<?php
/**
* @file
* Contains helper functions related to program-specific advanced options.
*/
/**
* @section
* BLASTn: Search a nucleotide database using a nucleotide query.
* ----------------------------------------------------------------------------
*/
/**
* Adds the BLASTn 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 $form.
*/
function blast_ui_blastn_advanced_options_form(&$form, $form_state) {
$all_job_data = variable_get('job_data', '');
if (isset($_GET['jid']) && isset($all_job_data)) {
$jid = base64_decode($_GET['jid']);
$job_data = $all_job_data[$jid];
}
else {
$job_data = array();
$jid = 0;
}
$defaults = _get_default_values($job_data, '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 aligned sequences to display'),
);
/*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',
'#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. <a href="http://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>'),
);
$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'),
);
$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,
);
$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.'),
);
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#options' => _get_gap('blastn'),
'#default_value' => $defaults['gap'],
'#description' => t('Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores.'),
);
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastn_advanced_options_form().
*/
function blast_ui_blastn_advanced_options_form_validate($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
$gap = _set_gap($form_state['values']['gapCost']);
// Expand Match/Mismatch option into penalty/reward values
$m_m = _set_match_mismatch($form_state['values']['M&MScores']);
// Limit number of query hits
$qRange = $form_state['values']['qRange'];
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'],
'culling_limit' => $qRange,
);
}//blast_ui_blastn_advanced_options_form_submit
/**
* @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) {
$all_job_data = variable_get('job_data', '');
if (isset($_GET['jid']) && isset($all_job_data)) {
$jid = base64_decode($_GET['jid']);
$job_data = $all_job_data[$jid];
}
else {
$job_data = array();
$jid = 0;
}
$defaults = _get_default_values($job_data, '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. <a href="http://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,
);
*/
$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' => $default['matrix'],
'#description' => t('Assigns a score for aligning pairs of residues, and determines overall alignment score..'),
'#ajax' => array(
'callback' => 'ajax_dependent_dropdown_callback',
'wrapper' => 'dropdown-second-replace',
),
);
$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
$form['ALG']['SParam']['M&MScores'] = array(
'#type' => 'select',
'#title' => t('Match/Mismatch Scores:'),
'#options' => array(
0 => t('No adjustment'),
1 => t('Composition-based statistics'),
2 => t('Conditional compositional score matrix adjustment'),
3 => t('Universal composition score matrix adjustment '),
),
'#default_value' => 2,
'#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
);
*/
}
/**
* Validate the advanced options provided by the BLASTn form above.
*
* @see blast_ui_blastx_advanced_options_form().
*/
function blast_ui_blastx_advanced_options_form_validate($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, $form_state) {
// Same as blastp form submit
return blast_ui_blastp_advanced_options_form_submit($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) {
$all_job_data = variable_get('job_data', '');
if (isset($_GET['jid']) && isset($all_job_data)) {
$jid = base64_decode($_GET['jid']);
$job_data = $all_job_data[$jid];
}
else {
$job_data = array();
$jid = 0;
}
$defaults = _get_default_values($job_data, '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'),
);
/*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',
'#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'),
);
$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,
);
$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' => 'ajax_dependent_dropdown_callback',
'wrapper' => 'dropdown-second-replace',
),
);
/*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
$form['ALG']['SParam']['M&MScores'] = array(
'#type' => 'select',
'#title' => t('Match/Mismatch Scores:'),
'#options' => array(
0 => t('No adjustment'),
1 => t('Composition-based statistics'),
2 => t('Conditional compositional score matrix adjustment'),
3 => t('Universal composition score matrix adjustment '),
),
'#default_value' => 2,
'#description' => t('Matrix adjustment method to compensate for amino acid composition of sequences'),
);
*/
}//blast_ui_blastp_advanced_options_form
/**
* Validate the advanced options provided by the BLASTp form above.
*
* @see blast_ui_blastp_advanced_options_form().
*/
function blast_ui_blastp_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the BLASTp form above.
*
* @see blast_ui_blastp_advanced_options_form().
*/
function blast_ui_blastp_advanced_options_form_submit($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 = $form_state['values']['Matrix'];
switch ($matrix) {
case '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 '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 '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 '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 '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 '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 '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 '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;
}
//eksc- need to implement query range limit
// q_range
return array(
'max_target_seqs' => $numAlign,
'evalue' => $eVal,
'word_size' => $wordSize,
'gapopen' => $gapOpen,
'gapextend' => $gapExtend,
'culling_limit' => $qRange,
'matrix' => $matrix,
);
}//blast_ui_blastp_advanced_options_form_submit
/**
* Fill the matrix dropdown list with appropriate options
*
* @return
* An array consisting of matrices name for the first dropdown list
*/
function _get_matrix_options() {
return drupal_map_assoc(array(
t('PAM30'),
t('PAM70'),
t('PAM250'),
t('BLOSUM80'),
t('BLOSUM62'),
t('BLOSUM45'),
t('BLOSUM50'),
t('BLOSUM90'),
));
}
/**
* Fill the gap penalty dropdown list with appropriate options given selected matrix
*
* @return
* An array containing open and extension gap values for the chosen matrix (to fill the second dropdown list)
*/
function _get_gap_for_matrix($key = '') {
$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();
}
}//_get_gap_for_matrix
/**
* Respond to Ajax dropdown call
*/
function ajax_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) {
$all_job_data = variable_get('job_data', '');
if (isset($_GET['jid']) && isset($all_job_data)) {
$jid = base64_decode($_GET['jid']);
$job_data = $all_job_data[$jid];
}
else {
$job_data = array();
$jid = 0;
}
$defaults = _get_default_values($job_data, '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. <a href="http://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,
);
*/
$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' => 'ajax_dependent_dropdown_callback',
'wrapper' => 'dropdown-second-replace',
),
);
$form['ALG']['SParam']['gapCost'] = array(
'#type' => 'select',
'#title' => t('Gap Costs:'),
'#prefix' => '<div id="dropdown-second-replace">',
'#suffix' => '</div>',
'#options' => _get_gap_for_matrix($$default['matrix']),
'#default_value' => 2,
'#description' => t('Cost to create and extend a gap in an alignment.'),
);
$form['ALG']['GParam']['qRange'] = array(
'#type' => 'textfield',
'#title' => t('Max matches in a query range'),
'#default_value' => $defaults['qRange'],
'#size' => 12,
'#maxlength' => 20,
'#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
);
}//blast_ui_tblastn_advanced_options_form
/**
* Validate the advanced options provided by the tBLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_validate($form, $form_state) { }
/**
* Processed the advanced options provided by the tBLASTn form above.
