Merge pull request #1 from bradfordcondon/advancedoptions

fix validator for proteins.  remove unused parameters in validate.

includes/blast_ui.form_advanced_options.inc

@@ -142,9 +142,6 @@ function blast_ui_blastn_advanced_options_form_submit($form, $form_state) {
   // Expand Match/Mismatch option into penalty/reward values
   $m_m = _set_match_mismatch($form_state['values']['M&MScores']);
 
-  // Limit number of query hits
-  $qRange = $form_state['values']['qRange'];
-
   return array(
     'max_target_seqs' => $numAlign,
     'evalue' => $eVal,
@@ -415,14 +412,16 @@ function blast_ui_blastp_advanced_options_form_submit($form, $form_state) {
   $wsKey = $form_state['values']['wordSize'];
   $wordSize = $form['ALG']['GParam']['wordSize']['#options'][$wsKey];
 
-/*eksc: removed as this is either equivalent to max_target_sequences or mis-implemented
-       as culling_limit
-  $qRange = $form_state['values']['qRange'];
-*/
+  //$qRange = $form_state['values']['qRange'];
+
   // Expand Gap Cost key into open and extend penalties
   $matrix = $form_state['values']['Matrix'];
   $gapKey = $form_state['values']['gapCost'];
-  $gap = _set_protein_gap($matrix, $gapKey);
+
+
+  $gap = _set_gap($gapKey);
+  $gapOpen = $gap['gapOpen'];
+  $gapExtend = $gap['gapExtend'];
 
   return array(
     'max_target_seqs' => $numAlign,
@@ -430,7 +429,7 @@ function blast_ui_blastp_advanced_options_form_submit($form, $form_state) {
     'word_size' => $wordSize,
     'gapopen' => $gapOpen,
     'gapextend' => $gapExtend,
-    'culling_limit' => $qRange,
+    //'culling_limit' => $qRange,
     'matrix' => $matrix,
   );
 }//blast_ui_blastp_advanced_options_form_submit
@@ -673,7 +672,7 @@ function _get_default_values($options, $program) {
     }
     else {
       if ($reward == 3) {
-        $matchmis = 4;
+        $matchmiss = 4;
       }
       else {
         if ($reward == 4) {
@@ -881,363 +880,6 @@ function _set_match_mismatch($m_m) {
   return array('penalty' => $penalty, 'reward' => $reward);
 }
 
