tripal_blast/includes/blast_ui.blastp.inc

<?php

/**
 * @file
 * Contains all functions for the Protein BLAST
 */


/**
 * Protein BLAST Submission Form
 *
 * @see blast_protein_form_validate()
 * @see blast_protein_form_submit()
 */
function blast_protein_form($form, &$form_state) {

	//  CSS support to the form
	$form['#attached']['css'] = array(
		drupal_get_path('module', 'blast_ui') . '/css/form.css',
		);

  // PROTEIN QUERY
  //.........................

  $form['query'] = array(
    '#type' => 'fieldset',
    '#title' => t('Enter Query Sequence'),
    '#description' => t('Enter one or more queries in the top text box or use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. In both cases, the data must be in FASTA format. <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml" target="_blank">More information..</a> '),
    '#collapsible' => TRUE,
    '#collapsed' => FALSE,
   	'#prefix' => '<div class="two-col">',
    '#suffix' => '</div>',
  );
  $form['query']['example_sequence'] = array(
    '#type' => 'button',
    '#button_type'=> 'button',
    '#limit_validation_errors' => array(),
    '#value' => t('Example Sequence'),
    '#prefix' => '<div class="center">',
    '#suffix' => '</div>',
    '#validate' => array(),
    '#ajax' => array(
    	'callback' => 'ajax_nucleotide_text_area_callback',
    	'wrapper'  => 'fasta_seq',
        'method'   => 'replace',
        'effect'   => 'fade',
        ),
	  '#attributes' => array('onclick' => 'return false;'),
  );


  $form['query']['FASTA'] = array(
    '#type' => 'textarea',
    '#title' => t('Enter FASTA sequence(s)'),
    '#description'=>t('Enter query sequence(s) in the text area.'),
    '#prefix' => '<div id="fasta_seq">',
    '#suffix' => '</div>',
  );

  // Upload a file as an alternative to enter a query sequence
  $form['#attributes']['enctype'] = 'multipart/form-data';
  $form['query']['UPLOAD'] = array(
  	'#prefix' => 'Or upload your query files:	',
  	'#type' => 'file',
  	'#description' => t('The file should be a plain-text FASTA file and not a .doc, .docx, etc. It cannot be greater than 10 Mb in size.'),
  );


	$form['query']['example_sequence'] = array(
			'#type' => 'button',
			'#button_type'=> 'button',
			'#limit_validation_errors' => array(),
			'#value' => t('Example Sequence'),
			'#prefix' => '<div class="center">',
			'#suffix' => '</div>',
			'#validate' => array(),
			'#ajax' => array(
				'callback' => 'ajax_protein_text_area_callback',
				'wrapper'  => 'fasta_seq',
					'method'   => 'replace',
					'effect'   => 'fade',
					),
		'#attributes' => array('onclick' => 'return false;'),
		);


  // BLAST DATABASE
  //.........................

  $form['DB'] = array(
    '#type' => 'fieldset',
    '#title' => t('Choose Search Set'),
    '#description' => t('Choose from one of the protein BLAST databases listed below. You can also use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. '),
    '#collapsible' => TRUE,
    '#collapsed' => FALSE,
  );

  $options = get_blast_database_options('p');
  $form['DB']['SELECT_DB'] = array(
  '#type' => 'select',
   '#title' => t('Protein BLAST Databases:'),
   '#options' => $options,
   '#default_value' => t('Select a database'),
  );

  // Upload a file as an alternative to enter a query sequence
  $form['#attributes']['enctype'] = 'multipart/form-data';
  $form['DB']['DBUPLOAD'] = array(
   '#prefix' => 'Or upload your own dataset:	',
  	'#type' => 'file',
  	'#description' => t('The file should be a plain-text FASTA file and not a .doc, .docx, etc. It cannot be greater than 10 Mb in size.'),
  );

  // ALGORITHM PARAMETERS
  //.........................

