'fieldset',
'#title' => t('General parameters'),
'#collapsible' => FALSE,
);
$form['ALG']['GParam']['maxTarget'] = array(
'#type' => 'select',
'#title' => t('Max target sequences:'),
'#options' => array(
0 => t('10'),
1 => t('50'),
2 => t('100'),
3 => t('250'),
4 => t('500'),
5 => t('1000'),
6 => t('5000'),
7 => t('10000'),
8 => t('20000'),
),
'#default_value' => 2,
'#description' => t('Select the maximum number of aligned sequences to display'),
);
$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',
'#title' => t('e-Value (Expected Threshold)'),
'#default_value' => 10,
'#size' => 12,
'#maxlength' => 20,
'#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. More Information | Expect value vedio tutorial'),
);
$form['ALG']['GParam']['wordSize'] = array(
'#type' => 'select',
'#title' => t('Word size:'),
'#options' => array(
0 => t('16'),
1 => t('20'),
2 => t('24'),
3 => t('28'),
4 => t('32'),
5 => t('48'),
6 => t('64'),
7 => t('128'),
8 => t('256'),
),
'#default_value' => 3,
'#description' => t('The length of the seed that initiates an alignment'),
);
$form['ALG']['GParam']['qRange'] = array(
'#type' => 'textfield',
'#title' => t('Max matches in a query range'),
'#default_value' => 0,
'#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,
);
$form['ALG']['SParam']['M&MScores'] = array(
'#type' => 'select',
'#title' => t('Match/Mismatch Scores:'),
'#options' => 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'),
),
'#default_value' => 0,
'#description' => t('Reward and penalty for matching and mismatching bases.'),
);
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#options' => array(
0 => t('Existence: 5 Extension: 2'),
1 => t('Existence: 2 Extension: 2'),
2 => t('Existence: 1 Extension: 2'),
3 => t('Existence: 0 Extension: 2'),
4 => t('Existence: 3 Extension: 1'),
5 => t('Existence: 2 Extension: 1'),
6 => t('Existence: 1 Extension: 1'),
),
'#default_value' => 0,
'#description' => t('Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores.'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastn_advanced_options_form().
*/
function blast_ui_blastn_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastn_advanced_options_form().
*/
function blast_ui_blastn_advanced_options_form_submit($form, $form_state) {
$eVal = $form_state['values']['eVal'];
$trgtKey = $form_state['values']['maxTarget'];
$numAlign = $form['ALG']['GParam']['maxTarget']['#options'][$trgtKey];
$wsKey = $form_state['values']['wordSize'];
$wordSize = $form['ALG']['GParam']['wordSize']['#options'][$wsKey];
// Expand Gap Cost key into open and extend penalties
$gapKey = $form_state['values']['gapCost'];
switch ($gapKey) {
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;
}
// Epand Match/Mismatch option into penalty/reward values
// @todo Amir: Is the switch supposed to be for $scoreKey?
$scoreKey = $form_state['values']['M&MScores'];
switch ($gapKey) {
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;
}
return array(
'evalue' => $eVal,
'word_size' => $wordSize,
'gapopen' => $gapOpen,
'gapextend' => $gapExtend,
'penalty' => $penalty,
'reward' => $reward
);
}
/**
* @section
* BLASTx: Search protein database using a translated nucleotide query.
* ----------------------------------------------------------------------------
*/
/**
* Adds the BLASTx Advanced Options to the passed in form.
*
* This form function is meant to be called within another form definition.
*
* @param $form
* The form the advanced options should be added to. This form already
* contains a $form['ALG'] fieldset meant to contain the advanced options.
* @param $formstate
* The current state fo the form passed in as $form.
