Re-factored BLAST submission form for code-reuse

includes/blast_ui.blastn.inc

@@ -1,502 +0,0 @@
-<?php
-
-/**
- * @file
- * Contains all functions for the Nucleotide BLAST
- */
-
-
-/**
- * Nucleotide BLAST Submission Form
- *
- * @see blast_nucleotide_form_validate()
- * @see blast_nucleotide_form_submit()
- */
-function blast_nucleotide_form($form, &$form_state) {
-	//  CSS support to the form
-	$form['#attached']['css'] = array(
-		drupal_get_path('module', 'blast_ui') . '/css/form.css',
-	);
-
-  // Add the sequence type to the form
-  $form['sequence_type'] = array(
-    '#type' => 'hidden',
-    '#value' => 'nucleotide'
-  );
-
-  // NUCLEOTIDE 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 <a href="@fasta-format-url" target="_blank">FASTA format</a>. ',
-        array(
-          '@fasta-format-url' => 'http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml'
-        )
-      ),
-    '#collapsible' => TRUE,
-    '#collapsed' => FALSE,
-  );
-
-  // Checkbox to show an example.
-  $form['query']['example_sequence'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Show an Example Sequence'),
-    '#prefix' => '<span style="float: right;">',
-    '#suffix' => '</span>',
-    '#ajax' => array(
-    	'callback' => 'ajax_blast_ui_example_sequence_callback',
-    	'wrapper'  => 'fasta-textarea',
-      'method'   => 'replace',
-      'effect'   => 'fade',
-    ),
-  );
-
-  // Textfield for submitting a mult-FASTA query
-  $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-textarea">',
-    '#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()),
-    ),
-  );
-
-
-  // BLAST DATABASE
-  //.........................
-
-  $form['DB'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Choose Search Set'),
-    '#description' => t('Choose from one of the nucleotide 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('n');
-  $form['DB']['SELECT_DB'] = array(
-    '#type' => 'select',
-    '#title' => t('Nucleotide BLAST Databases:'),
-    '#options' => $options,
-    '#default_value' => 0,
-  );
-
-  // Upload a file as an alternative to selecting an existing BLAST database
-  $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 (Expected Threshold)'),
-    '#default_value' => 10,
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Expected number of chance matches in a random model. This number should be give in a decimal format. <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' => array(
-      0 => t('16'),
-      1 => t('20'),
-      2 => t('24'),
-      3 => t('28'),
-      4 => t('32'),
-      5 => t('48'),
-      6 => t('64'),
-      7 => t('128'),
-      8 => t('256'),
-    ),
-    '#default_value' => 3,
-    '#description' => t('The length of the seed that initiates an alignment'),
-  );
-
-  $form['ALG']['GParam']['qRange'] = array(
-    '#type' => 'textfield',
-    '#title' => t('Max matches in a query range'),
-    '#default_value' => 0,
-    '#size' => 12,
-    '#maxlength' => 20,
-    '#description' => t('Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query.'),
-  );
-
-  // Scoring parameters
-
-  $form['ALG']['SParam'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Scoring parameters'),
-    '#collapsible' => FALSE,
-  );
-
-  $form['ALG']['SParam']['M&MScores'] = array(
-    '#type' => 'select',
-    '#title' => t('Match/Mismatch Scores:'),
-    '#options' => array(
-       0 => t('1,-2'),
-       1 => t('1,-3'),
-       2 => t('1,-4'),
-       3 => t('2,-3'),
-       4 => t('4,-5'),
-       5 => t('1,-1'),
-     ),
-    '#default_value' => 0,
-    '#description' => t('Reward and penalty for matching and mismatching bases.'),
-   );
-
-   $form['ALG']['SParam']['gapCost'] = array(
-    '#type' => 'select',
-    '#title' => t('Gap Costs:'),
-    '#options' => array(
-      0 => t('Existence: 5 Extension: 2'),
-      1 => t('Existence: 2 Extension: 2'),
-      2 => t('Existence: 1 Extension: 2'),
-      3 => t('Existence: 0 Extension: 2'),
-      4 => t('Existence: 3 Extension: 1'),
-      5 => t('Existence: 2 Extension: 1'),
-      6 => t('Existence: 1 Extension: 1'),
-    ),
-    '#default_value' => 0,
-    '#description' => t('Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores.'),
-  );
-
-  // Submit
-  $form['submit'] = array(
-    '#type' => 'submit',
-    '#default_value' => ' BLAST ',
-  );
-
-  return $form;
-}
-
-/**
- * Form validation handler for blast_nucleotide_form().
- *
- * @see blast_nucleotide_form().
- */
-function blast_nucleotide_form_validate($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('nBLAST', 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('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.'));
-  }
-
-  // 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'])) {
-    $form_state['dbFlag'] = 'blastdb';
-  }
-  // Otherwise they didn't select a database!!
-  else {
-    form_set_error('DB', t('No database selected. Either choose a database from the list or upload one of your own.'));
-  }
-
-}
-
-/**
- * Form submission handler for blast_nucleotide_form().
- *
- * @see blast_nucleotide_form().
- */
-function blast_nucleotide_form_submit($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 = $form_state['values']['gapCost'];
-  switch ($gapKey) {
-   case 0:
-      $gapOpen = 5;
-      $gapExtend = 2;
-      break;
-   case 1:
-      $gapOpen = 2;
-      $gapExtend = 2;
-      break;
-   case 2:
-      $gapOpen = 1;
-      $gapExtend = 2;
-      break;
-   case 3:
-      $gapOpen = 0;
-      $gapExtend = 2;
-      break;
-   case 4:
-      $gapOpen = 3;
-      $gapExtend = 1;
-      break;
-   case 5:
-      $gapOpen = 2;
-      $gapExtend = 1;
-      break;
-   case 6:
-      $gapOpen = 1;
-      $gapExtend = 1;
-      break;
-  }
-
-  // Epand Match/Mismatch option into penalty/reward values
-  // @todo Amir: Is the switch supposed to be for $scoreKey?
-  $scoreKey = $form_state['values']['M&MScores'];
-  switch ($gapKey) {
-   case 0:
-      $penalty = -2;
-      $reward = 1;
-      break;
-   case 1:
-      $penalty = -3;
-      $reward = 1;
-      break;
-   case 2:
-      $penalty = -4;
-      $reward = 1;
-      break;
-   case 3:
-      $penalty = -3;
-      $reward = 2;
-      break;
-   case 4:
-      $penalty = -5;
-      $reward = 4;
-      break;
-   case 5:
-      $penalty = -1;
-      $reward = 1;
-      break;
-  }
-
-  // If the query was submitted via the texrfield then create a file containing it
-  if ( isset($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 nucl -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 = $blastdb_with_path . '.nsq';
-  if (is_readable($blastdb_with_suffix)) {
-    global $user;
-    $output_filestub = date('YMd_His');
-    $job_args = array(
-      'program' => 'blastn',
-      'query' => $query,
-      'database' => $blastdb_with_path,
-      'output_filename' => $output_filestub,
-      'options' => array(
-        'evalue' => $eVal,
-        'word_size' => $wordSize,
-        'gapopen' => $gapOpen,
-        'gapextend' => $gapExtend,
-        'penalty' =>  $penalty,
-        'reward' => $reward
-      )
-    );
-    $job_id = tripal_add_job("BLAST (blastn): $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)/';
-	$fastaSeqRegEx = '/[^acgntuACGNTU\n\r]/';
-	if ( preg_match($fastaSeqRegEx,$sequence) && !(preg_match($fastaIdRegEx,$sequence)) ) {
-      $flag = 1;
-  } else {
-   $flag = 0;
-  }
-
-  return $flag;
-}

