight_input( current_from, current_to, 0)
   }
   highlight_input( from, to, 1)
   current_from = from;
@@ -534,7 +534,7 @@ function highlight_input( from, to, on_off ) {
   }
 }
 
-// 
+//
 // VISUALIZATION OF CHART CELLS
 //
 
@@ -570,7 +570,7 @@ function annotate_cells_with_rulecount() {
 function annotate_cells_with_derivation_score() {
   for (var from=0;from<length;from++) {
     for(var width=1; width<=length-from; width++) {
-      var to = from + width - 1;      
+      var to = from + width - 1;
       var score = cell_derivation_score[from][to];
       if (score < -9e9) { score = "dead end"; }
       annotate_cell( from, to, score, 15 )
@@ -596,12 +596,12 @@ function annotate_cell( from, to, label, font_size ) {
     cell_label.setAttribute("pointer-events", "none");
     cell_label.setAttribute("text-anchor", "middle");
     var content = document.createTextNode(line[i]);
-    cell_label.appendChild( content );  
+    cell_label.appendChild( content );
     cell_label_group.appendChild( cell_label );
   }
 
   var cell = document.getElementById("cell-" + from + "-" + to);
-  cell.appendChild( cell_label_group );  
+  cell.appendChild( cell_label_group );
 }
 
 function unannotate_cells() {
@@ -624,7 +624,7 @@ function unannotate_cell( from, to ) {
 function non_terminal_treemap( with_hyps ) {
   for (var from=0;from<length;from++) {
     for(var width=1; width<=length-from; width++) {
-      var to = from + width - 1;      
+      var to = from + width - 1;
       // get nt counts
       var lhs = new Array();
       var lhs_list = new Array();
@@ -639,7 +639,7 @@ function non_terminal_treemap( with_hyps ) {
           lhs[nt]++;
         }
       }
-      // sort 
+      // sort
       function sortByCount(a,b) {
         return lhs[b] - lhs[a];
       }
@@ -652,7 +652,7 @@ function non_terminal_treemap( with_hyps ) {
 function remove_non_terminal_treemap()  {
   for (var from=0;from<length;from++) {
     for(var width=1; width<=length-from; width++) {
-      var to = from + width - 1;      
+      var to = from + width - 1;
       var cell = document.getElementById("cell-" + from + "-" + to);
       var done = false;
       var j=0;
@@ -693,7 +693,7 @@ function treemap_cell( from, to, label, count, total, with_hyps ) {
     rect.setAttribute("stroke", "black");
     rect.setAttribute("stroke-width", "0.5");
     rect.setAttribute("onclick","click_menu(" + id + ",0);")
-    cell.appendChild( rect );  
+    cell.appendChild( rect );
     x += width * count[label[i]] / total;
   }
 }
@@ -749,7 +749,7 @@ function treemap_squarify( from, to, label, count, total, with_hyps ) {
         rect.setAttribute("pointer-events", "none");
         rect.setAttribute("stroke", "black");
         rect.setAttribute("stroke-width", "0.5");
-        cell.appendChild( rect );  
+        cell.appendChild( rect );
         // hypotheses
         if (with_hyps) {
           var hyp_list = Array();
@@ -760,15 +760,15 @@ function treemap_squarify( from, to, label, count, total, with_hyps ) {
               hyp_list.push( id );
             }
           }
-          hypothesis_in_rect( this_width * scale_factor - 2, 
-                              this_height * scale_factor - 2, 
-                              CELL_MARGIN + (offset_x + cum_x) * scale_factor + 1, 
-                              CELL_MARGIN + (offset_y + cum_y) * scale_factor + 1, 
+          hypothesis_in_rect( this_width * scale_factor - 2,
+                              this_height * scale_factor - 2,
+                              CELL_MARGIN + (offset_x + cum_x) * scale_factor + 1,
+                              CELL_MARGIN + (offset_y + cum_y) * scale_factor + 1,
                               cell, hyp_list );
         }
         // label
         var font_size = Math.min( Math.round(this_width * scale_factor / label[j].length * 1.3),
-                                  Math.round(this_height * scale_factor )); 
+                                  Math.round(this_height * scale_factor ));
         if (font_size > 20) { font_size = 20; }
         if (font_size >= 3) {
           var rect_label = document.createElementNS(xmlns,"text");
@@ -782,7 +782,7 @@ function treemap_squarify( from, to, label, count, total, with_hyps ) {
           rect_label.setAttribute("pointer-events", "none");
           var content = document.createTextNode( label[j] );
           rect_label.appendChild( content );
-          cell.appendChild( rect_label );  
+          cell.appendChild( rect_label );
         }
         if (adding_on_left) { cum_y += this_height; }
         else                { cum_x += this_width; }
@@ -829,7 +829,7 @@ function best_derivation( on_off ) {
   best_derivation_recurse( best_id, on_off, -1, -1, 0 );
 }
 