	$form['ALG'] = array(
    '#type' => 'fieldset',
    '#title' => t('Algorithm parameters'),
    '#collapsible' => TRUE,
    '#collapsed' => TRUE,
  );

  //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',
    ),
  );

  $form['ALG']['SParam']['gapCost'] = array(
    '#type' => 'select',
    '#title' => t('Gap Costs:'),
    '#prefix' => '<div id="dropdown-second-replace">',
    '#suffix' => '</div>',
    '#options' => _ajax_example_get_second_dropdown_options($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'),
  );

  //Submit
  $form['submit'] = array(
    '#type' => 'submit',
    '#default_value' => ' BLAST ',
  );

  return $form;
}

/**
 * Form validation handler for blast_protein_form().
 *
 * @see blast_protein_form_validate()
 */
function blast_protein_form_validate($form, &$form_state) {
  // Get the sequence 
  $fastaSeq = $form_state['values']['FASTA'];
  $upQuery = file_save_upload('UPLOAD', array('file_validate_extensions' => array('txt fasta fa fna'),
  																						), FILE_EXISTS_RENAME);
  // Check if the sequence is empty																					
  if(empty($fastaSeq) && empty($upQuery)) {
  	form_set_error('query', t('No query sequence given. Only raw sequence or sequence of type FASTA can be read. 
  								Enter sequence in the box provided or upload a plain text file.'));
  }
   
  // Get the DB
  $db_selected = $form_state['values']['SELECT_DB']; 
  $upDB = file_save_upload('DB', array('file_validate_extensions' => array('txt fasta fa fna'),
  																						), FILE_EXISTS_RENAME);
  // Check if the database is selected or not																						
  if(empty($upDB) && $db_selected == 0) {
  	form_set_error('DB', t('Select the database from the list or upload the FASTA file'));
  }
  

  // Validate query sequence
  if (isset($fastaSeq)) {
    if (validateFasta($fastaSeq)){
      form_set_error('FASTA', t('Error: Failed to read the Blast query: Wrong format provided for FASTA protein sequence'));
    }
    else {
      $form_state['qFlag'] = 'seqQuery';
    }
  }

  // Validate Query Upload
  if ($upQuery) {
    $upQuery_uri = $upQuery->uri;
    $form_state['upQuery_path'] = drupal_realpath($upQuery_uri);
    $upQuery_content = file_get_contents($form_state['upQuery_path']);
    if(validateFasta($upQuery_content)){
      form_set_error('UPLOAD', t('Error: Failed to upload the Blast query: Wrong format provided for FASTA protein sequence'));
    }
    else {
      $form_state['qFlag'] = 'upQuery';
    }
  }

  // Validate uploaded database
  if ($upDB) {
    $upDB_uri = $upDB->uri;
    $form_state['upDB_path'] = drupal_realpath($upDB_uri);
    $upDB_content = file_get_contents($form_state['upDB_path']);
    if(validateFasta($upDB_content)){
      form_set_error('SELECT_DB', t('Error: Failed to upload the Blast subject sequence file: Wrong format provided for FASTA protein sequence'));
    }
    else {
      $form_state['dbFlag'] = 'upQuery';
    }
  }
  else {
    $form_state['dbFlag'] = 'blastdb';
  }
}

/**
 * Form submition handler for blast_protein_form().
 *
 * @see blast_protein_form_submit()
 */
function blast_protein_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;
  }

  // If the query was submitted via the texrfield then create a file containing it
  if ( isset($form_state['qFlag']) ) {
    if ( $form_state['qFlag'] == 'seqQuery' ) {
      $seq_content = $form_state['values']['FASTA'];
	    $query = '/tmp/' . date('YMd_His') . '_query.fasta';
      file_put_contents ( $query , $seq_content);
    }
    elseif ( $form_state['qFlag'] == 'upQuery' ) {
      $query = $form_state['upQuery_path'];
    }
  }

  // If the BLAST database was uploaded then use it to run the BLAST
  if ($form_state['dbFlag'] == 'upQuery') {

    // Since we only support using the -db flag (not -subject) we need to create a
    // blast database for the FASTA uploaded.
    // NOTE: We can't support subject because we need to generate the ASN.1+ format
    // to provide multiple download type options from the same BLAST
    $blastdb_with_path = $form_state['upDB_path'];
    system("makeblastdb -in $blastdb_with_path -dbtype prot -parse_seqids");