*/
function blast_ui_blastx_advanced_options_form(&$form, $form_state) {
$form['ALG']['GParam'] = array(
'#type' => 'fieldset',
'#title' => t('General parameters'),
'#collapsible' => FALSE,
);
$form['ALG']['GParam']['maxTarget'] = array(
'#type' => 'select',
'#title' => t('Max target sequences:'),
'#options' => array(
0 => t('10'),
1 => t('50'),
2 => t('100'),
3 => t('250'),
4 => t('500'),
5 => t('1000'),
6 => t('5000'),
7 => t('10000'),
8 => t('20000'),
),
'#default_value' => 2,
'#description' => t('Select the maximum number of aligned sequences to display'),
);
$form['ALG']['GParam']['eVal'] = array(
'#type' => 'textfield',
'#title' => t('e-Value (Expected Threshold)'),
'#default_value' => 10,
'#size' => 12,
'#maxlength' => 20,
'#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. More Information | Expect value vedio tutorial'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastx_advanced_options_form().
*/
function blast_ui_blastx_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the BLASTx form above.
*
* @see blast_ui_blastx_advanced_options_form().
*/
function blast_ui_blastx_advanced_options_form_submit($form, $form_state) {
$eVal = $form_state['values']['eVal'];
$trgtKey = $form_state['values']['maxTarget'];
$numAlign = $form['ALG']['GParam']['maxTarget']['#options'][$trgtKey];
return array(
'evalue' => $eVal,
);
}
/**
* @section
* BLASTp: Search protein database using a protein query.
* ----------------------------------------------------------------------------
*/
/**
* Adds the BLASTp Advanced Options to the passed in form.
*
* This form function is meant to be called within another form definition.
*
* @param $form
* The form the advanced options should be added to. This form already
* contains a $form['ALG'] fieldset meant to contain the advanced options.
* @param $formstate
* The current state fo the form passed in as $form.
*/
function blast_ui_blastp_advanced_options_form(&$form, $form_state) {
//General parameters
$form['ALG']['GParam'] = array(
'#type' => 'fieldset',
'#title' => t('General parameters'),
'#collapsible' => FALSE,
);
$form['ALG']['GParam']['maxTarget'] = array(
'#type' => 'select',
'#title' => t('Max target sequences:'),
'#options' => array(
0 => t('10'),
1 => t('50'),
2 => t('100'),
3 => t('250'),
4 => t('500'),
5 => t('1000'),
6 => t('5000'),
7 => t('10000'),
8 => t('20000'),
),
'#default_value' => 2,
'#description' => t('Select the maximum number of aligned sequences to display'),
);
$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',
'#title' => t('e-value(Expect threshold)'),
'#default_value' => 10,
'#size' => 12,
'#maxlength' => 20,
'#description' => t('Expected number of chance matches in a random model.'),
);
$form['ALG']['GParam']['wordSize'] = array(
'#type' => 'select',
'#title' => t('Word size:'),
'#options' => array(
0 => t('2'),
1 => t('3'),
),
'#default_value' => 1,
'#description' => t('The length of the seed that initiates an alignment'),
);
$form['ALG']['GParam']['qRange'] = array(
'#type' => 'textfield',
'#title' => t('Max matches in a query range'),
'#default_value' => 0,
'#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,
);
$options_first = _ajax_example_get_first_dropdown_options();
$selected = isset($form_state['values']['MATRIX'] ) ? $form_state['values']['MATRIX'] : key($options_first);
$form['ALG']['SParam']['MATRIX'] = array(
'#type' => 'select',
'#title' => 'Matrix',
'#options' => $options_first,
'#default_value' => $selected,
'#description' => t('Assigns a score for aligning pairs of residues, and determines overall alignment score..'),
'#ajax' => array(
'callback' => 'ajax_example_dependent_dropdown_callback',
'wrapper' => 'dropdown-second-replace',
),
);
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#prefix' => '',
'#suffix' => '
',
'#options' => _ajax_example_get_second_dropdown_options($selected),
'#default_value' => 2,
'#description' => t('Cost to create and extend a gap in an alignment.'),
);
$form['ALG']['SParam']['M&MScores'] = array(
'#type' => 'select',
'#title' => t('Match/Mismatch Scores:'),
'#options' => array(
0 => t('No adjustment'),
1 => t('Composition-based statistics'),
2 => t('Conditional compositional score matrix adjustment'),
3 => t('Universal composition score matrix adjustment '),
),
'#default_value' => 2,
'#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastp_advanced_options_form().
