Merge branch '7.x-1.x' into cvitjs

includes/blast_ui.form_advanced_options.inc

@@ -38,9 +38,9 @@ function blast_ui_blastn_advanced_options_form(&$form, $form_state) {
   //.........................
 
   $form['ALG']['GParam'] = array(
-   '#type' => 'fieldset',
-   '#title' => t('General parameters'),
-   '#collapsible' => FALSE,
+    '#type' => 'fieldset',
+    '#title' => t('General parameters'),
+    '#collapsible' => FALSE,
   );
 
   $form['ALG']['GParam']['maxTarget'] = array(
@@ -51,13 +51,13 @@ function blast_ui_blastn_advanced_options_form(&$form, $form_state) {
     '#description' => t('Select the maximum number of unique target sequences per query sequence to show results for.'),
   );
 
-/*eksc: remove until we learn how this is implemented by NCBI
-  $form['ALG']['GParam']['shortQueries'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Automatically adjust parameters for short input sequences'),
-    '#default_value' => $short_queries,
-  );
-*/
+  /*eksc: remove until we learn how this is implemented by NCBI
+    $form['ALG']['GParam']['shortQueries'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Automatically adjust parameters for short input sequences'),
+      '#default_value' => $short_queries,
+    );
+  */
 
   $form['ALG']['GParam']['eVal'] = array(
     '#type' => 'textfield',
@@ -76,17 +76,17 @@ function blast_ui_blastn_advanced_options_form(&$form, $form_state) {
     '#description' => t('The length of the seed that initiates an alignment'),
   );
 
-/*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
-       as culling_limit, which is something else entirely
-  $form['ALG']['GParam']['qRange'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
-    '#default_value' => $defaults['qRange'],
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
-  );
-*/
+  /*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
+         as culling_limit, which is something else entirely
+    $form['ALG']['GParam']['qRange'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Max matches in a query range'),
+      '#default_value' => $defaults['qRange'],
+      '#size' => 12,
+      '#maxlength' => 20,
+      '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
+    );
+  */
   // Scoring parameters
   //.........................
 
@@ -102,14 +102,25 @@ function blast_ui_blastn_advanced_options_form(&$form, $form_state) {
     '#options' => _get_match_mismatch('blastn'),
     '#default_value' => $defaults['matchmiss'],
     '#description' => t('Reward and penalty for matching and mismatching bases.'),
-   );
+    '#ajax' => array(
+      'callback' => 'gap_cost_callback',
+      'wrapper' => 'gap_cost_wrapper',
+    ),
+  );
 
-   $form['ALG']['SParam']['gapCost'] = array(
+  $m_m_set = $defaults['matchmiss'];
+  if (isset($form_state['values']) && isset($form_state['values']['M&MScores'])) {
+    $m_m_set = $form_state['values']['M&MScores'];
+  }
+
+  $form['ALG']['SParam']['gapCost'] = array(
     '#type' => 'select',
     '#title' => t('Gap Costs:'),
-    '#options' => _get_gap_options('blastn'),
+    '#options' => _get_gap_options('blastn', $m_m_set),
     '#default_value' => $defaults['gap'],
     '#description' => t('Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores.'),
+    '#prefix' => '<div id="gap_cost_wrapper">',
+    '#suffix' => '</div>',
   );
 }
 
@@ -129,13 +140,14 @@ function blast_ui_blastn_advanced_options_form_validate($form, $form_state) {
     form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, <em>0.001</em> or, even better, <em>1e-10</em>.');
   }
 
-/*eksc: removed until/unless it can be properly implemented
-  // Next textfield up, "Max matches in a query range" which is also expected
-  // to be a positive number.
-  if (!is_numeric($form_state['values']['qRange'])) {
-    form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
-  }
-*/
+
+  /*eksc: removed until/unless it can be properly implemented
+    // Next textfield up, "Max matches in a query range" which is also expected
+    // to be a positive number.
+    if (!is_numeric($form_state['values']['qRange'])) {
+      form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
+    }
+  */
 }
 
 /**
@@ -163,12 +175,12 @@ function blast_ui_blastn_advanced_options_form_submit($form, $form_state) {
 
   return array(
     'max_target_seqs' => $numAlign,
-    'evalue'          => $eVal,
-    'word_size'       => $wordSize,
-    'gapopen'         => $gap['gapOpen'],
-    'gapextend'       => $gap['gapExtend'],
-    'penalty'         => $m_m['penalty'],
-    'reward'          => $m_m['reward'],
+    'evalue' => $eVal,
+    'word_size' => $wordSize,
+    'gapopen' => $gap['gapOpen'],
+    'gapextend' => $gap['gapExtend'],
+    'penalty' => $m_m['penalty'],
+    'reward' => $m_m['reward'],
   );
 }
 
@@ -201,10 +213,10 @@ function blast_ui_blastx_advanced_options_form(&$form, $form_state) {
     $defaults = _get_default_values(array(), 'blastx');
   }
 
-   $form['ALG']['GParam'] = array(
-   '#type' => 'fieldset',
-   '#title' => t('General parameters'),
-   '#collapsible' => FALSE,
+  $form['ALG']['GParam'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('General parameters'),
+    '#collapsible' => FALSE,
   );
 
   $form['ALG']['GParam']['maxTarget'] = array(
@@ -224,13 +236,13 @@ function blast_ui_blastx_advanced_options_form(&$form, $form_state) {
     '#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. <a href="https://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect" target="_blank">More Information</a> | <a href="https://www.youtube.com/watch?v=nO0wJgZRZJs" target="_blank">Expect value vedio tutorial</a>'),
   );
 
