options, 'blastn');
}
else {
$defaults = _get_default_values(array(), 'blastn');
}
// 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' => _get_max_target('blastn'),
'#default_value' => $defaults['max_target_seqs'],
'#description' => t('Select the maximum number of unique target sequences per query sequence to show results for.'),
);
$form['ALG']['GParam']['eVal'] = array(
'#type' => 'textfield',
'#title' => t('e-Value (Expected Threshold)'),
'#default_value' => $defaults['evalue'],
'#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 video tutorial'),
);
$form['ALG']['GParam']['wordSize'] = array(
'#type' => 'select',
'#title' => t('Word size:'),
'#options' => _get_word_size('blastn'),
'#default_value' => $defaults['word_size'],
'#description' => t('The length of the seed that initiates an alignment'),
);
// 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' => _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',
),
);
$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', $m_m_set),
'#default_value' => $defaults['gap'],
'#description' => t('Cost to create and extend a gap in an alignment.'),
'#prefix' => '',
'#suffix' => '
',
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastn_advanced_options_form().
*/
function blast_ui_blastn_advanced_options_form_validate($form, $form_state) {
// Ensure that our textfields are what we expect them to be since we will
// use them to generate the BLAST command.
// First up, e-value. We expect the evalue to be a very small yet still
// positive number. It may be given in scientific notation which is
// luckily supported by is_numeric().
if (!is_numeric($form_state['values']['eVal'])) {
form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, 0.001 or, even better, 1e-10.');
}
}
/**
* 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
$gap = _set_gap($form_state['values']['gapCost']);
// Expand Match/Mismatch option into penalty/reward values
$m_m = _set_match_mismatch($form_state['values']['M&MScores']);
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'],
);
}
/**
* @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, $form_state) {
// Edit and Resubmit functionality.
// We want to pull up the details from a previous blast and fill them in as defaults
// for this blast.
if (isset($form_state['prev_blast'])) {
$defaults = _get_default_values($form_state['prev_blast']->options, 'blastx');
}
else {
$defaults = _get_default_values(array(), 'blastx');
}
$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' => _get_max_target('blastx'),
'#default_value' => $defaults['max_target_seqs'],
'#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' => $defaults['evalue'],
'#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' => _get_word_size('blastx'),
'#default_value' => $defaults['word_size'],
'#description' => t('The length of the seed that initiates an alignment'),
);
// Scoring parameters
//.........................
$form['ALG']['SParam'] = array(
'#type' => 'fieldset',
'#title' => t('Scoring parameters'),
'#collapsible' => FALSE,
);
$matrix_options = _get_matrix_options();
$form['ALG']['SParam']['Matrix'] = array(
'#type' => 'select',
'#title' => 'Matrix',
'#options' => $matrix_options,
'#default_value' => $defaults['matrix'],
'#description' => t('Assigns a score for aligning pairs of residues, and determines overall alignment score..'),
'#ajax' => array(
'callback' => 'matrix_gap_cost_callback',
'wrapper' => 'gap_cost_wrapper',
),
);
$matrix_set = $defaults['matrix'];
if (isset($form_state['values']) && isset($form_state['values']['Matrix'])) {
$matrix_set = $form_state['values']['Matrix'];
}
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#prefix' => '',
'#suffix' => '
',
'#options' => _get_gap_for_matrix($matrix_set),
'#default_value' => $defaults['gap'],
'#description' => t('Cost to create and extend a gap in an alignment.'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastx_advanced_options_form().
*/
function blast_ui_blastx_advanced_options_form_validate($form, $form_state) {
// Ensure that our textfields are what we expect them to be since we will
// use them to generate the BLAST command.
// First up, e-value. We expect the evalue to be a very small yet still
// positive number. It may be given in scientific notation which is
// luckily supported by is_numeric().
if (!is_numeric($form_state['values']['eVal'])) {
form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, 0.001 or, even better, 1e-10.');
}
}
/**
* 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, $form_state) {
// Same as blastp form submit
return blast_ui_blastp_advanced_options_form_submit($form, $form_state);
}
/**
* @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, $form_state) {
// Edit and Resubmit functionality.
