Removed duplicated function getGap()

includes/blast_ui.services.inc

@@ -640,375 +640,6 @@ function getBlastData( $job_id )
    return $result;
  }
 
-/*
- **Method Used for tblastn and blastx
- **  @return  int $gapOpen and $gapExtend
- */
-
-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:
-               $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
-   );
- }
-
 /*
  ** Used for tblastn
  */