Initial commit.

blast_ui/blast_ui.info

@@ -0,0 +1,4 @@
+name = BLAST UI
+description = Provides a user interface to allow your users to utilize NCBI's BLAST+ on your server
+package = Tripal Extensions
+core = 7.x

blast_ui/blast_ui.install

@@ -0,0 +1,8 @@
+<?php
+
+/**
+ * @file
+ * Contains hooks to handle installation of this module
+ */
+
+tripal_create_files_dir('tripal_blast');

blast_ui/blast_ui.module

@@ -0,0 +1,40 @@
+<?php
+
+require_once 'includes/blast_ui.blastn.inc';
+require_once 'includes/blast_ui.blastp.inc';
+require_once 'includes/blast_ui.node.inc';
+
+function blast_ui_menu() {
+
+  $items['blast'] = array(
+    'title' => 'BLAST',
+    'page callback' => 'drupal_get_form',
+    // Add in a page callback/aguements for a drupal form letting you choose nucl. or protein and then redirecting you
+    'page arguments' => array('blast_nucleotide_form'),
+    'access arguments' => array('access content'),
+    'type' => MENU_NORMAL_ITEM,
+    'expanded' => TRUE
+  );
+
+  $items['blast/blastn'] = array(
+    'title' => 'Nucleotide BLAST',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('blast_nucleotide_form'), //Need to change these to use the blast_ui prefix instead of just blast
+
+    // Added the following
+    'access arguments' => array('access content'),
+    'type' => MENU_NORMAL_ITEM
+  );
+
+  $items['blast/blastp'] = array(
+    'title' => 'Protein BLAST',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('blast_protein_form'), //Need to change these to use the blast_ui prefix instead of just blast
+
+    // Added the following
+    'access arguments' => array('access content'),
+    'type' => MENU_NORMAL_ITEM
+  );
+
+  return $items;
+}

