Renamed getGap() to _set_match_mismatch() for clarity of purpose

includes/blast_ui.form_advanced_options.inc

@@ -495,7 +495,7 @@ function blast_ui_blastp_advanced_options_form_submit($form, $form_state) {
   // Expand Gap Cost key into open and extend penalties
   $matrix = $form_state['values']['Matrix'];
   $gapKey = $form_state['values']['gapCost'];
-  $gap    = getGap($matrix, $gapKey);
+  $gap    = _set_protein_gap($matrix, $gapKey);
 
 //eksc- need to implement query range limit
 //  q_range
@@ -946,356 +946,446 @@ function _get_match_mismatch($which) {
   }//switch
 }
 
+/**
+ * Get a list of options for gaps.
+ */
+function _get_gap_options($which) {
+  switch ($which) {
+    case 'blastn':
+      return array(
+        0 => t('Existence: 5 Extension: 2'),
+        1 => t('Existence: 2 Extension: 2'),
+        2 => t('Existence: 1 Extension: 2'),
+        3 => t('Existence: 0 Extension: 2'),
+        4 => t('Existence: 3 Extension: 1'),
+        5 => t('Existence: 2 Extension: 1'),
+        6 => t('Existence: 1 Extension: 1'),
+      );
+   }//switch
+}
+
+/**
+ * Translate above gap options into blast gap open and extend costs.
+ */
+function _set_gap($gap_key) {
+ switch ($gap_key) {
+   case 0:
+      $gapOpen = 5;
+      $gapExtend = 2;
+      break;
+   case 1:
+      $gapOpen = 2;
+      $gapExtend = 2;
+      break;
+   case 2:
+      $gapOpen = 1;
+      $gapExtend = 2;
+      break;
+   case 3:
+      $gapOpen = 0;
+      $gapExtend = 2;
+      break;
+   case 4:
+      $gapOpen = 3;
+      $gapExtend = 1;
+      break;
+   case 5:
+      $gapOpen = 2;
+      $gapExtend = 1;
+      break;
+   case 6:
+      $gapOpen = 1;
+      $gapExtend = 1;
+      break;
+  }//switch
+
+  return array('gapOpen' => $gapOpen, 'gapExtend' => $gapExtend);
+}
+
+/**
+ * Translate mismatch/match ratio option into blast penalty/reward options.
+ */
+function _set_match_mismatch($m_m) {
+  switch ($m_m) {
+   case 0:
+      $penalty = -2;
+      $reward = 1;
+      break;
+   case 1:
+      $penalty = -3;
+      $reward = 1;
+      break;
+   case 2:
+      $penalty = -4;
+      $reward = 1;
+      break;
+   case 3:
+      $penalty = -3;
+      $reward = 2;
+      break;
+   case 4:
+      $penalty = -5;
+      $reward = 4;
+      break;
+   case 5:
+      $penalty = -1;
+      $reward = 1;
+      break;
+  }//switch
+
+  return array('penalty' => $penalty, 'reward' => $reward);
+}
+
+
 /** 
  * Get gap values based on matrix and selected gap "key"
  */
-function getGap($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:
+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:
+          case 1:
                $gapOpen   = 14;
                $gapExtend = 3;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 13;
                $gapExtend = 3;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 12;
                $gapExtend = 3;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 11;
                $gapExtend = 3;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 17;
                $gapExtend = 2;
                break;
-            case 6:
+          case 6:
                $gapOpen   = 16;
                $gapExtend = 2;
                break;
-            case 7:
+          case 7:
                $gapOpen   = 15;
                $gapExtend = 2;
                break;
-            case 8:
+          case 8:
                $gapOpen   = 14;
                $gapExtend = 2;
                break;
-            case 9:
+          case 9:
                $gapOpen   = 13;
                $gapExtend = 2;
                break;
-            case 10:
+          case 10:
                $gapOpen   = 21;
                $gapExtend = 1;
                break;
-            case 11:
+          case 11:
                $gapOpen   = 20;
                $gapExtend = 1;
                break;
-            case 12:
+          case 12:
                $gapOpen   = 19;
                $gapExtend = 1;
                break;
-            case 13:
+          case 13:
                $gapOpen   = 18;
                $gapExtend = 1;
                break;
-            case 14:
+          case 14:
                $gapOpen   = 17;
                $gapExtend = 1;
                break;
-         }
-         break;
-      case 'BLOSUM80':
-         switch ($gapKey) {
-            case 0:
+      }
+      break;
+    case 'BLOSUM80':
+       switch ($gapKey) {
+          case 0:
                $gapOpen   = 8;
                $gapExtend = 2;
                break;
-            case 1:
+          case 1:
                $gapOpen   = 7;
                $gapExtend = 2;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 6;
                $gapExtend = 2;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 11;
                $gapExtend = 1;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 10;
                $gapExtend = 1;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 9;
                $gapExtend = 1;
                break;
-         }
-         break;
-      case 'BLOSUM62':
-         switch ($gapKey) {
-            case 0:
+      }
+      break;
+    case 'BLOSUM62':
+       switch ($gapKey) {
+          case 0:
                $gapOpen   = 11;
                $gapExtend = 2;
                break;
-            case 1:
+          case 1:
                $gapOpen   = 10;
                $gapExtend = 2;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 9;
                $gapExtend = 2;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 8;