-/*eksc- need to learn how this is implemented for blastx
-  $form['ALG']['GParam']['shortQueries'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Automatically adjust parameters for short input sequences'),
-    '#default_value' => TRUE,
-  );
-*/
+  /*eksc- need to learn how this is implemented for blastx
+    $form['ALG']['GParam']['shortQueries'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Automatically adjust parameters for short input sequences'),
+      '#default_value' => TRUE,
+    );
+  */
 
   $form['ALG']['GParam']['wordSize'] = array(
     '#type' => 'select',
@@ -262,33 +274,33 @@ function blast_ui_blastx_advanced_options_form(&$form, $form_state) {
     ),
   );
 
-/*eksc: removed as this is either equivalent to max_target_sequences or mis-implemented
-       as culling_limit
-  $form['ALG']['GParam']['qRange'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
-    '#default_value' => $defaults['qRange'],
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
-  );
-*/
-
-/*eksc: NOT match/mismatch but instead computational adjustments;
-        need to learn how there are implemented for blastx
-  $form['ALG']['SParam']['M&MScores'] = array(
-    '#type' => 'select',
-    '#title' => t('Match/Mismatch Scores:'),
-    '#options' => array(
-        0 => t('No adjustment'),
-        1 => t('Composition-based statistics'),
-        2 => t('Conditional compositional score matrix adjustment'),
-        3 => t('Universal composition score matrix adjustment '),
-      ),
-    '#default_value' => 2,
-    '#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
-  );
-*/
+  /*eksc: removed as this is either equivalent to max_target_sequences or mis-implemented
+         as culling_limit
+    $form['ALG']['GParam']['qRange'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Max matches in a query range'),
+      '#default_value' => $defaults['qRange'],
+      '#size' => 12,
+      '#maxlength' => 20,
+      '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
+    );
+  */
+
+  /*eksc: NOT match/mismatch but instead computational adjustments;
+          need to learn how there are implemented for blastx
+    $form['ALG']['SParam']['M&MScores'] = array(
+      '#type' => 'select',
+      '#title' => t('Match/Mismatch Scores:'),
+      '#options' => array(
+          0 => t('No adjustment'),
+          1 => t('Composition-based statistics'),
+          2 => t('Conditional compositional score matrix adjustment'),
+          3 => t('Universal composition score matrix adjustment '),
+        ),
+      '#default_value' => 2,
+      '#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
+    );
+  */
 }
 
 /**
@@ -307,13 +319,13 @@ function blast_ui_blastx_advanced_options_form_validate($form, $form_state) {
     form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, <em>0.001</em> or, even better, <em>1e-10</em>.');
   }
 
-/*eksc: removed until/unless we know how to properly implement
-  // Next textfield up, "Max matches in a query range" which is also expected
-  // to be a positive number.
-  if (!is_numeric($form_state['values']['qRange'])) {
-    form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
-  }
-*/
+  /*eksc: removed until/unless we know how to properly implement
+    // Next textfield up, "Max matches in a query range" which is also expected
+    // to be a positive number.
+    if (!is_numeric($form_state['values']['qRange'])) {
+      form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
+    }
+  */
 }
 
 /**
@@ -373,13 +385,13 @@ function blast_ui_blastp_advanced_options_form(&$form, $form_state) {
     '#description' => t('Select the maximum number of aligned sequences to display'),
   );
 
-/*eksc: remove until we learn how this is implemented
-  $form['ALG']['GParam']['shortQueries'] = array(
-   '#type' => 'checkbox',
-   '#title' => t('Automatically adjust parameters for short input sequences'),
-   '#default_value' => TRUE,
-  );
-*/
+  /*eksc: remove until we learn how this is implemented
+    $form['ALG']['GParam']['shortQueries'] = array(
+     '#type' => 'checkbox',
+     '#title' => t('Automatically adjust parameters for short input sequences'),
+     '#default_value' => TRUE,
+    );
+  */
 
   $form['ALG']['GParam']['eVal'] = array(
     '#type' => 'textfield',
@@ -398,23 +410,23 @@ function blast_ui_blastp_advanced_options_form(&$form, $form_state) {
     '#description' => t('The length of the seed that initiates an alignment'),
   );
 
-/*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
-       as culling_limit, which is something else entirely
-  $form['ALG']['GParam']['qRange'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
-    '#default_value' => $defaults['qRange'],
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
-  );
-*/
+  /*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
+         as culling_limit, which is something else entirely
+    $form['ALG']['GParam']['qRange'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Max matches in a query range'),
+      '#default_value' => $defaults['qRange'],
+      '#size' => 12,
+      '#maxlength' => 20,
+      '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
+    );
+  */
   // Scoring parameters
 
   $form['ALG']['SParam'] = array(
-   '#type' => 'fieldset',
-   '#title' => t('Scoring parameters'),
-   '#collapsible' => FALSE,
+    '#type' => 'fieldset',
+    '#title' => t('Scoring parameters'),
+    '#collapsible' => FALSE,
   );
 
   $matrix_options = _get_matrix_options();
@@ -430,33 +442,33 @@ function blast_ui_blastp_advanced_options_form(&$form, $form_state) {
     ),
   );
 