-/**
- * Get gap values based on matrix and selected gap "key"
- */
-function _set_protein_gap($matrix, $gapKey) {
-  switch ($matrix) {
-    case 'PAM30':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 7;
-          $gapExtend = 2;
-          break;
-        case 1:
-          $gapOpen = 6;
-          $gapExtend = 2;
-          break;
-        case 2:
-          $gapOpen = 5;
-          $gapExtend = 2;
-          break;
-        case 3:
-          $gapOpen = 10;
-          $gapExtend = 1;
-          break;
-        case 4:
-          $gapOpen = 9;
-          $gapExtend = 1;
-          break;
-        case 5:
-          $gapOpen = 8;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'PAM70':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 8;
-          $gapExtend = 2;
-          break;
-        case 1:
-          $gapOpen = 7;
-          $gapExtend = 2;
-          break;
-        case 2:
-          $gapOpen = 6;
-          $gapExtend = 2;
-          break;
-        case 3:
-          $gapOpen = 11;
-          $gapExtend = 1;
-          break;
-        case 4:
-          $gapOpen = 10;
-          $gapExtend = 1;
-          break;
-        case 5:
-          $gapOpen = 9;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'PAM250':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 15;
-          $gapExtend = 3;
-          break;
-        case 1:
-          $gapOpen = 14;
-          $gapExtend = 3;
-          break;
-        case 2:
-          $gapOpen = 13;
-          $gapExtend = 3;
-          break;
-        case 3:
-          $gapOpen = 12;
-          $gapExtend = 3;
-          break;
-        case 4:
-          $gapOpen = 11;
-          $gapExtend = 3;
-          break;
-        case 5:
-          $gapOpen = 17;
-          $gapExtend = 2;
-          break;
-        case 6:
-          $gapOpen = 16;
-          $gapExtend = 2;
-          break;
-        case 7:
-          $gapOpen = 15;
-          $gapExtend = 2;
-          break;
-        case 8:
-          $gapOpen = 14;
-          $gapExtend = 2;
-          break;
-        case 9:
-          $gapOpen = 13;
-          $gapExtend = 2;
-          break;
-        case 10:
-          $gapOpen = 21;
-          $gapExtend = 1;
-          break;
-        case 11:
-          $gapOpen = 20;
-          $gapExtend = 1;
-          break;
-        case 12:
-          $gapOpen = 19;
-          $gapExtend = 1;
-          break;
-        case 13:
-          $gapOpen = 18;
-          $gapExtend = 1;
-          break;
-        case 14:
-          $gapOpen = 17;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'BLOSUM80':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 8;
-          $gapExtend = 2;
-          break;
-        case 1:
-          $gapOpen = 7;
-          $gapExtend = 2;
-          break;
-        case 2:
-          $gapOpen = 6;
-          $gapExtend = 2;
-          break;
-        case 3:
-          $gapOpen = 11;
-          $gapExtend = 1;
-          break;
-        case 4:
-          $gapOpen = 10;
-          $gapExtend = 1;
-          break;
-        case 5:
-          $gapOpen = 9;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'BLOSUM62':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 11;
-          $gapExtend = 2;
-          break;
-        case 1:
-          $gapOpen = 10;
-          $gapExtend = 2;
-          break;
-        case 2:
-          $gapOpen = 9;
-          $gapExtend = 2;
-          break;
-        case 3:
-          $gapOpen = 8;
-          $gapExtend = 2;
-          break;
-        case 4:
-          $gapOpen = 7;
-          $gapExtend = 2;
-          break;
-        case 5:
-          $gapOpen = 6;
-          $gapExtend = 2;
-          break;
-        case 6:
-          $gapOpen = 13;
-          $gapExtend = 1;
-          break;
-        case 7:
-          $gapOpen = 12;
-          $gapExtend = 1;
-          break;
-        case 8:
-          $gapOpen = 11;
-          $gapExtend = 1;
-          break;
-        case 9:
-          $gapOpen = 10;
-          $gapExtend = 1;
-          break;
-        case 10:
-          $gapOpen = 9;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'BLOSUM45':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 13;
-          $gapExtend = 3;
-          break;
-        case 1:
-          $gapOpen = 12;
-          $gapExtend = 3;
-          break;
-        case 2:
-          $gapOpen = 11;
-          $gapExtend = 3;
-          break;
-        case 3:
-          $gapOpen = 10;
-          $gapExtend = 3;
-          break;
-        case 4:
-          $gapOpen = 15;
-          $gapExtend = 2;
-          break;
-        case 5:
-          $gapOpen = 14;
-          $gapExtend = 2;
-          break;
-        case 6:
-          $gapOpen = 13;
-          $gapExtend = 2;
-          break;
-        case 7:
-          $gapOpen = 12;
-          $gapExtend = 2;
-          break;
-        case 8:
-          $gapOpen = 19;
-          $gapExtend = 1;
-          break;
-        case 9:
-          $gapOpen = 18;
-          $gapExtend = 1;
-          break;
-        case 10:
-          $gapOpen = 17;
-          $gapExtend = 1;
-          break;
-        case 11:
-          $gapOpen = 16;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'BLOSUM50':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 13;
-          $gapExtend = 3;
-          break;
-        case 1:
-          $gapOpen = 12;
-          $gapExtend = 3;
-          break;
-        case 2:
-          $gapOpen = 11;
-          $gapExtend = 3;
-          break;
-        case 3:
-          $gapOpen = 10;
-          $gapExtend = 3;
-          break;
-        case 4:
-          $gapOpen = 9;
-          $gapExtend = 3;
-          break;
-        case 5:
-          $gapOpen = 16;
-          $gapExtend = 2;
-          break;
-        case 6:
-          $gapOpen = 15;
-          $gapExtend = 2;
-          break;
-        case 7:
-          $gapOpen = 14;
-          $gapExtend = 2;
-          break;
-        case 8:
-          $gapOpen = 13;
-          $gapExtend = 2;
-          break;
-        case 9:
-          $gapOpen = 12;
-          $gapExtend = 2;
-          break;
-        case 10:
-          $gapOpen = 19;
-          $gapExtend = 1;
-          break;
-        case 11:
-          $gapOpen = 18;
-          $gapExtend = 1;
-          break;
-        case 12:
-          $gapOpen = 17;
-          $gapExtend = 1;
-          break;
-        case 13:
-          $gapOpen = 16;
-          $gapExtend = 1;
-          break;
-        case 14:
-          $gapOpen = 15;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-    case 'BLOSUM90':
-      switch ($gapKey) {
-        case 0:
-          $gapOpen = 9;
-          $gapExtend = 2;
-          break;
-        case 1:
-          $gapOpen = 8;
-          $gapExtend = 2;
-          break;
-        case 2:
-          $gapOpen = 7;
-          $gapExtend = 2;
-          break;
-        case 3:
-          $gapOpen = 6;
-          $gapExtend = 2;
-          break;
-        case 4:
-          $gapOpen = 11;
-          $gapExtend = 1;
-          break;
-        case 5:
-          $gapOpen = 10;
-          $gapExtend = 1;
-          break;
-        case 6:
-          $gapOpen = 9;
-          $gapExtend = 1;
-          break;
-      }
-      break;
-  }
-
-  return array(
-    'gapOpen' => $gapOpen,
-    'gapExtend' => $gapExtend,
-  );
-}
-
 /**
  * AJAX callback for match and gap cost.
  * @param $form