  }
  // Otherwise, we are using one of the website provided BLAST databases so form the
  // BLAST command accordingly
  elseif ($form_state['dbFlag'] == 'blastdb') {

     $selected_db = $form_state['values']['SELECT_DB'];
     $blastdb_node = node_load($selected_db);
     $blastdb_with_path = $blastdb_node->db_path;

  }

  // Actually submit the BLAST Tripal Job
  // NOTE: Tripal jobs needs to be executed from the command-line before it will be run!!
  $blastdb_with_suffix = $blastdb_with_path . '.psq';
  if (is_readable($blastdb_with_suffix)) {
    global $user;
    $output_filestub = date('YMd_His');
    $job_args = array(
      'program' => 'blastp',
      'query' => $query,
      'database' => $blastdb_with_path,
      'output_filename' => $output_filestub,
      'options' => array(
        'evalue' => $eVal,
        'word_size' => $wordSize,
        'gapopen' => $gapOpen,
        'gapextend' => $gapExtend,
        'matrix' => $matrix
      )
    );
    $job_id = tripal_add_job("BLAST (blastp): $query",'blast_job','run_BLAST_tripal_job', $job_args, $user->uid);

    // Redirect to the BLAST results page
    drupal_goto("blast/report/$job_id");
  }
  else {
    $dbfile_uploaded_msg = ($form_state['dbFlag'] == 'upQuery') ? 'The BLAST database was submitted via user upload.' : 'Existing BLAST Database was chosen';
    tripal_report_error(
      'blast_ui',
      TRIPAL_ERROR,
      "BLAST database %db unaccessible. $dbfile_uploaded_msg",
      array('%db' => $blastdb_with_path)
    );
    drupal_set_message('BLAST database unaccessible. Please contact the site administrator.','error');
  }
}


/**
 * FASTA validating parser
 *
 * @param $sequence
 *  A string of characters to be validated. A sequence in FASTA format begins with a single-line description, followed by lines of sequence data.
 *  The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column.
 *  The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional).
 *  There should be no space between the ">" and the first letter of the identifier. The sequence ends if another line starting with a ">" appears;
 *  this indicates the start of another sequence.
 *
 * @return
 *  Return a boolean. 1 if the sequence does not pass the format valifation stage and 0 otherwise.
 *
 */
function validateFasta($sequence) {
	$fastaIdRegEx = '/^>.*(\\n|\\r)/';
	$fastaSeqRegEx = '/[^acgturykmswbdhvnxACGTURYKMSWBDHVNX\*\-\n\r]/';
	if ( preg_match($fastaSeqRegEx,$sequence) && !(preg_match($fastaIdRegEx,$sequence)) ) {
    $flag = 1;
  } else {
    $flag = 0;
  }

  return $flag;
}

/**
 * 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'];
}


// call back function for example sequence
function ajax_protein_text_area_callback($form, $form_state) {
 $element = $form['query']['FASTA']; // Get example Protein sequence

$element['#value'] =
	'>gi|166477|gb|AAA96434.1| resveratrol synthase [Arachis hypogaea]
MVSVSGIRKVQRAEGPATVLAIGTANPPNCIDQSTYADYYFRVTNSEHMTDLKKKFQRICERTQIKNRHM
YLTEEILKENPNMCAYKAPSLDAREDMMIREVPRVGKEAATKAIKEWGQPMSKITHLIFCTTSGVALPGV
DYELIVLLGLDPCVKRYMMYHQGCFAGGTVLRLAKDLAENNKDARVLIVCSENTAVTFRGPSETDMDSLV
GQALFADGAAAIIIGSDPVPEVEKPIFELVSTDQKLVPGSHGAIGGLLREVGLTFYLNKSVPDIISQNIN
DALNKAFDPLGISDYNSIFWIAHPGGRAILDQVEQKVNLKPEKMKATRDVLSNYGNMSSACVFFIMDLMR
KRSLEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI';

return $element;
}