-/*eksc: probably not used for blastp
-  $form['ALG']['SParam']['gapCost'] = array(
-    '#type' => 'select',
-    '#title' => t('Gap Costs:'),
-    '#prefix' => '<div id="dropdown-second-replace">',
-    '#suffix' => '</div>',
-    '#options' => _get_gap_for_matrix($selected),
-    '#default_value' => 2,
-    '#description' => t('Cost to create and extend a gap in an alignment.'),
-  );
-*/
-
-/*eksc: NOT match/mismatch but instead computational adjustments;
-        need to learn how there are implemented for blastp
-  $form['ALG']['SParam']['M&MScores'] = array(
-    '#type' => 'select',
-    '#title' => t('Match/Mismatch Scores:'),
-    '#options' => array(
-      0 => t('No adjustment'),
-      1 => t('Composition-based statistics'),
-      2 => t('Conditional compositional score matrix adjustment'),
-      3 => t('Universal composition score matrix adjustment '),
-    ),
-    '#default_value' => 2,
-    '#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
-  );
-*/
+  /*eksc: probably not used for blastp
+    $form['ALG']['SParam']['gapCost'] = array(
+      '#type' => 'select',
+      '#title' => t('Gap Costs:'),
+      '#prefix' => '<div id="dropdown-second-replace">',
+      '#suffix' => '</div>',
+      '#options' => _get_gap_for_matrix($selected),
+      '#default_value' => 2,
+      '#description' => t('Cost to create and extend a gap in an alignment.'),
+    );
+  */
+
+  /*eksc: NOT match/mismatch but instead computational adjustments;
+          need to learn how there are implemented for blastp
+    $form['ALG']['SParam']['M&MScores'] = array(
+      '#type' => 'select',
+      '#title' => t('Match/Mismatch Scores:'),
+      '#options' => array(
+        0 => t('No adjustment'),
+        1 => t('Composition-based statistics'),
+        2 => t('Conditional compositional score matrix adjustment'),
+        3 => t('Universal composition score matrix adjustment '),
+      ),
+      '#default_value' => 2,
+      '#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
+    );
+  */
 }
 
 /**
@@ -475,13 +487,13 @@ function blast_ui_blastp_advanced_options_form_validate($form, $form_state) {
     form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, <em>0.001</em> or, even better, <em>1e-10</em>.');
   }
 
-/*eksc: remove until/unless we know how to correctly implement it
-  // Next textfield up, "Max matches in a query range" which is also expected
-  // to be a positive number.
-  if (!is_numeric($form_state['values']['qRange'])) {
-    form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
-  }
-*/
+  /*eksc: remove until/unless we know how to correctly implement it
+    // Next textfield up, "Max matches in a query range" which is also expected
+    // to be a positive number.
+    if (!is_numeric($form_state['values']['qRange'])) {
+      form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
+    }
+  */
 }
 
 /**
@@ -507,18 +519,19 @@ 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'];
-  $gap    = _set_protein_gap($matrix, $gapKey);
+  $gap = _set_protein_gap($matrix, $gapKey);
 
 //eksc- need to implement query range limit
 //  q_range
 
   return array(
     'max_target_seqs' => $numAlign,
-    'evalue'          => $eVal,
-    'word_size'       => $wordSize,
-    'gapopen'         => $gap['gapOpen'],
-    'gapextend'       => $gap['gapExtend'],
-    'matrix'          => $matrix,
+    'evalue' => $eVal,
+    'word_size' => $wordSize,
+    'gapopen' => $gapOpen,
+    'gapextend' => $gapExtend,
+    'culling_limit' => $qRange,
+    'matrix' => $matrix,
   );
 }//blast_ui_blastp_advanced_options_form_submit
 
@@ -542,10 +555,12 @@ function _get_matrix_options() {
 }
 
 /**
- * Fill the gap penalty dropdown list with appropriate options given selected matrix
+ * Fill the gap penalty dropdown list with appropriate options given selected
+ * matrix
  *
  * @return
- * An array containing open and extension gap values for the chosen matrix (to fill the second dropdown list)
+ * An array containing open and extension gap values for the chosen matrix (to
+ *   fill the second dropdown list)
  */
 function _get_gap_for_matrix($key = '') {
   $options = array(
@@ -556,7 +571,7 @@ function _get_gap_for_matrix($key = '') {
       t('Existence: 10 Extension: 1'),
       t('Existence: 9 Extension: 1'),
       t('Existence: 8 Extension: 1'),
-     )),
+    )),
     t('PAM70') => drupal_map_assoc(array(
       t('Existence: 8 Extension: 2'),
       t('Existence: 7 Extension: 2'),
@@ -660,6 +675,7 @@ function ajax_dependent_dropdown_callback($form, $form_state) {
   return $form['ALG']['SParam']['gapCost'];
 }
 
+
 /**
  * @section
  * tBLASTn: Search translated nucleotide database using a protein query.
@@ -690,9 +706,9 @@ function blast_ui_tblastn_advanced_options_form(&$form, $form_state) {
   }
 
   $form['ALG']['GParam'] = array(
-   '#type' => 'fieldset',
-   '#title' => t('General parameters'),
-   '#collapsible' => FALSE,
+    '#type' => 'fieldset',
+    '#title' => t('General parameters'),
+    '#collapsible' => FALSE,
   );
 
   $form['ALG']['GParam']['maxTarget'] = array(
@@ -712,13 +728,13 @@ function blast_ui_tblastn_advanced_options_form(&$form, $form_state) {
     '#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. <a href="https://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect" target="_blank">More Information</a> | <a href="https://www.youtube.com/watch?v=nO0wJgZRZJs" target="_blank">Expect value vedio tutorial</a>'),
   );
 
-/*eksc: need to learn how this is implemented for tblastn
-  $form['ALG']['GParam']['shortQueries'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Automatically adjust parameters for short input sequences'),
-    '#default_value' => TRUE,
-  );
-*/
+  /*eksc: need to learn how this is implemented for tblastn
+    $form['ALG']['GParam']['shortQueries'] = array(
+      '#type' => 'checkbox',
+      '#title' => t('Automatically adjust parameters for short input sequences'),
+      '#default_value' => TRUE,
+    );
+  */
 
   $form['ALG']['GParam']['wordSize'] = array(
     '#type' => 'select',
@@ -760,17 +776,17 @@ function blast_ui_tblastn_advanced_options_form(&$form, $form_state) {
     '#description' => t('Cost to create and extend a gap in an alignment.'),
   );
 
