Added admin UI to set example sequences

blast_ui.module

@@ -18,6 +18,9 @@ require_once 'theme/blast_ui.theme.inc';
 // Application Programmers Interface
 require_once 'api/blast_ui.api.inc';
 
+// Administration
+require_once 'includes/blast_ui.admin.inc';
+
 /**
  * Implements hook_menu().
  */
@@ -51,16 +54,6 @@ function blast_ui_menu() {
     'type' => MENU_NORMAL_ITEM
   );
 
-  // Ajax path for the BLAST example sequence.
-  // Arguement is expected to be either 'nucleotide' or 'protein'.
-  $items['blast/example_sequence/%'] = array(
-    'title' => 'Example Sequence',
-    'page callback' => 'ajax_blast_ui_example_sequence_callback',
-    'page arguments' => array(2),
-    'access arguments' => array('access content'),
-    'type' => MENU_CALLBACK,
-  );
-
   // BLAST Results page
   $items['blast/report/%'] = array(
     'title' => 'BLAST Results',
@@ -70,6 +63,16 @@ function blast_ui_menu() {
     'type' => MENU_CALLBACK,
   );
 
+  // BLAST Admin
+  $items['admin/tripal/extension/blast_ui'] = array(
+    'title' => 'BLAST User Interface',
+    'description' => 'Provides an interface allowing users to execute their own BLASTs.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('blast_ui_admin_form'),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_NORMAL_ITEM,
+  );
+
   return $items;
 }
 

includes/blast_ui.admin.inc

@@ -0,0 +1,90 @@
+<?php
+
+/**
+ * @file
+ * Administrative interface for the BLAST UI
+ */
+
+/**
+ *
+ */
+function blast_ui_admin_form($form, $form_state) {
+
+  $form['example_sequence'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Set Example Sequences',
+    '#description' => 'There is the ability to show example sequences built-in to the various BLAST forms. Use the following fields to set these example sequences. This allows you to provide more relevant examples to your users.'
+  );
+
+  $nucleotide_default = '>partial lipoxygenase Glyma15g03040
+TTTCGTATGA GATTAAAATG TGTGAAATTT TGTTTGATAG GACATGGGAA
+AGGAAAAGTT GGAAAGGCTA CAAATTTAAG AGGACAAGTG TCGTTACCAA
+CCTTGGGAGC TGGCGAAGAT GCATACGATG TTCATTTTGA ATGGGACAGT
+GACTTCGGAA TTCCCGGTGC ATTTTACATT AAGAACTTCA TGCAAGTTGA
+GTTCTATCTC AAGTCTCTAA CTCTCGAAGA CATTCCAAAC CACGGAACCA
+TTCACTTCGT ATGCAACTCC TGGGTTTACA ACTCAAAATC CTACCATTCT
+GATCGCATTT TCTTTGCCAA CAATGTAAGC TACTTAAATA CTGTTATACA
+TTGTCTAACA TCTTGTTAGA GTCTTGCATG ATGTGTACCG TTTATTGTTG
+TTGTTGAACT TTACCACATG GCATGGATGC AAAAGTTGTT ATACACATAA
+ATTATAATGC AGACATATCT TCCAAGCGAG ACACCGGCTC CACTTGTCAA
+GTACAGAGAA GAAGAATTGA AGAATGTAAG AGGGGATGGA ACTGGTGAGC
+GCAAGGAATG GGATAGGATC TATGATTATG ATGTCTACAA TGACTTGGGC
+GATCCAGATA AGGGTGAAAA GTATGCACGC CCCGTTCTTG GAGGTTCTGC
+CTTACCTTAC CCTCGCAGAG GAAGAACCGG AAGAGGAAAA ACTAGAAAAG
+GTTTCTCACT AGTCACTAAT TTATTACTTT TTAATGTTTG TTTTTAGGCA
+TCTTTTCTGA TGAAATGTAT ACTTTTGATG TTTTTTTGTT TTAGCATAAC
+TGAATTAGTA AAGTGTGTTG TGTTCCTTAG AAGTTAGAAA AGTACTAAGT
+ATAAGGTCTT TGAGTTGTCG TCTTTATCTT AACAGATCCC AACAGTGAGA
+AGCCCAGTGA TTTTGTTTAC CTTCCGAGAG ATGAAGCATT TGGTCACTTG
+AAGTCATCAG ATTTTCTCGT TTATGGAATC AAATCAGTGG CTCAAGACGT
+CTTGCCCGTG TTGACTGATG CGTTTGATGG CAATCTTTTG AGCCTTGAGT
+TTGATAACTT TGCTGAAGTG CGCAAACTCT ATGAAGGTGG AGTTACACTA
+CCTACAAACT TTCTTAGCAA GATCGCCCCT ATACCAGTGG TCAAGGAAAT
+TTTTCGAACT GATGGCGAAC AGTTCCTCAA GTATCCACCA CCTAAAGTGA
+TGCAGGGTAT GCTACATATT TTGAATATGT AGAATATTAT CAATATACTC
+CTGTTTTTAT TCAACATATT TAATCACATG GATGAATTTT TGAACTGTTA';
+  $form['example_sequence']['nucleotide_example'] = array(
+    '#type' => 'textarea',
+    '#title' => 'Nucleotide Example',
+    '#description' => t('Enter a complete nucleotide FASTA record including the header. More information: <a href="@fasta-format-url" target="_blank">FASTA format</a>.',
+      array('@fasta-format-url' => 'http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml')),
+    '#default_value' => variable_get(
+        'blast_ui_nucleotide_example_sequence',
+        $nucleotide_default
+      )
+  );
+
+  $protein_default = '>gi|166477|gb|AAA96434.1| resveratrol synthase [Arachis hypogaea]
+MVSVSGIRKVQRAEGPATVLAIGTANPPNCIDQSTYADYYFRVTNSEHMTDLKKKFQRICERTQIKNRHM
+YLTEEILKENPNMCAYKAPSLDAREDMMIREVPRVGKEAATKAIKEWGQPMSKITHLIFCTTSGVALPGV
+DYELIVLLGLDPCVKRYMMYHQGCFAGGTVLRLAKDLAENNKDARVLIVCSENTAVTFRGPSETDMDSLV
+GQALFADGAAAIIIGSDPVPEVEKPIFELVSTDQKLVPGSHGAIGGLLREVGLTFYLNKSVPDIISQNIN
+DALNKAFDPLGISDYNSIFWIAHPGGRAILDQVEQKVNLKPEKMKATRDVLSNYGNMSSACVFFIMDLMR
+KRSLEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI';
+  $form['example_sequence']['protein_example'] = array(
+    '#type' => 'textarea',
+    '#title' => 'Protein Example',
+    '#description' => t('Enter a complete protein FASTA record including the header. More information: <a href="@fasta-format-url" target="_blank">FASTA format</a>.',
+      array('@fasta-format-url' => 'http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml')),
+    '#default_value' => variable_get(
+        'blast_ui_protein_example_sequence',
+        $protein_default
+      )
+  );
+
+  $form['submit'] = array(
+    '#type' => 'submit',
+    '#value' => 'Save Configuration'
+  );
+
+  return $form;
+}
+
+/**
+ *
+ */
+function blast_ui_admin_form_submit($form, $form_state) {
+
+  variable_set('blast_ui_nucleotide_example_sequence', $form_state['values']['nucleotide_example']);
+  variable_set('blast_ui_protein_example_sequence', $form_state['values']['protein_example']);
+}