-function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos ) {  
+function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos ) {
   var from = edge[id][FROM];
   var to = edge[id][TO];
 
@@ -846,10 +846,10 @@ function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos
   else {
     unannotate_cell( from, to );
   }
-  
+
   // highlight hyp
   highlight_hyp( id, on_off );
-  
+
   // arrow to parent
   if (parent_from >= 0) {
     if (on_off) {
@@ -860,7 +860,7 @@ function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos
       chart.removeChild(arrow);
     }
   }
-  
+
   var child_order = Array();
   if (edge[id][ALIGNMENT] != "") {
     var alignment = edge[id][ALIGNMENT].split(" ");
@@ -880,7 +880,7 @@ function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos
       child_order[target_source[1]] = i;
     }
   }
-  
+
   // recurse
   var covered = new Array;
   var children = get_children( id );
@@ -888,7 +888,7 @@ function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos
     var child = children[c];
     for( var i=edge[child][FROM]; i<=edge[child][TO]; i++ ) {
       covered[i] = 1;
-    } 
+    }
     best_derivation_recurse( child, on_off, from, to, children.length == 1 ? 0.5 : child_order[c]/(children.length-1.0) );
   }
 
@@ -900,10 +900,10 @@ function best_derivation_recurse( id, on_off, parent_from, parent_to, child_pos
       }
       else {
         var arrow = document.getElementById("arrow-word-" + i);
-        chart.removeChild(arrow);        
+        chart.removeChild(arrow);
       }
     }
-  } 
+  }
 }
 
 function make_arrow( id, parent_from, parent_to, from, to, word_flag, position ) {
@@ -1034,7 +1034,7 @@ function hypothesis_in_rect( width, height, offset_x, offset_y, parent_element,
 
   for (var i=0; i<hyp_list.length;i++) {
     id = hyp_list[i];
-        
+
     //alert("adding circle (" + (x + diameter/2) + "," + (y + diameter/2) + ") - " + (diameter/2) );
     var hyp = document.createElementNS(xmlns,"circle");
     hyp.setAttribute("id", "hyp-" + id);
@@ -1045,7 +1045,7 @@ function hypothesis_in_rect( width, height, offset_x, offset_y, parent_element,
 	  hyp.setAttribute("onmouseover","hover_hyp(" + id + ");")
 	  hyp.setAttribute("onmouseout","unhover_hyp(" + id + ");")
 	  parent_element.appendChild( hyp );
-	  
+
 	  x += diameter;
     if (++column >= row_size) {
       column = 0;
@@ -1114,7 +1114,7 @@ function hyp_color( id, on_off ) {
   if (on_off) {
     var color = "#ff0000";
     if (edge[id][RECOMBINED]>0) { color = "#808080"; }
-    else if (id in reachable) { color = "#00c000"; }    
+    else if (id in reachable) { color = "#00c000"; }
     return color;
   }
   var color = "#ffc0c0";
@@ -1136,26 +1136,26 @@ function get_rule( id ) {
     var source_target = alignment[i].split("-");
     nt_label.push(output[source_target[1]]);
   }
-  
+
   var rule = edge[id][LHS]+"\u2192";
   var children = get_children(id);
   var pos = edge[id][FROM];
   for (var i=0; i<children.length; i++) {
     if (pos != edge[id][FROM]) { rule += " "; }
     var child = children[i];
-    for(;pos<edge[child][FROM];pos++) { 
-      rule += (input[pos].length <= 10) ? input[pos] : input[pos].substr(0,8) + "."; 
+    for(;pos<edge[child][FROM];pos++) {
+      rule += (input[pos].length <= 10) ? input[pos] : input[pos].substr(0,8) + ".";
       rule += " ";
     }
     rule += nt_label[i];
-    rule += (edge[child][FROM] == edge[child][TO]) ? 
+    rule += (edge[child][FROM] == edge[child][TO]) ?
       "[" + edge[child][FROM] + "]" :
       "[" + edge[child][FROM] + "-" + edge[child][TO] + "]";
     pos = edge[child][TO]+1;
   }
-  for(;pos<=edge[id][TO];pos++) { 
+  for(;pos<=edge[id][TO];pos++) {
     if (pos != edge[id][FROM]) { rule += " "; }
-    rule += (input[pos].length <= 10) ? input[pos] : input[pos].substr(0,8) + "."; 
+    rule += (input[pos].length <= 10) ? input[pos] : input[pos].substr(0,8) + ".";
   }
 