-/*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
-       as culling_limit, which is something else entirely
-  $form['ALG']['GParam']['qRange'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
-    '#default_value' => $defaults['qRange'],
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
-  );
-*/
+  /*eksc: remove this as it is either the same as max_target_seqs, or miss-implemented
+         as culling_limit, which is something else entirely
+    $form['ALG']['GParam']['qRange'] = array(
+      '#type' => 'textfield',
+      '#title' => t('Max matches in a query range'),
+      '#default_value' => $defaults['qRange'],
+      '#size' => 12,
+      '#maxlength' => 20,
+      '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
+    );
+  */
 }
 
 /**
@@ -789,13 +805,13 @@ function blast_ui_tblastn_advanced_options_form_validate($form, $form_state) {
     form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, <em>0.001</em> or, even better, <em>1e-10</em>.');
   }
 
-/*eksc: remove until/unless we know how to correctly implement it
-  // Next textfield up, "Max matches in a query range" which is also expected
-  // to be a positive number.
-  if (!is_numeric($form_state['values']['qRange'])) {
-    form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
-  }
-*/
+  /*eksc: remove until/unless we know how to correctly implement it
+    // Next textfield up, "Max matches in a query range" which is also expected
+    // to be a positive number.
+    if (!is_numeric($form_state['values']['qRange'])) {
+      form_set_error('qRange', 'The "Max matches in a query range" should be a positive integer.');
+    }
+  */
 }
 
 /**
@@ -816,69 +832,96 @@ function blast_ui_tblastn_advanced_options_form_submit($form, $form_state) {
 function _get_default_values($options) {
   // restore previous values or set to default
   $max_target = (isset($options['max_target_seqs']))
-            ? $options['max_target_seqs'] : 500;
+    ? $options['max_target_seqs'] : 500;
   $short_queries = (isset($options['shortQueries']))
-            ? $options['shortQueries'] : true;
+    ? $options['shortQueries'] : TRUE;
   $evalue = (isset($options['evalue']))
-            ? $options['evalue'] : variable_get('eVal', 0.001);
+    ? $options['evalue'] : variable_get('eVal', 0.001);
   $word_size = (isset($options['word_size']))
-            ? $options['word_size'] : 11;
+    ? $options['word_size'] : 11;
 
   $matchmiss = 0;
   $reward = (isset($options['reward']))
-            ? $options['reward'] : 1;
+    ? $options['reward'] : 1;
   $penalty = (isset($options['penalty']))
-            ? $options['penalty'] : -2;
+    ? $options['penalty'] : -2;
   if ($reward == 1) {
     switch ($penalty) {
-      case -1: $matchmiss = 5; break;
-      case -2: $matchmiss = 0; break;
-      case -3: $matchmiss = 1; break;
-      case -4: $matchmiss = 2; break;
+      case -1:
+        $matchmiss = 5;
+        break;
+      case -2:
+        $matchmiss = 0;
+        break;
+      case -3:
+        $matchmiss = 1;
+        break;
+      case -4:
+        $matchmiss = 2;
+        break;
     }
   }
-  else if ($reward == 2) {
-    $matchmiss = 3;
-  }
-  else if ($reward == 3) {
-     $matchmis = 4;
-  }
-  else if ($eward == 4) {
-     $matchmiss = 5;
+  else {
+    if ($reward == 2) {
+      $matchmiss = 3;
+    }
+    else {
+      if ($reward == 3) {
+        $matchmis = 4;
+      }
+      else {
+        if ($reward == 4) {
+          $matchmiss = 5;
+        }
+      }
+    }
   }
 
   $gap = 0;
   $gapopen = (isset($options['gapopen']))
-            ? $options['gapopen'] : 5;
+    ? $options['gapopen'] : 5;
   $gapextend = (isset($options['gapextend']))
-            ? $options['gapextend'] : 2;
+    ? $options['gapextend'] : 2;
   if ($gapextend == 2) {
     switch ($gapopen) {
-      case 5: $gap = 0; break;
-      case 2: $gap = 1; break;
-      case 1: $gap = 2; break;
-      case 0: $gap = 3; break;
+      case 5:
+        $gap = 0;
+        break;
+      case 2:
+        $gap = 1;
+        break;
+      case 1:
+        $gap = 2;
+        break;
+      case 0:
+        $gap = 3;
+        break;
     }
   }
-  else if ($gapextend == 1) {
-    switch ($gapopen) {
-      case 3: $gap = 4;
-      case 2: $gap = 5;
-      case 1: $gap = 6;
+  else {
+    if ($gapextend == 1) {
+      switch ($gapopen) {
+        case 3:
+          $gap = 4;
+        case 2:
+          $gap = 5;
+        case 1:
+          $gap = 6;
+      }
     }
   }
 
   $matrix = (isset($options['matrix']))
-            ? $options['matrix'] : 'PAM30';
+    ? $options['matrix'] : 'PAM30';
+
   return array(
     'max_target_seqs' => $max_target,
-    'short_queries'   => $short_queries,
-    'word_size'       => $word_size,
-    'evalue'          => $evalue,
-    'matchmiss'       => $matchmiss,
-    'gap'             => $gap,
-//    'qRange'          => $qRange,
-    'matrix'          => $matrix,
+    'short_queries' => $short_queries,
+    'word_size' => $word_size,
+    'evalue' => $evalue,
+    'matchmiss' => $matchmiss,
+    'gap' => $gap,
+    'matrix' => $matrix,
   );
 }//_get_default_values
 