blast_ui/includes/blast_ui.blastn.inc

@@ -0,0 +1,327 @@
+<?php
+
+function blast_nucleotide_form($form, &$form_state) {
+  
+//Nucleotide BLAST
+
+$form['nBLAST'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Standard Nucleotide BLAST'),
+    '#collapsible' => TRUE, 
+    '#collapsed' => FALSE,  
+  );
+$form['nBLAST']['FASTA'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Enter FASTA sequence(s)'),
+    '#description'=>t('Enter query sequence(s) in the text area.'),
+  );
+
+// Upload a file as an alternative to enter a query sequence 
+$form['#attributes']['enctype'] = 'multipart/form-data';
+$form['nBLAST']['UPLOAD'] = array(
+  	'#prefix' => 'Or upload your query files:	',
+  	'#type' => 'file',
+  	'#description' => t('Please give a text a FASTA file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+
+
+//DATABASE//
+
+$form['DB'] = array(
+  '#type' => 'fieldset',
+  '#title' => t('BLAST Assembled KnowPulse Genomes'),
+  '#collapsible' => TRUE, 
+  '#collapsed' => FALSE,  
+);
+  
+//$options =  _DB_options(); 
+$form['DB']['SELECT_DB'] = array(
+ '#type' => 'select',
+ '#title' => t('KnowPulse Databases:'),
+ '#options' => 'TEST',
+ '#default_value' => NULL,
+);
+  
+// Upload a file as an alternative to enter a query sequence 
+$form['#attributes']['enctype'] = 'multipart/form-data';
+$form['DB']['DBUPLOAD'] = array(
+   '#prefix' => 'Or upload your own dataset:	',
+  	'#type' => 'file',
+  	'#description' => t('Please give a text or a FASTA file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+  
+//Algorithm parameters
+
+$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('Expect threshold'), 
+  '#default_value' => 10, 
+  '#size' => 12, 
+  '#maxlength' => 20, 
+  '#description' => t('Expected number of chance matches in a random model.'),
+);
+	
+$form['ALG']['GParam']['wordSize'] = array(
+    '#type' => 'select',
+    '#title' => t('Word size:'),
+    '#options' => array(
+       0 => t('16'),
+       1 => t('20'),
+       2 => t('24'),
+       3 => t('28'),
+       4 => t('32'),
+       5 => t('48'),
+       6 => t('64'),
+       7 => t('128'),
+       8 => t('256'),
+    ),
+    '#default_value' => 3,
+    '#description' => t('The length of the seed that initiates an alignment'),
+   );
+  
+$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 $form;
+}
+
+function blast_nucleotide_form_validate($form, &$form_state) {
+   $fastaSeq = $form_state['input']['FASTA'];
+   if (isset($fastaSeq)) {
+      if(_validateFasta($fastaSeq)){
+          form_set_error('nBLAST', t('Error: Failed to read the Blast query: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         $form_state['flag'] = 'seqQuery';
+      }  
+   }
+   $upQuery = file_save_upload('UPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
+   if ($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('nBLAST', t('Error: Failed to upload the Blast query: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         $form_state['qFlag'] = 'upQuery';
+      }
+   }
+   
+   $upDB = file_save_upload('DBUPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
+   if ($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('DB', t('Error: Failed to upload the Blast subject sequence file: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         $form_state['dbFlag'] = 'upQuery';
+      }
+   }
+   
+}
+
+function blast_nucleotide_form_submit($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];
+  
+  $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;
+  }
+  
+  $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;
+      $reward = 1;
+      break;
+  }
+  
+  if ( isset($form_state['qFlag']) ) {
+     if ( $form_state['qFlag'] == 'seqQuery' ) {
+        $query = $form_state['values']['FASTA'];
+     } elseif ( $form_state['qFlag'] == 'upQuery' ) {
+        $query = $form_state['upQuery_path'];
+     }
+  }
+  
+  if ( isset($form_state['dbFlag']) ) {
+     if ( $form_state['dbFlag'] == 'upQuery') {
+        $subjectSeq = $form_state['upDB_path'];
+        $subSeqOut = drupal_basename($form_state['upDB_path']);
+        //shell_exec("blastn -query $query -subject $subjectSeq -out /tmp/$subSeqOut.blastn -evalue $eVal -word_size $wordSize -gapopen $gapOpen -gapextend $gapExtend -penalty $penalty -reward $reward -num_alignments $numAlign -outfmt 7 ");
+        shell_exec("blastn -query $query -subject $subjectSeq -out /home/amm072/kp-amir/sites/default/files/tripal/tripal_blast/$subSeqOut.blastn.html -evalue $eVal -word_size $wordSize -gapopen $gapOpen -gapextend $gapExtend -penalty $penalty -reward $reward -num_alignments 100 -html");
+     } else {
+        $db = $form['values']['SELECT_DB'];
+        //$output = shell_exec("blastn -query $query -db $db -out <> -evalue $eVal -word_size <> -gapopen <> -gapextend <> -penalty <> -reward <>");
+     }
+  }
+
+
+}
+
+// 
+// output file name 
+
+function _validateFasta($sequence) {
+	$fastaIdRegEx = '/^>.*(\\n|\\r)/';
+	$fastaSeqRegEx = '/[^acgntuACGNTU\n\r]/';
+	if ( preg_match($fastaSeqRegEx,$sequence) && !(preg_match($fastaIdRegEx,$sequence)) ) {
+      $flag = 1;
+  } else {
+   $flag = 0;
+  }
+	
+  return $flag;
+}
+
+function _DB_options() {
+  $type = 'BLASTDB';
+  $nodes  = node_load_multiple(array(), array('type' => $type));
+  return $nodes;
+
+}