*/
function blast_ui_blastp_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the BLASTp form above.
*
* @see blast_ui_blastp_advanced_options_form().
*/
function blast_ui_blastp_advanced_options_form_submit($form, $form_state) {
$eVal = $form_state['values']['eVal'];
$trgtKey = $form_state['values']['maxTarget'];
$numAlign = $form['ALG']['GParam']['maxTarget']['#options'][$trgtKey];
$wsKey = $form_state['values']['wordSize'];
$wordSize = $form['ALG']['GParam']['wordSize']['#options'][$wsKey];
// Expand Gap Cost key into open and extend penalties
$gapKey = $form_state['values']['MATRIX'];
switch ($gapKey) {
case 0:
$matrix ="PAM30";
$gapKey = $form_state['values']['gapCost'];
switch ($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 1:
$matrix ="PAM70";
$gapKey = $form_state['values']['gapCost'];
switch ($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 2:
$matrix ="PAM250";
$gapKey = $form_state['values']['gapCost'];
switch ($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 3:
$matrix ="BLOSUM80";
$gapKey = $form_state['values']['gapCost'];
switch ($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 4:
$matrix ="BLOSUM62";
$gapKey = $form_state['values']['gapCost'];
switch ($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 5:
$matrix ="BLOSUM45";
$gapKey = $form_state['values']['gapCost'];
switch ($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 6:
$matrix ="BLOSUM50";
$gapKey = $form_state['values']['gapCost'];
switch ($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 7:
$matrix ="BLOSUM90";
$gapKey = $form_state['values']['gapCost'];
switch ($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(
'evalue' => $eVal,
'word_size' => $wordSize,
'gapopen' => $gapOpen,
'gapextend' => $gapExtend,
'matrix' => $matrix
);
}
/**
* Fill the first dropdown list with appropriate options
*
* @return
* An array consisting of matrices name for the first dropdown list
*/
function _ajax_example_get_first_dropdown_options() {
return drupal_map_assoc(array(
t('PAM30'),
t('PAM70'),
t('PAM250'),
t('BLOSUM80'),
t('BLOSUM62'),
t('BLOSUM45'),
t('BLOSUM50'),
t('BLOSUM90'),
));
}
/**
* Fill the second dropdown list with appropriate options
*
* @return
* An array containing open and extension gap values for the chosen matrix (to fill the second dropdown list)
*/
function _ajax_example_get_second_dropdown_options($key = '') {
$options = array(
t('PAM30') => drupal_map_assoc(array(
t('Existence: 7 Extension: 2'),
t('Existence: 6 Extension: 2'),
t('Existence: 5 Extension: 2'),
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'),
t('Existence: 6 Extension: 2'),
t('Existence: 11 Extension: 1'),
t('Existence: 10 Extension: 1'),
t('Existence: 9 Extension: 1'),
)),
t('PAM250') => drupal_map_assoc(array(
t('Existence: 15 Extension: 3'),
t('Existence: 14 Extension: 3'),
t('Existence: 13 Extension: 3'),
t('Existence: 12 Extension: 3'),
t('Existence: 11 Extension: 3'),
t('Existence: 17 Extension: 2'),
t('Existence: 16 Extension: 2'),
t('Existence: 15 Extension: 2'),
t('Existence: 14 Extension: 2'),
t('Existence: 13 Extension: 2'),
t('Existence: 21 Extension: 1'),
t('Existence: 20 Extension: 1'),
t('Existence: 19 Extension: 1'),
t('Existence: 18 Extension: 1'),
t('Existence: 17 Extension: 1'),
)),
t('BLOSUM80') => drupal_map_assoc(array(
t('Existence: 8 Extension: 2'),
t('Existence: 7 Extension: 2'),
t('Existence: 6 Extension: 2'),
t('Existence: 11 Extension: 1'),
t('Existence: 10 Extension: 1'),
t('Existence: 9 Extension: 1'),
)),
t('BLOSUM62') => drupal_map_assoc(array(
t('Existence: 11 Extension: 2'),