@@ -915,25 +958,25 @@ function _get_max_target($which) {
 function _get_word_size($which) {
   switch ($which) {
     case 'blastn':
-       return array(
-         7 => t('7'),
-         11 => t('11'),
-         15 => t('15'),
-         16 => t('16'),
-         20 => t('20'),
-         24 => t('24'),
-         28 => t('28'),
-         32 => t('32'),
-         48 => t('48'),
-         64 => t('64'),
-          128 => t('128'),
-         256 => t('256'),
+      return array(
+        7 => t('7'),
+        11 => t('11'),
+        15 => t('15'),
+        16 => t('16'),
+        20 => t('20'),
+        24 => t('24'),
+        28 => t('28'),
+        32 => t('32'),
+        48 => t('48'),
+        64 => t('64'),
+        128 => t('128'),
+        256 => t('256'),
       );
     case 'blastx':
     case 'blastp':
     case 'tblastn':
       return array(
-      //  2 => t('2'),
+        //  2 => t('2'),
         3 => t('3'),
         6 => t('6'),
       );
@@ -947,23 +990,28 @@ function _get_match_mismatch($which) {
   switch ($which) {
     case 'blastn':
       return array(
-         0 => t('1,-2'),
-         1 => t('1,-3'),
-         2 => t('1,-4'),
-         3 => t('2,-3'),
-         4 => t('4,-5'),
-         5 => t('1,-1'),
+        0 => t('1,-2'),
+        1 => t('1,-3'),
+        2 => t('1,-4'),
+        3 => t('2,-3'),
+        4 => t('4,-5'),
+        5 => t('1,-1'),
       );
   }//switch
 }
 
 /**
- * Get a list of options for gaps.
+ * @param $which - the blast program being run
+ * @param $m_m - the match mismatch scores.
+ *
+ * @return array
  */
-function _get_gap_options($which) {
+function _get_gap_options($which, $m_m) {
+
   switch ($which) {
     case 'blastn':
-      return array(
+
+      $base = array(
         0 => t('Existence: 5 Extension: 2'),
         1 => t('Existence: 2 Extension: 2'),
         2 => t('Existence: 1 Extension: 2'),
@@ -972,42 +1020,128 @@ function _get_gap_options($which) {
         5 => t('Existence: 2 Extension: 1'),
         6 => t('Existence: 1 Extension: 1'),
       );
-   }//switch
+
+      $two_neg_three = [
+        0 => t('Existence: 5 Extension: 2'),
+        1 => t('Existence: 2 Extension: 2'),
+        7 => t('Existence: 4 Extension: 4'),
+        8 => t('Existence: 2 Extension: 4'),
+        9 => t('Existence: 0 Extension: 4'),
+        10 => t('Existence: 3 Extension: 3'),
+        11 => t('Existence: 6 Extension: 3'),
+        12 => t('Existence: 4 Extension: 2'),
+      ];
+
+      $four_neg_five = [
+        13 => t('Existence: 12 Extension: 8'),
+        14 => t('Existence: 6 Extension: 5'),
+        15 => t('Existence: 5 Extension: 5'),
+        16 => t('Existence: 4 Extension: 5'),
+        17 => t('Existence: 3 Extension: 5'),
+      ];
+
+
+      switch ($m_m) {
+        case 0: //1, -2
+          return $base;
+        case 1: //1, -3
+          unset($base[4]);
+          return $base;
+        case 2: // 1, -4
+          unset($base[1]);
+          unset($base[4]);
+          return $base;
+        case 3://2, -3
+          return $two_neg_three;
+        case 4://4, -5
+          return $four_neg_five;
+        case 5: //1, -1
+          unset($base[6]);
+          $base[18]= t("Existence: 3 Extension 2");
+          $base[19]= t("Existence: 4 Extension 1");
+          return $base;
+      }
+  }
 }
 
 /**
  * Translate above gap options into blast gap open and extend costs.
  */
 function _set_gap($gap_key) {
- switch ($gap_key) {
-   case 0:
+  switch ($gap_key) {
+    case 0:
       $gapOpen = 5;
       $gapExtend = 2;
       break;
-   case 1:
+    case 1:
       $gapOpen = 2;
       $gapExtend = 2;
       break;
-   case 2:
+    case 2:
       $gapOpen = 1;
       $gapExtend = 2;
       break;
-   case 3:
+    case 3:
       $gapOpen = 0;
       $gapExtend = 2;
       break;
-   case 4:
+    case 4:
       $gapOpen = 3;
       $gapExtend = 1;
       break;
-   case 5:
+    case 5:
       $gapOpen = 2;
       $gapExtend = 1;
       break;
-   case 6:
+    case 6:
       $gapOpen = 1;
       $gapExtend = 1;
       break;
+    case 7:
+      $gapOpen = 4;
+      $gapExtend = 4;
+      break;
+    case 8:
+      $gapOpen = 2;
+      $gapExtend = 4;
+      break;
+    case 9:
+      $gapOpen = 0;
+      $gapExtend = 4;
+      break;
+    case 10:
+      $gapOpen = 3;
+      $gapExtend = 3;
+      break;
+    case 11:
+      $gapOpen = 6;
+      $gapExtend = 3;
+      break;
+    case 12:
+      $gapOpen = 4;
+      $gapExtend = 2;
+      break;
+    case 13:
+      $gapOpen = 12;
+      $gapExtend = 8;
+      break;
+    case 14:
+      $gapOpen = 6;
+      $gapExtend = 5;
+      break;
+    case 15:
+      $gapOpen = 5;
+      $gapExtend = 5;
+      break;
+    case 16:
+      $gapOpen = 4;
+      $gapExtend = 5;
+      break;
+    case 17:
+      $gapOpen = 3;
+      $gapExtend = 5;
+      break;
+
   }//switch
 
   return array('gapOpen' => $gapOpen, 'gapExtend' => $gapExtend);
@@ -1018,27 +1152,27 @@ function _set_gap($gap_key) {
  */
 function _set_match_mismatch($m_m) {
   switch ($m_m) {
-   case 0:
+    case 0:
       $penalty = -2;
       $reward = 1;
       break;
-   case 1:
+    case 1:
       $penalty = -3;
       $reward = 1;
       break;
-   case 2:
+    case 2:
       $penalty = -4;
       $reward = 1;
       break;
-   case 3:
+    case 3:
       $penalty = -3;
       $reward = 2;
       break;
-   case 4:
+    case 4:
       $penalty = -5;
       $reward = 4;
       break;
-   case 5:
+    case 5:
       $penalty = -1;
       $reward = 1;
       break;
@@ -1048,361 +1182,373 @@ function _set_match_mismatch($m_m) {
 }
 