blast_ui/includes/blast_ui.blastn.inc_COPY

@@ -0,0 +1,238 @@
+<?php
+
+function blast_nucleotide_form($form, &$form_state) {
+  
+//Nucleotide BLAST
+
+$form['nBLAST'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Standard Nucleotide BLAST'),
+    '#collapsible' => TRUE, 
+    '#collapsed' => FALSE,  
+  );
+$form['nBLAST']['FASTA'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Enter FASTA sequence(s)'),
+    '#description'=>t('Enter query sequence(s) in the text area.'),
+  );
+
+// Upload a file as an alternative to enter a query sequence 
+$form['#attributes']['enctype'] = 'multipart/form-data';
+$form['nBLAST']['UPLOAD'] = array(
+  	'#prefix' => 'Or upload your query files:	',
+  	'#type' => 'file',
+  	'#description' => t('Please give a text a FASTA file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+
+
+//DATABASE//
+
+	$form['DB'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('BLAST Assembled KnowPulse Genomes'),
+    '#collapsible' => TRUE, 
+    '#collapsed' => FALSE,  
+  );
+  
+//  //$options =  _DB_options(); 
+//  $form['DB']['SELECT_DB'] = array(
+//       '#type' => 'select',
+//       '#title' => t('KnowPulse Databases:'),
+//       '#options' => $options,
+//       '#default_value' => NULL,
+//   );
+  
+// 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('Please give a text or a FASTA file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+  
+//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('Expect threshold'), 
+  '#default_value' => 10, 
+  '#size' => 12, 
+  '#maxlength' => 20, 
+  '#description' => t('Expected number of chance matches in a random model.'),
+);
+	
+	 $form['ALG']['GParam']['wordSize'] = array(
+       '#type' => 'select',
+       '#title' => t('Word size:'),
+       '#options' => array(
+          0 => t('16'),
+          1 => t('20'),
+          2 => t('24'),
+          3 => t('28'),
+          4 => t('32'),
+          5 => t('48'),
+          6 => t('64'),
+          7 => t('128'),
+          8 => t('256'),
+       ),
+       '#default_value' => 3,
+       '#description' => t('The length of the seed that initiates an alignment'),
+   );
+  
+$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('Linear'),
+          1 => t('Extension: 5 Extension: 2'),
+          2 => t('Extension: 2 Extension: 2'),
+          3 => t('Extension: 1 Extension: 2'),
+          4 => t('Extension: 0 Extension: 2'),
+          5 => t('Extension: 3 Extension: 1'),
+          6 => t('Extension: 2 Extension: 1'),
+          7 => t('Extension: 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 $form;
+}
+
+function blast_nucleotide_form_validate($form, &$form_state) {
+   $fastaSeq = $form_state['input']['FASTA'];
+   dpm($form_state, $name = NULL);
+   if (isset($fastaSeq)) {
+      if(_validateFasta($fastaSeq)){
+          form_set_error('nBLAST', t('Error: Failed to read the Blast query: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         //
+      }  
+   }
+   $upQuery = file_save_upload('UPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
+   if ($upQuery) {
+      $upQuery_uri = $upQuery->uri;
+      $upQuery_path = drupal_realpath($upQuery_uri);
+      $upQuery_content = file_get_contents($upQuery_path);
+      if(_validateFasta($upQuery_content)){
+          form_set_error('nBLAST', t('Error: Failed to upload the Blast query: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         //
+      }
+   }
+   
+   $upDB = file_save_upload('DBUPLOAD', array('file_validate_extensions' => array('txt fasta fa fna')), FILE_EXISTS_RENAME);
+   if ($upDB) {
+      $upDB_uri = $upDB->uri;
+      $upDB_path = drupal_realpath($upDB_uri);
+      $upDB_content = file_get_contents($upDB_path); 
+      if(_validateFasta($upDB_content)){
+          form_set_error('DB', t('Error: Failed to upload the Blast reference file: Wrong format provided for FASTA nucleotide sequence'));
+      } else {
+         //Build a Blast DB?
+      }
+   }
+   
+}
+
+function blast_nucleotide_form_submit($form, &$form_state) {
+  //dpm($form_state['values'], $name = NULL);
+  //$output = shell_exec("water -asequence $aSeq -bsequence $selectedDB -gapopen 10 -gapextend 2 -outfile /tmp/$jobID.water ");
+}
+
+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;
+}
+
+function _DB_options() {
+  $type = 'BLASTDB';
+  $nodes  = node_load_multiple(array(), array('type' => $type));
+  return $nodes;
+
+}

