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(
    '#title' => 'Or upload your own query FASTA:	',
    '#type' => 'managed_file',
    '#description' => t('The file should be a plain-text FASTA
(.fasta, .fna, .fa) file. In other words, it cannot have formatting as is the
case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater
than %max_size in size. <strong>Don\'t forget to press the Upload button before
attempting to submit your BLAST.</strong>',
      array(
        '%max_size' => round(file_upload_max_size() / 1024 / 1024,1) . 'MB'
      )
    ),
    '#upload_validators' => array(
      'file_validate_extensions' => array('fasta fna fa'),
      'file_validate_size' => array(file_upload_max_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(
    '#title' => 'Or upload your own dataset:	',
    '#type' => 'managed_file',
    '#description' => t('The file should be a plain-text FASTA
(.fasta, .fna, .fa) file. In other words, it cannot have formatting as is the
case with MS Word (.doc, .docx) or Rich Text Format (.rtf). It cannot be greater
than %max_size in size. <strong>Don\'t forget to press the Upload button before
attempting to submit your BLAST.</strong>',
      array(
        '%max_size' => round(file_upload_max_size() / 1024 / 1024,1) . 'MB'
      )
    ),
    '#upload_validators' => array(
      'file_validate_extensions' => array('fasta fna fa'),
      'file_validate_size' => array(file_upload_max_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) {

  // Validate Query
  //----------------
  // @todo: We are currently not validating uploaded files are valid FASTA.
  // First check to see if we have an upload & if so then validate it.
  $file = file_load($form_state['values']['UPLOAD']);
  // If the $file is populated then this is a newly uploaded, temporary file.
  if (is_object($file)) {
    $form_state['qFlag'] = 'upQuery';
    $form_state['upQuery_path'] = drupal_realpath($file->uri);
  }
  // Otherwise there was no file uploaded.
  // Check if there was a query sequence entered in the texfield.
  elseif (!empty($form_state['input']['FASTA'])) {
    // Check to ensure that the query sequence entered is valid FASTA.
    if (validateFasta($form_state['input']['FASTA'])){
      form_set_error('pBLAST', t('You need to provide a valid FASTA sequence
for the query.'));
    }
    else {
      $form_state['qFlag'] = 'seqQuery';
    }
  }
  // Otherwise they didn't enter a query!!
  else {
    form_set_error('pBLAST', t('You must either enter a FASTA sequence in the
text field or upload one of your own.'));
  }

  // Validate Database
  //-------------------
  // @todo: We are currently not validating uploaded files are valid FASTA.
  // First check to see if we have an upload & if so then validate it.
  $file = file_load($form_state['values']['DBUPLOAD']);
  // If the $file is populated then this is a newly uploaded, temporary file.
  if (is_object($file)) {
    $form_state['dbFlag'] = 'upDB';
    $form_state['upDB_path'] = drupal_realpath($file->uri);
  }
  // Otherwise there was no file uploaded
  // Check if there was a database choosen from the list instead
  elseif (!empty($form_state['values']['SELECT_DB'])) {
    $form_state['dbFlag'] = 'blastdb';
  }
  // Otherwise they didn't select a database!!
  else {
    form_set_error('DB', t('You must either choose a database from the list or upload one of your own.'));
  }
}

/**
 * Form submition handler for blast_protein_form().
 *
 * @see blast_protein_form_submit()
 */
function blast_protein_form_submit($form, &$form_state) {

  $error = FALSE;

  $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'] == 'upDB') {

    // 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'];
    $result = NULL;
    exec("makeblastdb -in $blastdb_with_path -dbtype prot -parse_seqids 2>&1", $result);

    // Check that the BLAST database was made correctly.
    $result = implode('<br />', $result);
    if (preg_match('/Error/', $result)) {
      drupal_set_message('Unable to generate a BLAST database from your uploaded
FASTA sequence. Please check that your file is a valid FASTA file and that if
your sequence headers include pipes (i.e.: | ) they adhere to '
. l('NCBI standards.', 'http://www.ncbi.nlm.nih.gov/books/NBK21097/table/A632/?report=objectonly', array('attributes' => array('target' => '_blank'))),
        'error'
      );

      $error = TRUE;
    }

  }
  // 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");
  }
  // We check if $error is set to TRUE because if so then the error has already
  // been reported.
  elseif (!$error) {
    $dbfile_uploaded_msg = ($form_state['dbFlag'] == 'upDB') ? '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;
}