// We want to pull up the details from a previous blast and fill them in as defaults
// for this blast.
if (isset($form_state['prev_blast'])) {
$defaults = _get_default_values($form_state['prev_blast']->options, 'blastp');
}
else {
$defaults = _get_default_values(array(), 'blastp');
}
//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' => _get_max_target('blastp'),
'#default_value' => $defaults['max_target_seqs'],
'#description' => t('Select the maximum number of aligned sequences to display'),
);
$form['ALG']['GParam']['eVal'] = array(
'#type' => 'textfield',
'#title' => t('e-value(Expect threshold)'),
'#default_value' => $defaults['evalue'],
'#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' => _get_word_size('blastp'),
'#default_value' => $defaults['word_size'],
'#description' => t('The length of the seed that initiates an alignment'),
);
// Scoring parameters
$form['ALG']['SParam'] = array(
'#type' => 'fieldset',
'#title' => t('Scoring parameters'),
'#collapsible' => FALSE,
);
$matrix_options = _get_matrix_options();
$form['ALG']['SParam']['Matrix'] = array(
'#type' => 'select',
'#title' => 'Matrix',
'#options' => $matrix_options,
'#default_value' => $defaults['matrix'],
'#description' => t('Assigns a score for aligning pairs of residues, and determines overall alignment score..'),
'#ajax' => array(
'callback' => 'matrix_gap_cost_callback',
'wrapper' => 'gap_cost_wrapper',
),
);
$matrix_set = $defaults['matrix'];
if (isset($form_state['values']) && isset($form_state['values']['Matrix'])) {
$matrix_set = $form_state['values']['Matrix'];
}
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#prefix' => '',
'#suffix' => '
',
'#options' => _get_gap_for_matrix($matrix_set),
'#default_value' => $defaults['gap'],
'#description' => t('Cost to create and extend a gap in an alignment.'),
);
}
/**
* Validate the advanced options provided by the BLASTp form above.
*
* @see blast_ui_blastp_advanced_options_form().
*/
function blast_ui_blastp_advanced_options_form_validate($form, $form_state) {
// Ensure that our textfields are what we expect them to be since we will
// use them to generate the BLAST command.
// First up, e-value. We expect the evalue to be a very small yet still
// positive number. It may be given in scientific notation which is
// luckily supported by is_numeric().
if (!is_numeric($form_state['values']['eVal'])) {
form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, 0.001 or, even better, 1e-10.');
}
}
/**
* 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];
//$qRange = $form_state['values']['qRange'];
// Expand Gap Cost key into open and extend penalties
$matrix = $form_state['values']['Matrix'];
$gapKey = $form_state['values']['gapCost'];
$gap = _set_gap($gapKey);
$gapOpen = $gap['gapOpen'];
$gapExtend = $gap['gapExtend'];
return array(
'max_target_seqs' => $numAlign,
'evalue' => $eVal,
'word_size' => $wordSize,
'gapopen' => $gapOpen,
'gapextend' => $gapExtend,
//'culling_limit' => $qRange,
'matrix' => $matrix,
);
}//blast_ui_blastp_advanced_options_form_submit
/**
* @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, $form_state) {
// Edit and Resubmit functionality.
// We want to pull up the details from a previous blast and fill them in as defaults
// for this blast.
if (isset($form_state['prev_blast'])) {
$defaults = _get_default_values($form_state['prev_blast']->options, 'tblastn');
}
else {
$defaults = _get_default_values(array(), 'tblastn');
}
$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' => _get_max_target('tblastn'),
'#default_value' => $defaults['max_target_seqs'],
'#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' => $defaults['evalue'],
'#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' => _get_word_size('tblastn'),
'#default_value' => $defaults['word_size'],
'#description' => t('The length of the seed that initiates an alignment'),
);
// Scoring parameters
//.........................
$form['ALG']['SParam'] = array(
'#type' => 'fieldset',
'#title' => t('Scoring parameters'),
'#collapsible' => FALSE,
);
$matrix_options = _get_matrix_options();
$form['ALG']['SParam']['Matrix'] = array(
'#type' => 'select',
'#title' => 'Matrix',
'#options' => $matrix_options,
'#default_value' => $defaults['matrix'],
'#description' => t('Assigns a score for aligning pairs of residues, and determines overall alignment score.'),
'#ajax' => array(
'callback' => 'matrix_gap_cost_callback',
'wrapper' => 'gap_cost_wrapper',
),
);
$matrix_set = $defaults['matrix'];
if (isset($form_state['values']) && isset($form_state['values']['Matrix'])) {
$matrix_set = $form_state['values']['Matrix'];
}
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#prefix' => '',
'#suffix' => '
',
'#options' => _get_gap_for_matrix($matrix_set),
'#default_value' => $defaults['gap'],
'#description' => t('Cost to create and extend a gap in an alignment.'),
);
}
/**
* Validate the advanced options provided by the tBLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_validate($form, $form_state) {
// Ensure that our textfields are what we expect them to be since we will
// use them to generate the BLAST command.