 
-/** 
+/**
  * Get gap values based on matrix and selected gap "key"
  */
-function _set_protein_gap($matrix, $gapkey) {
+function _set_protein_gap($matrix, $gapKey) {
   switch ($matrix) {
     case 'PAM30':
       switch ($gapKey) {
         case 0:
-             $gapOpen   = 7;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 7;
+          $gapExtend = 2;
+          break;
         case 1:
-             $gapOpen   = 6;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 6;
+          $gapExtend = 2;
+          break;
         case 2:
-             $gapOpen   = 5;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 5;
+          $gapExtend = 2;
+          break;
         case 3:
-             $gapOpen   = 10;
-             $gapExtend = 1;
-             break;
+          $gapOpen = 10;
+          $gapExtend = 1;
+          break;
         case 4:
-             $gapOpen   = 9;
-             $gapExtend = 1;
-             break;
+          $gapOpen = 9;
+          $gapExtend = 1;
+          break;
         case 5:
-             $gapOpen   = 8;
-             $gapExtend = 1;
-             break;
+          $gapOpen = 8;
+          $gapExtend = 1;
+          break;
       }
       break;
     case 'PAM70':
       switch ($gapKey) {
         case 0:
-             $gapOpen   = 8;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 8;
+          $gapExtend = 2;
+          break;
         case 1:
-             $gapOpen   = 7;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 7;
+          $gapExtend = 2;
+          break;
         case 2:
-             $gapOpen   = 6;
-             $gapExtend = 2;
-             break;
+          $gapOpen = 6;
+          $gapExtend = 2;
+          break;
         case 3:
-             $gapOpen   = 11;
-             $gapExtend = 1;
-             break;
+          $gapOpen = 11;
+          $gapExtend = 1;
+          break;
         case 4:
-             $gapOpen   = 10;
-             $gapExtend = 1;
-             break;
+          $gapOpen = 10;
+          $gapExtend = 1;
+          break;
         case 5:
-             $gapOpen   = 9;
-             $gapExtend = 1;
-             break;
+          $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;
-               $gapExtend = 1;
-               break;
+      switch ($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;
-               $gapExtend = 1;
-               break;
+      switch ($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;
-               $gapExtend = 1;
-               break;
+      switch ($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;
-               $gapExtend = 1;
-               break;
+      switch ($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;
-               $gapExtend = 1;
-               break;
+      switch ($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;
-               $gapExtend = 1;
-               break;
+      switch ($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 
-   );
- }
+  }
+
+  return array(
+    'gapOpen' => $gapOpen,
+    'gapExtend' => $gapExtend,
+  );
+}
+
+/**
+ * AJAX callback for match and gap cost.
+ * @param $form
+ * @param $form_state
+ *
+ * @return mixed
+ */
+function gap_cost_callback($form, &$form_state) {
+
+  return $form['B']['ALG']['SParam']['gapCost'];
+}
 
 

includes/blast_ui.linkouts.inc

@@ -64,7 +64,7 @@ function blast_ui_blast_linkout_info() {
     'require_regex' => FALSE,
     'require_db' => FALSE,
   );
-  
+
   $types['link'] = array(
     // Human-readable Type name to display to users in the BLAST Database
     // create/edit form.
@@ -73,7 +73,7 @@ function blast_ui_blast_linkout_info() {
     // This function will have full access to the blast hit and database
     // prefix information and is expected to return a URL.
     'process function' => 'tripal_blast_generate_linkout_link',
-    // Help text to show in the BLAST Database create/edit form so that 
+    // Help text to show in the BLAST Database create/edit form so that
     // users will know how to use this link-out type. Specifically, info
     // about your assumptions for the URL prefix are very helpful.
     // HTML is aloud but do not enclose in <p>.
@@ -214,13 +214,13 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   // calculate the smallest and largest coordinate.
   $coords = array();
   foreach($info['HSPs'] as $hsp) {
-  
+
     $start = min($hsp['Hsp_hit-from'], $hsp['Hsp_hit-to']);
     $stop = max($hsp['Hsp_hit-from'], $hsp['Hsp_hit-to']);
-    
+
     // Format the hsp for inclusion in the new track later.
     array_push($ranges, "$start..$stop");
-    
+
     // Add both the start & stop to the coordinate list.
     array_push($coords, $start, $stop);
   }
@@ -245,7 +245,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
       '!hspcoords' => join ("," , $ranges),
     )
   );
-  
+
   // Highlight our newly added feature.
   $query['h_feat'] = 'BlastHit';
 
@@ -253,16 +253,16 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
   $url = l(
     $hit->{'linkout_id'},
     $hit_url,
-    array( 
+    array(
       'query' => $query,
       'attributes' => array('target' => '_blank')
     )
   );
-  
-  // For some reason GBrowse expects semi-colons (;&) to delineate query paramters 
+
+  // For some reason GBrowse expects semi-colons (;&) to delineate query paramters
   // whereas Drupal throws ampherstands (&) in. This is to fix that.
   $url = str_replace('&',';&', $url);
-  
+
   return $url;
 