*
* @see blast_ui_tblastn_advanced_options_form().
*/
function blast_ui_tblastn_advanced_options_form_submit($form, $form_state) {
return blast_ui_blastp_advanced_options_form_submit($form, $form_state);
}
/*
* Get default form values; may come from saved job data if user is re-running
* a previous job.
*/
function _get_default_values($job_data) {
// restore previous values or set to default
$max_target = (isset($job_data['options']['max_target_seqs']))
? $job_data['options']['max_target_seqs'] : 10;
$short_queries = (isset($job_data['options']['shortQueries']))
? $job_data['options']['shortQueries'] : true;
$evalue = (isset($job_data['options']['evalue']))
? $job_data['options']['evalue'] : .001;
$word_size = (isset($job_data['options']['word_size']))
? $job_data['options']['word_size'] : 11;
$qRange = (isset($job_data['options']['culling_limit']))
? $job_data['options']['culling_limit'] : 0;
$matchmiss = 0;
$reward = (isset($job_data['options']['reward']))
? $job_data['options']['reward'] : 1;
$penalty = (isset($job_data['options']['penalty']))
? $job_data['options']['penalty'] : -2;
if ($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) {
$matchmis = 4;
}
else if ($eward == 4) {
$matchmiss = 5;
}
$gap = 0;
$gapopen = (isset($job_data['options']['gapopen']))
? $job_data['options']['gapopen'] : 5;
$gapextend = (isset($job_data['options']['gapextend']))
? $job_data['options']['gapextend'] : 2;
if ($gapextend == 2) {
switch ($gapopen) {
case 5: $gap = 0; break;
case 2: $gap = 1; break;
case 1: $gap = 2; break;
case 0: $gap = 3; break;
}
}
else if ($gapextend == 1) {
switch ($gapopen) {
case 3: $gap = 4;
case 2: $gap = 5;
case 1: $gap = 6;
}
}
// eksc- need to implement query range limit
// $q_range = 0;
$matrix = (isset($job_data['options']['matrix']))
? $job_data['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' => $matrix,
);
}//_get_default_values
function _get_max_target($which) {
switch ($which) {
case 'blastn':
case 'blastx':
case 'blastp':
case 'tblastn':
return array(
10 => t('10'),
50 => t('50'),
100 => t('100'),
250 => t('250'),
500 => t('500'),
1000 => t('1000'),
5000 => t('5000'),
10000 => t('10000'),
20000 => t('20000'),
);
}//switch
}
function _get_word_size($which) {
switch ($which) {
case 'blastn':
return array(
7 => t('7'),
11 => t('11'),
15 => t('15'),
16 => t('16'),
20 => t('20'),
24 => t('24'),
28 => t('28'),
32 => t('32'),
48 => t('48'),
64 => t('64'),
128 => t('128'),
256 => t('256'),
);
case 'blastx':
case 'blastp':
case 'tblastn':
return array(
2 => t('2'),
3 => t('3'),
6 => t('6'),
);
}//switch
}
function _get_match_mismatch($which) {
switch ($which) {
case 'blastn':
return array(
0 => t('1,-2'),
1 => t('1,-3'),
2 => t('1,-4'),
3 => t('2,-3'),
4 => t('4,-5'),
5 => t('1,-1'),
);
}//switch
}
function _get_gap($which) {
switch ($which) {
case 'blastn':
return array(
0 => t('Existence: 5 Extension: 2'),
1 => t('Existence: 2 Extension: 2'),
2 => t('Existence: 1 Extension: 2'),
3 => t('Existence: 0 Extension: 2'),
4 => t('Existence: 3 Extension: 1'),
5 => t('Existence: 2 Extension: 1'),
6 => t('Existence: 1 Extension: 1'),
);
}//switch
}
function _set_gap($gap_key) {
switch ($gap_key) {
case 0:
$gapOpen = 5;
$gapExtend = 2;
break;
case 1:
$gapOpen = 2;
$gapExtend = 2;
break;
case 2:
$gapOpen = 1;
$gapExtend = 2;
break;
case 3:
$gapOpen = 0;
$gapExtend = 2;
break;
case 4:
$gapOpen = 3;
$gapExtend = 1;
break;
case 5:
$gapOpen = 2;
$gapExtend = 1;
break;
case 6:
$gapOpen = 1;
$gapExtend = 1;
break;
}//switch
return array('gapOpen' => $gapOpen, 'gapExtend' => $gapExtend);
}
function _set_match_mismatch($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);
}