// First up, e-value. We expect the evalue to be a very small yet still
// positive number. It may be given in scientific notation which is
// luckily supported by is_numeric().
if (!is_numeric($form_state['values']['eVal'])) {
form_set_error('eVal', 'The e-value should be a very small number (scientific notation is supported). For example, 0.001 or, even better, 1e-10.');
}
}
/**
* Processed the advanced options provided by the tBLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_submit($form, $form_state) {
return blast_ui_blastp_advanced_options_form_submit($form, $form_state);
}
/**
* Fill the matrix dropdown list with appropriate options
*
* @return
* An array consisting of matrices name for the first dropdown list
*/
function _get_matrix_options() {
return drupal_map_assoc(array(
t('PAM30'),
t('PAM70'),
t('PAM250'),
t('BLOSUM80'),
t('BLOSUM62'),
t('BLOSUM45'),
t('BLOSUM50'),
t('BLOSUM90'),
));
}
/**
* Fill the gap penalty dropdown list with appropriate options given selected
* matrix
*
* @return
* An array containing open and extension gap values for the chosen matrix (to
* fill the second dropdown list)
*/
function _get_gap_for_matrix($key = '') {
switch ($key) {
case 'PAM30':
return _make_gaps(array('7_2', '6_2', '5_2', '10_1', '8_1', '13_3', '15_3', '14_1',
'14_2')
);
case 'PAM70':
return _make_gaps(array('8_2', '7_2', '6_2', '11_1', '10_1', '9_1', '12_3', '11_2'));
case 'PAM250':
return _make_gaps(array('15_3', '14_3', '13_3', '12_3', '11_3', '17_2', '16_2',
'15_2', '14_2', '13_2', '21_1', '20_1', '19_1', '18_1',
'17_1')
);
case 'BLOSUM80':
return _make_gaps(array('8_2', '7_2', '6_2', '11_1', '10_1', '9_1'));
case 'BLOSUM62':
return _make_gaps(array('11_2', '10_2', '9_2', '8_2', '7_2', '6_2', '13_1',
'12_1', '11_1', '10_1', '9_1')
);
case 'BLOSUM45':
return _make_gaps(array('13_3', '12_3', '11_3', '10_3', '15_2', '14_2', '13_2',
'12_2', '19_1', '18_1', '17_1', '16_1')
);
case 'BLOSUM50':
return _make_gaps(array('13_3', '12_3', '11_3', '10_3', '9_3', '16_2', '15_2',
'14_2', '13_2', '12_2', '19_1', '18_1', '17_1', '16_1',
'15_1')
);
case 'BLOSUM90':
return _make_gaps(array('9_2', '8_2', '7_2', '6_2', '11_1', '10_1', '9_1'));
}
}//_get_gap_for_matrix
/**
* Respond to Ajax dropdown call
*/
function matrix_gap_cost_callback($form, &$form_state) {
return $form['B']['ALG']['SParam']['gapCost'];
}
/**
* Get default form values; may come from saved job data if user is re-running
* a previous job.
*/
function _get_default_values($options, $program) {
// restore previous values or set to default
$max_target = (isset($options['max_target_seqs']))
? $options['max_target_seqs'] : 500;
$short_queries = (isset($options['shortQueries']))
? $options['shortQueries'] : TRUE;
$evalue = (isset($options['evalue']))
? $options['evalue'] : variable_get('eVal', 0.001);
$word_size = (isset($options['word_size']))
? $options['word_size'] : 11;
// match/mismatch
$matchmiss = 0;
$reward = (isset($options['reward']))
? $options['reward'] : 1;
$penalty = (isset($options['penalty']))
? $options['penalty'] : -2;
if ($reward == 1) {
switch ($penalty) {
case -1:
$matchmiss = 5;
break;
case -2:
$matchmiss = 0;
break;
case -3:
$matchmiss = 1;
break;
case -4:
$matchmiss = 2;
break;
}
}
else {
if ($reward == 2) {
$matchmiss = 3;
}
else {
if ($reward == 3) {
$matchmiss = 4;
}
else {
if ($reward == 4) {
$matchmiss = 5;
}
}
}
}
// gap
if (isset($options['gapopen']) && isset($options['gapextend'])) {
$gapopen = $options['gapopen'];
$gapextend = $options['gapextend'];
}
else {
switch ($program) {
case 'blastn':
$gapopen = 5;
$gapextend = 2;
break;
case 'blastp':
case 'blastx':
case 'tblastn':
$gapopen = 11;
$gapextend = 1;
break;
}
}
$gap = $gapopen.'_'.$gapextend;
// matrix
$matrix = (isset($options['matrix']))
? $options['matrix'] : 'BLOSUM62';
// all done
return array(
'max_target_seqs' => $max_target,
'short_queries' => $short_queries,
'word_size' => $word_size,
'evalue' => $evalue,
'matchmiss' => $matchmiss,
'gap' => $gap,
'matrix' => $matrix,
);
}//_get_default_values
/**
* Get a list of options for the max_target_seq blast option.