 }
@@ -276,7 +276,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
  *  allow your default tracks to be visible and give contect to your blast hit. You
  *  should include "blast" in your jbrowse.conf default track list to ensure your
  *  users can always see their hits. If you don't have access to the jbrowse.conf,
- *  you can place the tracks you want to see including 'blast' in the url prefix 
+ *  you can place the tracks you want to see including 'blast' in the url prefix
  *  (see example below under @param $url_prefix).
  *
  * @param $url_prefix
@@ -285,7 +285,7 @@ function tripal_blast_generate_linkout_gbrowse($url_prefix, $hit, $info, $option
  *   For example,
  *     http://myserver.com/jbrowse/databasica/?
  *     http://myserver.com/jbrowse/databasica/?tracks=myfavtrack,anoktrack,blast&
- * 
+ *
  * @param $hit
  *   The blast XML hit object. This object has the following keys based on the
  *   XML: Hit_num, Hit_id, Hit_def, Hit_accession, Hit_len and Hit_hsps.
@@ -314,20 +314,22 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
   // calculate the smallest and largest coordinate.
   $coords = array();
   $count = 0;
+  $strands = array();
   foreach($info['HSPs'] as $hsp) {
     $count++;
-    
+
     $strand = '1';
     $hsp_start = $hsp['Hsp_hit-from'];
     $hsp_end = $hsp['Hsp_hit-to'];
-    
+    $strands[] = $strand;
+
     // Handle alignments on the negative strand.
     if (($hsp_end - $hsp_start) < 0) {
       $strand = '-1';
       $hsp_start = $hsp['Hsp_hit-to'];
       $hsp_end = $hsp['Hsp_hit-from'];
     }
-    
+
     // Add both the start & stop to the coordinate list.
     array_push($coords,$hsp['Hsp_hit-from'] , $hsp['Hsp_hit-to'] );
 
@@ -346,8 +348,8 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
   // Calculate the minimum & maximum coordinates.
   $min = min($coords);
   $max = max($coords);
-  
-  // We also want some white-space on either side of out hit 
+
+  // We also want some white-space on either side of out hit
   // when we show it in the JBrowse. To make this generic,
   // we want our blast hit to take up 2/3 of the screen thus
   // we have 1/6 per side for white-space.
@@ -367,19 +369,37 @@ function tripal_blast_generate_linkout_jbrowse($url_prefix, $hit, $info, $option
     )
   );
 
-  // Next we want to add our BLAST hit to the JBrowse.
-  $jbrowse_query['addFeatures'] = format_string(
-    'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","subfeatures":[!hspcoords]}]',
-    array(
-      '!id' => $hit->{'linkout_id'},
-      '!name' => $info['query_name'] . ' Blast Hit',
-      '!min' => $min,
-      '!max' => $max,
-      '!hspcoords' => join ("," , $ranges)
-    ));
+  $unique_strands = array_unique($strands);
+  if (count($unique_strands) === 1) {
+    $strand = end($strands);
+    // Next we want to add our BLAST hit to the JBrowse.
+    $jbrowse_query['addFeatures'] = format_string(
+      'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","strand":!strand,"subfeatures":[!hspcoords]}]',
+      array(
+        '!id' => $hit->{'linkout_id'},
+        '!name' => $info['query_name'] . ' Blast Hit',
+        '!min' => $min,
+        '!max' => $max,
+        '!hspcoords' => join(",", $ranges),
+        '!strand' => $strand,
+      )
+    );
+  }
+  else {
+    $jbrowse_query['addFeatures'] = format_string(
+      'addFeatures=[{"seq_id":"!id","start":!min,"end":!max,"name":"!name","subfeatures":[!hspcoords]}]',
+      array(
+        '!id' => $hit->{'linkout_id'},
+        '!name' => $info['query_name'] . ' Blast Hit',
+        '!min' => $min,
+        '!max' => $max,
+        '!hspcoords' => join(",", $ranges),
+      )
+    );
+  }
 
   // Then add a track to display our new feature.
-  $jbrowse_query['addTracks'] = 'addTracks=[{"label":"blast","key":"BLAST Result","type":"JBrowse/View/Track/HTMLFeatures","store":"url"}]';
+  $jbrowse_query['addTracks'] = 'addTracks=[{"label":"blast","key":"BLAST Result","type":"JBrowse/View/Track/CanvasFeatures","store":"url"}]';
 
   $url_postfix = implode('&', $jbrowse_query);
 

theme/blast_report.tpl.php

@@ -232,11 +232,17 @@ $no_hits = TRUE;
               $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps,
                                        $target_size, $query_size, $q_name, $hit_name_short);
 
+
+              // get blast program
+              $blast_cmd_arr = explode(' ',trim($blast_job->blast_cmd));
+              $blast_cmd_program =  $blast_cmd_arr[0];
+
+
               // State what should be in the alignment row for theme_table() later.
               $alignment_row = array(
                 'data' => array(
                   'arrow' => array(
-                    'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img)),
+                    'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img, 'blast_program' => $blast_cmd_program)),
                     'colspan' => 5,
                   ),
                 ),

theme/blast_report_alignment_row.tpl.php

@@ -12,7 +12,7 @@
 <div class="alignment-row-section hit-visualization" title="Your query sequence is shown at the bottom and the target sequence it aligned to is shown at the top. The shape connecting them indicates how much of the target and query are represented by the hit.">
   <div class="title">Hit Visualization</div>
   <img src="data:image/png;base64,<?php print $hit_visualization;?>"/>
-  <p>The image above shows the relationship between query and target for this 
+  <p>The image above shows the relationship between query and target for this
     particular BLAST hit.</p>
 </div>
 <div class="alignment-row-section alignment">
@@ -39,7 +39,7 @@
     </div>
     <div class="alignment">
       <div class="alignment-row">
-        <?php 
+        <?php
         // We want to display the alignment with a max 60 residues per line with line numbers indicated.
         // First break up the strings.
         $query = str_split($hsp['Hsp_qseq'], 60);
@@ -49,39 +49,75 @@
         $coord_length = strlen($hsp['Hsp_hit-from']) + 3;
         $coord_length = (strlen($hsp['Hsp_query-to']) + 3 > $coord_length) ? strlen($hsp['Hsp_query-to']) + 3 : $coord_length;
 