   return rule;
@@ -1176,10 +1176,10 @@ function show_rules( from, to ) {
   cell.setAttribute("stroke-width", "3");
   current_rule_from = from;
   current_rule_to = to;
-  
+
   best_hyp_score = -9e9;
   best_derivation_score = cell_derivation_score[from][to];
-  
+
   var rule_hash = Array();
   var rule_count = Array();
   rule_list = Array();
@@ -1196,16 +1196,16 @@ function show_rules( from, to ) {
       rule_count[rule_hash[rule]]++;
     }
     edge2rule[id] = rule_hash[rule];
-    
-    if (edge[id][HYP_SCORE] > best_hyp_score) { 
-      best_hyp_score = edge[id][HYP_SCORE]; 
+
+    if (edge[id][HYP_SCORE] > best_hyp_score) {
+      best_hyp_score = edge[id][HYP_SCORE];
     }
   }
   function sortByRuleCount( a, b ) {
     return rule_count[rule_hash[b]] - rule_count[rule_hash[a]];
   }
   rule_list = rule_list.sort(sortByRuleCount);
-  
+
   RULE_HEIGHT = 15;
   RULE_FONT_SIZE = 11;
   // squeeze if too many rules
@@ -1214,7 +1214,7 @@ function show_rules( from, to ) {
     RULE_HEIGHT = Math.floor( RULE_HEIGHT * factor );
     RULE_FONT_SIZE = Math.ceil( RULE_FONT_SIZE * factor );
   }
-  
+
   draw_rule_options();
   for(var i=-1; i<rule_list.length; i++) {
     draw_rule(from, to, i);
@@ -1243,7 +1243,7 @@ function unshow_rules() {
   finished = 0;
   for(var i=1; !finished; i++) {
     var old = document.getElementById("rule-option-" + i);
-    if (old != null) { 
+    if (old != null) {
       chart.removeChild( old );
       var old = document.getElementById("rule-option-label-" + i);
       chart.removeChild( old );
@@ -1306,12 +1306,12 @@ function click_rule( from, to, rule_id ) {
   // highlight current rule
   if (current_rule_id>=0) {
     var rule_label = document.getElementById("rule-"+current_rule_id);
-    rule_label.setAttribute("style", "font-size: "+RULE_FONT_SIZE+"; font-family: Verdana, Arial;");    
+    rule_label.setAttribute("style", "font-size: "+RULE_FONT_SIZE+"; font-family: Verdana, Arial;");
   }
   var rule_label = document.getElementById("rule-"+rule_id);
   rule_label.setAttribute("style", "font-size: "+RULE_FONT_SIZE+"; font-family: Verdana, Arial; font-weight: bold;");
   current_rule_id = rule_id;
-  
+
   // first get all the data
   output_list = Array();
   var output_hash = Array();
@@ -1332,7 +1332,7 @@ function click_rule( from, to, rule_id ) {
       // create index for children
       var children = get_children( id );
       for(var j=0;j<children.length;j++) {
-        // init children indices if needed 
+        // init children indices if needed
         if (j > children_list.length-1) {
           children_hash.push([]);
           children_list.push([]);
@@ -1346,7 +1346,7 @@ function click_rule( from, to, rule_id ) {
       }
     }
   }
-  
+
   // sort
   function sortBySecond(a,b) {
     asplit = a.split("|");
@@ -1361,7 +1361,7 @@ function click_rule( from, to, rule_id ) {
   for(var i=0;i<children.length;i++) {
     children_list[i].sort(sortHypByScore);
   }
-  
+
   // select dimensions of rule cube
   axis = Array();
   axis.push(output_list);
@@ -1394,7 +1394,7 @@ function draw_rule_cube(z_pos_string) {
   if (z_pos_string != "") {
     z_pos = z_pos_string.split(",");
   }
-  
+
   // draw rube cube
   var old = document.getElementById("rule-cube");
   if (old != null) { chart.removeChild( old ); }
@@ -1439,7 +1439,7 @@ function draw_rule_cube(z_pos_string) {
   }
   else if (max_length+8 > CHART_HEIGHT/9) {
     RULE_CUBE_HYP_SIZE = 9;
-    RULE_CUBE_FONT_SIZE = 7;    
+    RULE_CUBE_FONT_SIZE = 7;
   }
   else {
     RULE_CUBE_HYP_SIZE = CHART_HEIGHT/(max_length+8);
@@ -1455,7 +1455,7 @@ function draw_rule_cube(z_pos_string) {
   rule_cube.setAttribute("x", CHART_WIDTH - 30);
   rule_cube.setAttribute("y", 0);
   chart.appendChild( rule_cube );
-  
+
   // draw y axis
   var label = get_rule_axis_name(dimension_order[0]);
   draw_rule_row(-1,label);
@@ -1470,7 +1470,7 @@ function draw_rule_cube(z_pos_string) {
   // draw x axis
   if (axis.length > 1) {
     var label = get_rule_axis_name(dimension_order[1]);
-    draw_rule_column(-1,label);  
+    draw_rule_column(-1,label);
     for(var x=0; x<axis[dimension_order[1]].length && x<CHART_HEIGHT/9-10; x++) {
       var label = get_rule_axis_label(dimension_order[1], x);
       draw_rule_column(x,label);
@@ -1478,7 +1478,7 @@ function draw_rule_cube(z_pos_string) {
     if (axis[dimension_order[1]].length > CHART_HEIGHT/9-10) {
       draw_rule_column(Math.ceil(CHART_HEIGHT/9-10),"(more, "+axis[dimension_order[1]].length+" total)");
     }
-  }  
+  }
 