                $gapExtend = 2;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 7;
                $gapExtend = 2;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 6;
                $gapExtend = 2;
                break;
-            case 6:
+          case 6:
                $gapOpen   = 13;
                $gapExtend = 1;
                break;
-            case 7:
+          case 7:
                $gapOpen   = 12;
                $gapExtend = 1;
                break;
-            case 8:
+          case 8:
                $gapOpen   = 11;
                $gapExtend = 1;
                break;
-            case 9:
+          case 9:
                $gapOpen   = 10;
                $gapExtend = 1;
                break;
-            case 10:
+          case 10:
                $gapOpen   = 9;
                $gapExtend = 1;
                break;
-         }
-         break;
-      case 'BLOSUM45':
-         switch ($gapKey) {
-            case 0:
+      }
+      break;
+    case 'BLOSUM45':
+       switch ($gapKey) {
+          case 0:
                $gapOpen   = 13;
                $gapExtend = 3;
                break;
-            case 1:
+          case 1:
                $gapOpen   = 12;
                $gapExtend = 3;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 11;
                $gapExtend = 3;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 10;
                $gapExtend = 3;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 15;
                $gapExtend = 2;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 14;
                $gapExtend = 2;
                break;
-            case 6:
+          case 6:
                $gapOpen   = 13;
                $gapExtend = 2;
                break;
-            case 7:
+          case 7:
                $gapOpen   = 12;
                $gapExtend = 2;
                break;
-            case 8:
+          case 8:
                $gapOpen   = 19;
                $gapExtend = 1;
                break;
-            case 9:
+          case 9:
                $gapOpen   = 18;
                $gapExtend = 1;
                break;
-            case 10:
+          case 10:
                $gapOpen   = 17;
                $gapExtend = 1;
                break;
-            case 11:
+          case 11:
                $gapOpen   = 16;
                $gapExtend = 1;
                break;
-         }
-         break;
-      case 'BLOSUM50':
-         switch ($gapKey) {
-            case 0:
+      }
+      break;
+    case 'BLOSUM50':
+       switch ($gapKey) {
+          case 0:
                $gapOpen   = 13;
                $gapExtend = 3;
                break;
-            case 1:
+          case 1:
                $gapOpen   = 12;
                $gapExtend = 3;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 11;
                $gapExtend = 3;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 10;
                $gapExtend = 3;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 9;
                $gapExtend = 3;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 16;
                $gapExtend = 2;
                break;
-            case 6:
+          case 6:
                $gapOpen   = 15;
                $gapExtend = 2;
                break;
-            case 7:
+          case 7:
                $gapOpen   = 14;
                $gapExtend = 2;
                break;
-            case 8:
+          case 8:
                $gapOpen   = 13;
                $gapExtend = 2;
                break;
-            case 9:
+          case 9:
                $gapOpen   = 12;
                $gapExtend = 2;
                break;
-            case 10:
+          case 10:
                $gapOpen   = 19;
                $gapExtend = 1;
                break;
-            case 11:
+          case 11:
                $gapOpen   = 18;
                $gapExtend = 1;
                break;
-            case 12:
+          case 12:
                $gapOpen   = 17;
                $gapExtend = 1;
                break;
-            case 13:
+          case 13:
                $gapOpen   = 16;
                $gapExtend = 1;
                break;
-            case 14:
+          case 14:
                $gapOpen   = 15;
                $gapExtend = 1;
                break;
-         }
-         break;
-      case 'BLOSUM90':
-         switch ($gapKey) {
-            case 0:
+      }
+      break;
+    case 'BLOSUM90':
+       switch ($gapKey) {
+          case 0:
                $gapOpen   = 9;
                $gapExtend = 2;
                break;
-            case 1:
+          case 1:
                $gapOpen   = 8;
                $gapExtend = 2;
                break;
-            case 2:
+          case 2:
                $gapOpen   = 7;
                $gapExtend = 2;
                break;
-            case 3:
+          case 3:
                $gapOpen   = 6;
                $gapExtend = 2;
                break;
-            case 4:
+          case 4:
                $gapOpen   = 11;
                $gapExtend = 1;
                break;
-            case 5:
+          case 5:
                $gapOpen   = 10;
                $gapExtend = 1;
                break;
-            case 6:
+          case 6:
                $gapOpen   = 9;
                $gapExtend = 1;
                break;
-         }
-         break;
-         
+      }
+      break;
    }
    