+        // We need to take into account that 3 nucleotides encode 1 amino acid when we are
+        // carying out a BLAST where query and subject types are different.
+        // Thus we use the blast program here to determine if the type of query != subject.
+        $query_multiplier = 1;
+        $hit_multiplier = 1;
+        // tblastn: query = protein, subject = nucleotide.
+        // Thus we need to adjust the hit/subject coordinates.
+        if ($blast_program == 'tblastn'){
+          $hit_multiplier = 3;
+        }
+        // blastx: query = nucleotide, subject = protein.
+        // Thus we need to adjust the query coordinates.
+        elseif ($blast_program == 'blastx'){
+          $query_multiplier = 3;
+        }
+
+        // Take into account that coordinates can increase or decrease
+        // from start to finish of the match (either query and/or subject/hit).
+        // By default, we assume everything is increasing then adjust as neccessary.
+        $h_from = $hsp['Hsp_hit-from'];
+        $h_to = $hsp['Hsp_hit-to'];
+        $q_from = $hsp['Hsp_query-from'];
+        $q_to = $hsp['Hsp_query-to'];
+        if ( $h_from > $h_to){
+          $h_to = $hsp['Hsp_hit-from'];
+          $h_from = $hsp['Hsp_hit-to'];
+        }
+        if ( $q_from > $q_to){
+          $q_to = $hsp['Hsp_query-from'];
+          $q_from = $hsp['Hsp_query-to'];
+        }
+
         // Now foreach chink determined above...
         foreach (array_keys($query) as $k) {
-          // Determine the current coordinates.
-          $coord['qstart'] = $hsp['Hsp_query-from'] + ($k * 60);
-          $coord['qstart'] = ($k == 0) ? $coord['qstart'] : $coord['qstart'];
-        
-          // code added to fix the range issue
-          // Cordinates can increase or decrease
-          if($hsp['Hsp_hit-from'] < $hsp['Hsp_hit-to']) {
-              $coord['hstart'] = $hsp['Hsp_hit-from'] + ($k * 60);    
-            }
-            else {
-              $coord['hstart'] = $hsp['Hsp_hit-from'] - ($k * 60);
-            }
-            $coord['qstop'] = $hsp['Hsp_query-from'] + (($k + 1) * 60) - 1;
-            $coord['qstop'] = ($coord['qstop'] > $hsp['Hsp_query-to']) ? $hsp['Hsp_query-to'] : $coord['qstop'];
-      
-            if ($hsp['Hsp_hit-from'] < $hsp['Hsp_hit-to']) {
-              $coord['hstop'] = $hsp['Hsp_hit-from'] + (($k + 1) * 60) - 1;
-              $coord['hstop'] = ($coord['hstop'] > $hsp['Hsp_hit-to']) ? $hsp['Hsp_hit-to'] : $coord['hstop'];
-          
-            }
-            else {
-              $coord['hstop'] = $hsp['Hsp_hit-from'] - (($k + 1) * 60) + 1;
-              $coord['hstop'] = ($coord['hstop'] < $hsp['Hsp_hit-to']) ? $hsp['Hsp_hit-to'] : $coord['hstop'];
-            }
-          
-            // Pad these coordinates to ensure columned display.
-            foreach ($coord as $ck => $val) {
-              $pad_type = (preg_match('/start/', $ck)) ? STR_PAD_LEFT : STR_PAD_RIGHT;
-              $coord[$ck] = str_pad($val, $coord_length, '#', $pad_type);
-              $coord[$ck] =  str_replace('#', '&nbsp', $coord[$ck]);
-            }
+
+          // Determine the query coordinates.
+          $qgap_count = substr_count($query[$k],'-');
+          // We also need to take into account the frame when determining the direction
+          // of the match. This if the frame is positive then when go from -> to...
+          if ($hsp['Hsp_query-frame'] >= 0){
+            $coord['qstart'] = ($k == 0) ? $q_from : $coord['qstop'] + 1;
+            $coord['qstop'] = $coord['qstart'] + strlen($query[$k]) * $query_multiplier - $qgap_count - 1;
+          }
+          // whereas, if the frame is negative then we go to -> from.
+          else{
+            $coord['qstart'] = ($k == 0) ? $q_to : $coord['qstop'] - 1;
+            $coord['qstop'] = $coord['qstart'] - strlen($query[$k]) * $query_multiplier - $qgap_count + 1;
+          }
+
+          // Determine the subject/hit coordinates.
+          $hgap_count = substr_count($hit[$k],'-');
+          // We also need to take into account the frame when determining the direction
+          // of the match. This if the frame is positive then when go from -> to...
+          if ($hsp['Hsp_hit-frame'] >= 0){
+            $coord['hstart'] = ($k == 0) ? $h_from : $coord['hstop'] + 1;
+            $coord['hstop'] = $coord['hstart'] + strlen($hit[$k]) * $hit_multiplier - $hgap_count - 1;
+          }
+          // whereas, if the frame is negative then we go to -> from.
+          else{
+            $coord['hstart'] = ($k == 0) ? $h_to : $coord['hstop'] - 1;
+            $coord['hstop'] = $coord['hstart'] - strlen($hit[$k]) * $hit_multiplier - $hgap_count + 1;
+          }
+
+          // Pad these coordinates to ensure columned display.
+          foreach ($coord as $ck => $val) {
+            $pad_type = (preg_match('/start/', $ck)) ? STR_PAD_LEFT : STR_PAD_RIGHT;
+            $coord[$ck] = str_pad($val, $coord_length, '#', $pad_type);
+            $coord[$ck] =  str_replace('#', '&nbsp', $coord[$ck]);
+          }
         ?>
           <div class="alignment-subrow">
             <div class="query">
@@ -109,4 +145,4 @@
   <?php
     }
   ?>
-</div>
+</div>