*
* The options are the same for all programs
* and describe the maximum number of aligned sequences to keep.
*/
function _get_max_target($which) {
switch ($which) {
case 'blastn':
case 'blastx':
case 'blastp':
case 'tblastn':
return array(
0 => t(' '),
10 => t('10'),
50 => t('50'),
100 => t('100'),
250 => t('250'),
500 => t('500'),
1000 => t('1000'),
5000 => t('5000'),
10000 => t('10000'),
20000 => t('20000'),
);
}//switch
}
/**
* Get a list of options for work size.
*/
function _get_word_size($which) {
switch ($which) {
case 'blastn':
return array(
7 => t('7'),
11 => t('11'),
15 => t('15'),
16 => t('16'),
20 => t('20'),
24 => t('24'),
28 => t('28'),
32 => t('32'),
48 => t('48'),
64 => t('64'),
128 => t('128'),
256 => t('256'),
);
case 'blastx':
case 'blastp':
case 'tblastn':
return array(
// 2 => t('2'),
3 => t('3'),
6 => t('6'),
);
}//switch
}
/**
* Get a list of options for match/mismatch ratio.
*/
function _get_match_mismatch($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'),
);
}//switch
}
/**
* @param $which - the blast program being run
* @param $m_m - the match mismatch scores.
*
* @return array
*/
function _get_gap_options($which, $m_m) {
switch ($which) {
case 'blastn':
switch ($m_m) {
case 0: //1, -2
return _make_gaps(array('5_2', '2_2', '1_2', '0_2', '3_1', '2_1', '1_1'));
case 1: //1, -3
return _make_gaps(array('5_2', '2_2', '1_2', '1_2', '0_2', '2_1', '1_1'));
case 2: // 1, -4
return _make_gaps(array('5_2', '1_2', '0_2', '2_1', '1_1'));
case 3: //2, -3
return _make_gaps(array('4_4', '2_4', '0_4', '3_3', '6_2', '5_2', '4_2', '2_2'));
case 4: //4, -5
return _make_gaps(array('12_8', '6_5', '5_5', '4_5', '3_5'));
case 5: //1, -1
return _make_gaps(array('5_2', '3_2', '2_2', '1_2', '0_2', '4_1', '3_1', '2_1'));
}
}
}
/**
* @param $gap_array - array of gap abbreviations
*
* @return array
*/
function _make_gaps($gap_array) {
$a = array();
foreach ($gap_array as $g) {
$parts = explode('_', $g);
$a[$g] = t("Existence: $parts[0] Extension: $parts[1]");
}
return $a;
}
/**
* Translate gap abbreviation into blast gap open and extend costs.
* @param $gap_key - a gap open/extend abbreviation
*/
function _set_gap($gap_key) {
$parts = explode('_', $gap_key);
return array('gapOpen' => $parts[0], 'gapExtend' => $parts[1]);
}
/**
* Translate mismatch/match ratio option into blast penalty/reward options.
*/
function _set_match_mismatch($m_m) {
switch ($m_m) {
case 0:
$penalty = -2;
$reward = 1;
break;
case 1:
$penalty = -3;
$reward = 1;
break;
case 2:
$penalty = -4;
$reward = 1;
break;
case 3:
$penalty = -3;
$reward = 2;
break;
case 4:
$penalty = -5;
$reward = 4;
break;
case 5:
$penalty = -1;
$reward = 1;
break;
}//switch
return array('penalty' => $penalty, 'reward' => $reward);
}
/**
* 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'];
}