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@@ -21,14 +21,14 @@ function blast_ui_admin_form($form, $form_state) {
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'#description' => t('You can ignore if your $PATH variable is set. Otherwise, enter the absoulte path to bin folder. For example, /opt/blast/2.2.29+/bin/'),
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'#default_value' => variable_get('blast_path', ''),
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);
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-
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+
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$form['general']['blast_threads']= array(
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'#type' => 'textfield',
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'#title' => t('Enter the number of CPU threads to use in blast search.'),
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'#description' => t('You can increase the number to reduce the search time. Before you increase, please check your hardware configurations . A value of one(1) can result in a slower search for some programs eg. tblastn.'),
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'#default_value' => variable_get('blast_threads', 1),
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);
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-
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+
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$form['general']['eVal']= array(
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'#type' => 'textfield',
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'#title' => t('e-Value (Expected Threshold)'),
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@@ -36,14 +36,14 @@ function blast_ui_admin_form($form, $form_state) {
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'#default_value' => variable_get('eVal', 0.001),
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//'#default_value' => variable_get('blast_threads', 1),
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);
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-
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+
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$form['general']['qRange']= array(
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'#type' => 'textfield',
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'#title' => t('Max matches in a query range'),
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'#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.'),
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'#default_value' => variable_get('qRange', 0),
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);
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-
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+
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$form['file_upload'] = array(
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'#type' => 'fieldset',
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'#title' => 'Allow File Upload',
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@@ -52,7 +52,7 @@ function blast_ui_admin_form($form, $form_state) {
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them to more conviently BLAST large sets of sequences. However, the size of the
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files could be problematic, storage-wise, on your server.<br />'
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);
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-
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+
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$form['file_upload']['query_upload'] = array(
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'#type' => 'checkbox',
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'#title' => 'Enable Query Sequence Upload',
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@@ -145,12 +145,12 @@ KRSLEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI';
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function blast_ui_admin_form_validate($form, &$form_state) {
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$blast_path = $form_state['values']['blast_path'];
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$blast_path .= 'blastn';
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- if(!empty($blast_path)) {
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+ if(!empty($form_state['values']['blast_path'])) {
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if(file_exists($blast_path) ) {
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variable_set('blast_path', $form_state['values']['blast_path']);
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}
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else {
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- form_set_error('blast_path', t('Please enter a valid path or you can leave it blank'));
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+ form_set_error('blast_path', t('Please enter a valid path not including the name of the blast program (ie: /urs/bin/). You can leave this blank if you have your $PATH variable set appropriately.'));
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}
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}
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@@ -163,13 +163,13 @@ function blast_ui_admin_form_submit($form, $form_state) {
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variable_set('blast_path', $form_state['values']['blast_path']);
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variable_set('blast_threads', $form_state['values']['blast_threads']);
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-
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+
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variable_set('eVal', $form_state['values']['eVal']);
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variable_set('qRange', $form_state['values']['qRange']);
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-
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- variable_set('blast_ui_allow_query_upload', $form_state['values']['query_upload']);
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+
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+ variable_set('blast_ui_allow_query_upload', $form_state['values']['query_upload']);
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variable_set('blast_ui_allow_target_upload', $form_state['values']['target_upload']);
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-
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+
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variable_set('blast_ui_nucleotide_example_sequence', $form_state['values']['nucleotide_example']);
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variable_set('blast_ui_protein_example_sequence', $form_state['values']['protein_example']);
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-}
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+}
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