   // draw hyps
   for(var y=0; y<axis[dimension_order[0]].length && y<(CHART_HEIGHT-Z_HEIGHT)/9-10; y++) {
@@ -1493,8 +1493,8 @@ function draw_rule_cube(z_pos_string) {
       }
     }
   }
-      
-  
+
+
   // draw z-axes
   var pos_offset = axis[dimension_order[0]].length+2;
   for(var z=2;z<dimension_order.length;z++) {
@@ -1506,7 +1506,7 @@ function draw_rule_cube(z_pos_string) {
     }
     pos_offset += axis[dimension_order[z]].length+2;
   }
-  
+
   // report summary statistics
   var message = output_list.length + " output phrases";
   message += "<br>DEBUG: " + axis.length;
@@ -1514,7 +1514,7 @@ function draw_rule_cube(z_pos_string) {
   for(var i=0;i<children_list.length;i++) {
     message += "<br>" + children_list[i].length + " hyps for NT" + (i+1);
   }
-  //draw_rule_message(message);  
+  //draw_rule_message(message);
 }
 
 function find_hyp_by_rule(position, dimension_order) {
@@ -1524,14 +1524,14 @@ function find_hyp_by_rule(position, dimension_order) {
     var match = 1;
     for(var p=0; p<position.length; p++) {
       if (dimension_order[p] == 0) {
-        if (output_list[position[p]] != edge[id][OUTPUT]+"|"+edge[id][HEURISTIC_RULE_SCORE]) { 
+        if (output_list[position[p]] != edge[id][OUTPUT]+"|"+edge[id][HEURISTIC_RULE_SCORE]) {
           match = 0;
         }
       }
       else {
         var nt_number = dimension_order[p]-1;
-        if (children_list[nt_number][position[p]] != children[nt_number]) { 
-          match = 0; 
+        if (children_list[nt_number][position[p]] != children[nt_number]) {
+          match = 0;
         }
       }
     }
@@ -1580,7 +1580,7 @@ function get_full_output( id ) {
     var source_target = alignment[i].split("-");
     nonterminal[source_target[1]] = children[i];
   }
-  
+
   var full_output = "";
   for(var i=0;i<output.length;i++) {
     if (nonterminal[i] === undefined) {
@@ -1647,7 +1647,7 @@ function draw_rule_z( z,total_z, z_pos, pos,pos_offset, label ) {
   else {
     rule_label.setAttribute("style", "font-size: "+(RULE_CUBE_FONT_SIZE-2)+"; font-family: Verdana, Arial; font-weight: bold;");
   }
-   
+
   var content = document.createTextNode( label );
   rule_label.appendChild( content );
   var rule_cube = document.getElementById("rule-cube");
@@ -1686,7 +1686,7 @@ function rule_hyp_color( id, on_off ) {
     }
     else {
       derivation_score_color = get_score_from_color(best_derivation_score-edge[id][DERIVATION_SCORE]);
-    }  
+    }
   }
   return "#" + inactive_color + derivation_score_color + hyp_score_color;
 }
diff --git a/scripts/ems/web/sgviz.php b/scripts/ems/web/sgviz.php
index bac9289ba..9fccadf60 100644
--- a/scripts/ems/web/sgviz.php
+++ b/scripts/ems/web/sgviz.php
@@ -39,7 +39,7 @@ new Ajax.Request('?analysis=sgviz_data'
     method: "post"
   });
 </script></body></html>
-<?php 
+<?php
 // read graph
 //$file = get_current_analysis_filename("basic","search-graph")."/graph.$sentence";
 //$handle = fopen($file,"r");
@@ -55,7 +55,7 @@ function sgviz_data($sentence) {
   $file = get_current_analysis_filename("basic","search-graph")."/graph.$sentence";
 
   $handle = fopen($file,"r");
-  while (($line = fgets($handle)) !== false) { 
+  while (($line = fgets($handle)) !== false) {
     $e = explode("\t",addslashes(chop($line)));
     $edge[$e[0]] = array($e[1],$e[2],$e[3],$e[4],$e[5],$e[6],$e[7],$e[8],$e[9],$e[10]);
   }