t('Existence: 10 Extension: 2'),
t('Existence: 9 Extension: 2'),
t('Existence: 8 Extension: 2'),
t('Existence: 7 Extension: 2'),
t('Existence: 6 Extension: 2'),
t('Existence: 13 Extension: 1'),
t('Existence: 12 Extension: 1'),
t('Existence: 11 Extension: 1'),
t('Existence: 10 Extension: 1'),
t('Existence: 9 Extension: 1'),
)),
t('BLOSUM45') => drupal_map_assoc(array(
t('Existence: 13 Extension: 3'),
t('Existence: 12 Extension: 3'),
t('Existence: 11 Extension: 3'),
t('Existence: 10 Extension: 3'),
t('Existence: 15 Extension: 2'),
t('Existence: 14 Extension: 2'),
t('Existence: 13 Extension: 2'),
t('Existence: 12 Extension: 2'),
t('Existence: 19 Extension: 1'),
t('Existence: 18 Extension: 1'),
t('Existence: 17 Extension: 1'),
t('Existence: 16 Extension: 1'),
)),
t('BLOSUM50') => drupal_map_assoc(array(
t('Existence: 13 Extension: 3'),
t('Existence: 12 Extension: 3'),
t('Existence: 11 Extension: 3'),
t('Existence: 10 Extension: 3'),
t('Existence: 9 Extension: 3'),
t('Existence: 16 Extension: 2'),
t('Existence: 15 Extension: 2'),
t('Existence: 14 Extension: 2'),
t('Existence: 13 Extension: 2'),
t('Existence: 12 Extension: 2'),
t('Existence: 19 Extension: 1'),
t('Existence: 18 Extension: 1'),
t('Existence: 17 Extension: 1'),
t('Existence: 16 Extension: 1'),
t('Existence: 15 Extension: 1'),
)),
t('BLOSUM90') => drupal_map_assoc(array(
t('Existence: 9 Extension: 2'),
t('Existence: 8 Extension: 2'),
t('Existence: 7 Extension: 2'),
t('Existence: 6 Extension: 2'),
t('Existence: 11 Extension: 1'),
t('Existence: 10 Extension: 1'),
t('Existence: 9 Extension: 1'),
)),
);
if (isset($options[$key])) {
return $options[$key];
} else {
return array();
}
}
/**
* Respond to Ajax dropdown call
*/
function ajax_example_dependent_dropdown_callback($form, $form_state) {
return $form['ALG']['SParam']['gapCost'];
}
/**
* @section
* tBLASTn: Search translated nucleotide database using a protein query.
* ----------------------------------------------------------------------------
*/
/**
* Adds the tBLASTn Advanced Options to the passed in form.
*
* This form function is meant to be called within another form definition.
*
* @param $form
* The form the advanced options should be added to. This form already
* contains a $form['ALG'] fieldset meant to contain the advanced options.
* @param $formstate
* The current state fo the form passed in as $form.
*/
function blast_ui_tblastn_advanced_options_form(&$form, $form_state) {
$form['ALG']['GParam'] = array(
'#type' => 'fieldset',
'#title' => t('General parameters'),
'#collapsible' => FALSE,
);
$form['ALG']['GParam']['maxTarget'] = array(
'#type' => 'select',
'#title' => t('Max target sequences:'),
'#options' => array(
0 => t('10'),
1 => t('50'),
2 => t('100'),
3 => t('250'),
4 => t('500'),
5 => t('1000'),
6 => t('5000'),
7 => t('10000'),
8 => t('20000'),
),
'#default_value' => 2,
'#description' => t('Select the maximum number of aligned sequences to display'),
);
$form['ALG']['GParam']['eVal'] = array(
'#type' => 'textfield',
'#title' => t('e-Value (Expected Threshold)'),
'#default_value' => 10,
'#size' => 12,
'#maxlength' => 20,
'#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. More Information | Expect value vedio tutorial'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the yBLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_submit($form, $form_state) {
$eVal = $form_state['values']['eVal'];
$trgtKey = $form_state['values']['maxTarget'];
$numAlign = $form['ALG']['GParam']['maxTarget']['#options'][$trgtKey];
return array(
'evalue' => $eVal,
);
}