    return array(
@@ -1305,92 +1395,3 @@ function getGap($matrix, $gapkey) {
  }
 
 
-/**
- * Get a list of options for gaps.
- */
-function _get_gap_options($which) {
-  switch ($which) {
-    case 'blastn':
-      return array(
-        0 => t('Existence: 5 Extension: 2'),
-        1 => t('Existence: 2 Extension: 2'),
-        2 => t('Existence: 1 Extension: 2'),
-        3 => t('Existence: 0 Extension: 2'),
-        4 => t('Existence: 3 Extension: 1'),
-        5 => t('Existence: 2 Extension: 1'),
-        6 => t('Existence: 1 Extension: 1'),
-      );
-   }//switch
-}
-
-/**
- * Translate above gap options into blast gap open and extend costs.
- */
-function _set_gap($gap_key) {
- switch ($gap_key) {
-   case 0:
-      $gapOpen = 5;
-      $gapExtend = 2;
-      break;
-   case 1:
-      $gapOpen = 2;
-      $gapExtend = 2;
-      break;
-   case 2:
-      $gapOpen = 1;
-      $gapExtend = 2;
-      break;
-   case 3:
-      $gapOpen = 0;
-      $gapExtend = 2;
-      break;
-   case 4:
-      $gapOpen = 3;
-      $gapExtend = 1;
-      break;
-   case 5:
-      $gapOpen = 2;
-      $gapExtend = 1;
-      break;
-   case 6:
-      $gapOpen = 1;
-      $gapExtend = 1;
-      break;
-  }//switch
-
-  return array('gapOpen' => $gapOpen, 'gapExtend' => $gapExtend);
-}
-
-/**
- * Translate mismatch/match ratio option into blast penalty/reward options.
- */
-function _set_match_mismatch($m_m) {
-  switch ($m_m) {
-   case 0:
-      $penalty = -2;
-      $reward = 1;
-      break;
-   case 1:
-      $penalty = -3;
-      $reward = 1;
-      break;
-   case 2:
-      $penalty = -4;
-      $reward = 1;
-      break;
-   case 3:
-      $penalty = -3;
-      $reward = 2;
-      break;
-   case 4:
-      $penalty = -5;
-      $reward = 4;
-      break;
-   case 5:
-      $penalty = -1;
-      $reward = 1;
-      break;
-  }//switch
-
-  return array('penalty' => $penalty, 'reward' => $reward);
-}