blast_ui/includes/blast_ui.blastp.inc

@@ -0,0 +1,275 @@
+<?php
+
+function blast_protein_form($form, &$form_state) {
+  
+
+//Protein BLAST
+
+  $form['pBLAST'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Standard Nucleotide BLAST'),
+    '#collapsible' => TRUE, 
+    '#collapsed' => FALSE,  
+  );
+$form['pBLAST']['FASTA'] = array(
+    '#type' => 'textarea',
+    '#title' => t('Enter FASTA sequence(s)'),
+    '#description'=>t('Enter query sequence(s) in the text area.'),
+  );
+
+
+// Upload a file as an alternative to enter a query sequence 
+  $form['#attributes']['enctype'] = 'multipart/form-data';
+  $form['pBLAST']['UPLOAD'] = array(
+  	'#prefix' => 'Or upload your query files:	',
+  	'#type' => 'file',
+  	'#description' => t('Please give a text file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+
+//// Job title 
+//  $form ['pBLAST']['JOB_ID'] = array(
+//    '#type' => 'textfield',
+//    '#title' => t('Job title'),
+//    '#suffix' => t('Enter a descriptive title for your pairwise alignment'),
+//  );
+
+
+//DATABASE//
+
+	$form['DB'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('BLAST Assembled KnowPulse Genomes'),
+    '#collapsible' => TRUE, 
+    '#collapsed' => FALSE,  
+  );
+  $form['DB']['SELECT_DB'] = array(
+       '#type' => 'select',
+       '#title' => t('KnowPulse Databases:'),
+       '#options' => array(
+          0 => t('Human immunodeficiency virus 1'),
+          1 => t('Human immunodeficiency virus 2'),
+          2 => t('Simian immunodeficiency virus'),
+          3 => t('Human herpesvirus 2'),
+          4 => t('Human herpesvirus 1'),
+       ),
+       '#default_value' => NULL,
+   );
+  
+// Upload a file as an alternative to enter a query sequence 
+  $form['#attributes']['enctype'] = 'multipart/form-data';
+  $form['DB']['UPLOAD'] = array(
+  	'#prefix' => 'Or upload your own dataset:	',
+  	'#type' => 'file',
+  	'#description' => t('Please give a text file, not a MS-Word or other document, you can upload up to 10 Mb.'),
+  );
+  
+//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('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['next'] = array(
+    '#type' => 'submit',
+    '#value' => ' BLAST ',
+  );
+  return $form;
+}
+
+function _ajax_example_get_first_dropdown_options() {
+  return drupal_map_assoc(array(
+  t('PAM30'),	
+  t('PAM70'),
+  t('PAM250'),
+  t('BLOSUM80'),
+  t('BLOSUM62'),
+  t('BLOSUM45'),
+  t('BLOSUM50'),
+  t('BLOSUM90'),
+  ));
+}
+
+function _ajax_example_get_second_dropdown_options($key = '') {
+  $options = array(
+    t('PAM30') => drupal_map_assoc(array(
+      t('Extension: 15 Extension: 3'),
+      t('Extension: 14 Extension: 3'),
+      t('Extension: 13 Extension: 3'),
+      t('Extension: 12 Extension: 3'),
+      t('Extension: 11 Extension: 3'),
+      t('Extension: 17 Extension: 2'),
+      t('Extension: 16 Extension: 2'), 
+      t('Extension: 15 Extension: 2'),
+      t('Extension: 14 Extension: 2'),
+      t('Extension: 13 Extension: 2'),
+      t('Extension: 21 Extension: 1'),
+      t('Extension: 20 Extension: 1'),
+      t('Extension: 19 Extension: 1'),
+      t('Extension: 18 Extension: 1'),
+      t('Extension: 17 Extension: 1'),
+    )),
+    t('PAM70') => drupal_map_assoc(array(
+      t('Flute'),
+      t('Clarinet'),
+      t('Oboe'),
+      t('Bassoon'),
+    )),
+    t('PAM250') => drupal_map_assoc(array(
+      t('Trumpet'),
+      t('Trombone'),
+      t('French Horn'),
+      t('Euphonium'),
+    )),
+    t('BLOSUM80') => drupal_map_assoc(array(
+      t('Bass Drum'),
+      t('Timpani'),
+      t('Snare Drum'),
+      t('Tambourine'),
+    )),
+    t('BLOSUM62') => drupal_map_assoc(array(
+      t('Bass Drum'),
+      t('Timpani'),
+      t('Snare Drum'),
+      t('Tambourine'),
+    )),
+    t('BLOSUM45') => drupal_map_assoc(array(
+      t('Bass Drum'),
+      t('Timpani'),
+      t('Snare Drum'),
+      t('Tambourine'),
+    )),
+    t('BLOSUM50') => drupal_map_assoc(array(
+      t('Bass Drum'),
+      t('Timpani'),
+      t('Snare Drum'),
+      t('Tambourine'),
+    )),
+    t('BLOSUM90') => drupal_map_assoc(array(
+      t('Bass Drum'),
+      t('Timpani'),
+      t('Snare Drum'),
+      t('Tambourine'),
+    )),
+    );
+    if (isset($options[$key])) {
+    	return $options[$key];
+    } else {
+    	return array();
+    }
+}
+
+function ajax_example_dependent_dropdown_callback($form, $form_state) {
+  return $form['ALG']['SParam']['gapCost'];
+}