includes/blast_ui.blastp.inc

@@ -1,940 +0,0 @@
-<?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',
-	);
-
-  // Add the sequence type to the form
-  $form['sequence_type'] = array(
-    '#type' => 'hidden',
-    '#value' => 'protein'
-  );
-
-  // 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 <a href="@fasta-format-url" target="_blank">FASTA format</a>. ',
-        array(
-          '@fasta-format-url' => 'http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml'
-        )
-      ),
-    '#collapsible' => TRUE,
-    '#collapsed' => FALSE,
-  );
-
-  // Checkbox to show an example.
-  $form['query']['example_sequence'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Show an Example Sequence'),
-    '#prefix' => '<span style="float: right;">',
-    '#suffix' => '</span>',
-    '#ajax' => array(
-    	'callback' => 'ajax_blast_ui_example_sequence_callback',
-    	'wrapper'  => 'fasta-textarea',
-      'method'   => 'replace',
-      'effect'   => 'fade',
-    ),
-  );
-
-
-  $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-textarea">',
-    '#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()),
-    ),
-  );
-
-  // 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('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.'));
-    }
-    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'])) {
-    $form_state['dbFlag'] = 'blastdb';
-  }
-  // Otherwise they didn't select a database!!
-  else {
-    form_set_error('DB', t('No database selected. Either choose a database from
-the list or upload one of your own.'));
-  }
-}
-
-/**
- * Form submition handler for blast_protein_form().
- *
- * @see blast_protein_form_submit()
- */
-function blast_protein_form_submit($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'];
-}