set_protein_gap removed

includes/blast_ui.form_advanced_options.inc

@@ -883,364 +883,6 @@ 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