blast_ui/includes/blast_ui.node.inc

@@ -0,0 +1,77 @@
+<?php
+
+/**
+ * @file
+ * Contains all functions for creating the blastdb node type
+ */
+
+function blast_ui_node_info() {
+  return array(
+    'blastdb' => array(
+      'name' => t('Blast Database'),
+      'base' => 'blastdb',
+      'description' => t('Registers a BLAST Database for use with the BLAST UI.'),
+    ),
+  );
+}
+
+function blastdb_node_access($node, $op, $account) {
+  $node_type = $node;
+  if (is_object($node)) {
+    $node_type = $node->type;
+  }
+
+  if($node_type == 'blastdb') {
+    if ($op == 'create') {
+      if (!user_access('create Blast Database', $account)) {
+        return NODE_ACCESS_DENY;
+      }
+      return NODE_ACCESS_ALLOW;
+    }
+    if ($op == 'update') {
+      if (!user_access('edit Blast Database', $account)) {
+        return NODE_ACCESS_DENY;
+      }
+    }
+    if ($op == 'delete') {
+      if (!user_access('delete Blast Database', $account)) {
+        return NODE_ACCESS_DENY;
+      }
+    }
+    if ($op == 'view') {
+      if (!user_access('access Blast Database', $account)) {
+        return NODE_ACCESS_DENY;
+      }
+    }
+
+    return NODE_ACCESS_IGNORE;
+  }
+}
+
+function blastdb_form($node, &$form_state) {
+  $form = array();
+
+  $form['db_name']= array(
+    '#type' => 'textfield',
+    '#title' => t('File Name'),
+    // Add a #description for each field
+    '#required' => TRUE,
+    '#default_value' => NULL,
+  );
+  $form['db_path']= array(
+    '#type' => 'textfield',
+    '#title' => t('File Address'),
+    '#required' => TRUE,
+    '#default_value' => NULL,
+  );
+
+  $form['db_common_name']= array(
+    '#type' => 'textfield',
+    // this is a description; you want something more succint for a title such as File Name
+    '#title' => t('Pick a friendly name for your file'),
+    '#required' => TRUE,
+    '#default_value' => NULL,
+  );
+
+  return $form;
+}