diff --git a/app/Http/Controllers/lib/Seq.php b/app/Http/Controllers/lib/Seq.php
index 629cb23a4a299d8821fa9fcf689493f7c2bdd084..85a4b1385d6deeb2e812636e4893e9accf61ac6e 100755
--- a/app/Http/Controllers/lib/Seq.php
+++ b/app/Http/Controllers/lib/Seq.php
@@ -57,21 +57,27 @@ function blast2cirdna($infile, $outfile, $start, $end){
$line = explode("\t", $newline);
$fullname = $line["1"];
- $names = explode("_FEATCAT_", $fullname);
+ $names = explode("_FEATCOLOR_", $fullname);
$featname = $names["0"];
- $featcat = $names["1"];
+ $featcolor = $names["1"];
// set color according to feature category
- if ($featcat == "PRO"){ $color = "9";
- } elseif ($featcat == "REG") { $color = "13";
- } elseif ($featcat == "TER") { $color = "9";
- } elseif ($featcat == "SEL") { $color = "1";
- } elseif ($featcat == "REP") { $color = "8";
- } elseif ($featcat == "TAG") { $color = "0";
- } elseif ($featcat == "LOC") { $color = "0";
- } elseif ($featcat == "ORI") { $color = "10";
- } elseif ($featcat == "HYB") { $color = "12";
- } elseif ($featcat == "OTH") { $color = "13";
- } else { $color = "14";
+ if ($featcolor == "black"){ $color = "0";
+ } elseif ($featcolor == "red") { $color = "1";
+ } elseif ($featcolor == "yellow") { $color = "2";
+ } elseif ($featcolor == "green") { $color = "3";
+ } elseif ($featcolor == "aquamarine") { $color = "4";
+ } elseif ($featcolor == "pink") { $color = "5";
+ } elseif ($featcolor == "wheat") { $color = "6";
+ } elseif ($featcolor == "grey") { $color = "7";
+ } elseif ($featcolor == "brown") { $color = "8";
+ } elseif ($featcolor == "blue") { $color = "9";
+ } elseif ($featcolor == "blueviolet") { $color = "10";
+ } elseif ($featcolor == "cyan") { $color = "11";
+ } elseif ($featcolor == "turquoise") { $color = "12";
+ } elseif ($featcolor == "magenta") { $color = "13";
+ } elseif ($featcolor == "salmon") { $color = "14";
+ } elseif ($featcolor == "white") { $color = "15";
+ } else { $color = "15";
}
$newtxt = "label" . "\n". "Block". "\t"; fwrite($output, $newtxt);
@@ -144,7 +150,7 @@ function update_blastdb_dnafeatures($storagedir){
** Create/Update the dnafeatures BLAST Database
** (including the feature's type in its name)
** with fasta file in format:
- ** >featurename_FEATCAT_featurecategory
+ ** >featurename_FEATCOLOR_color
*/
$dnafeatures = DnaFeature::all();
// Create an updated fasta file of all DNA features
@@ -153,7 +159,7 @@ function update_blastdb_dnafeatures($storagedir){
foreach ($dnafeatures as $dnafeature) {
// remove white spaces from name
$namenospace = str_replace(" ", "", $dnafeature->name);
- $extendedname = $namenospace . "_FEATCAT_" . $dnafeature->category;
+ $extendedname = $namenospace . "_FEATCOLOR_" . $dnafeature->color;
fwrite($FastaFile, ">$extendedname\n");
$toprint = Convert2Fasta($dnafeature->sequence);
for ($i=0; $i< count($toprint); $i++) {
diff --git a/database/migrations/2021_04_20_104452_add_color_column_to_dnafeatures_table.php b/database/migrations/2021_04_20_104452_add_color_column_to_dnafeatures_table.php
new file mode 100644
index 0000000000000000000000000000000000000000..039e6655b0617b211d54f91a4b58cb06abca284c
--- /dev/null
+++ b/database/migrations/2021_04_20_104452_add_color_column_to_dnafeatures_table.php
@@ -0,0 +1,32 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+
+class AddColorColumnToDnafeaturesTable extends Migration
+{
+ /**
+ * Run the migrations.
+ *
+ * @return void
+ */
+ public function up()
+ {
+ Schema::table('dna_features', function (Blueprint $table) {
+ $table->string('color',30)->nullable($value = true)->default("black");
+ });
+ }
+
+ /**
+ * Reverse the migrations.
+ *
+ * @return void
+ */
+ public function down()
+ {
+ Schema::table('dna_features', function (Blueprint $table) {
+ $table->dropColumn('color');
+ });
+ }
+}
diff --git a/database/seeders/FunctionalityTrackingByIseedDataRowsTableSeeder.php b/database/seeders/FunctionalityTrackingByIseedDataRowsTableSeeder.php
index 729cd08ca08979f957f3c5a45c7412e1b967002b..c787258cf4667ab84fa11e46c311d469035e9cd3 100755
--- a/database/seeders/FunctionalityTrackingByIseedDataRowsTableSeeder.php
+++ b/database/seeders/FunctionalityTrackingByIseedDataRowsTableSeeder.php
@@ -1579,7 +1579,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'delete' => 0,
'details' => '{}',
'display_name' => 'Id (required)',
- 'edit' => 0,
+ 'edit' => 1,
'field' => 'id',
'id' => 143,
'order' => 1,
@@ -1606,7 +1606,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
99 =>
array (
'add' => 1,
- 'browse' => 1,
+ 'browse' => 0,
'data_type_id' => 28,
'delete' => 1,
'details' => '{}',
@@ -1630,7 +1630,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'edit' => 1,
'field' => 'comments',
'id' => 147,
- 'order' => 6,
+ 'order' => 7,
'read' => 1,
'required' => 0,
'type' => 'text_area',
@@ -1638,7 +1638,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
101 =>
array (
'add' => 0,
- 'browse' => 1,
+ 'browse' => 0,
'data_type_id' => 28,
'delete' => 1,
'details' => '{}',
@@ -1646,7 +1646,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'edit' => 1,
'field' => 'created_at',
'id' => 148,
- 'order' => 8,
+ 'order' => 9,
'read' => 1,
'required' => 1,
'type' => 'timestamp',
@@ -1662,7 +1662,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'edit' => 0,
'field' => 'updated_at',
'id' => 149,
- 'order' => 9,
+ 'order' => 10,
'read' => 1,
'required' => 1,
'type' => 'timestamp',
@@ -2442,7 +2442,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'data_type_id' => 28,
'delete' => 1,
'details' => '{}',
- 'display_name' => 'Name',
+ 'display_name' => 'Name (short)',
'edit' => 1,
'field' => 'name',
'id' => 235,
@@ -2550,7 +2550,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
158 =>
array (
'add' => 1,
- 'browse' => 1,
+ 'browse' => 0,
'data_type_id' => 28,
'delete' => 1,
'details' => '{"sort":{"key":"name","direction":"desc"},"model":"App\\\\DnafeatCategory","table":"dnafeat_categories","type":"belongsTo","column":"category","key":"category","label":"name","pivot_table":"antibodies","pivot":"0","taggable":"0"}',
@@ -2662,7 +2662,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
165 =>
array (
'add' => 1,
- 'browse' => 1,
+ 'browse' => 0,
'data_type_id' => 28,
'delete' => 1,
'details' => '{}',
@@ -2670,7 +2670,7 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'edit' => 1,
'field' => 'author',
'id' => 249,
- 'order' => 7,
+ 'order' => 8,
'read' => 1,
'required' => 0,
'type' => 'text',
@@ -2723,6 +2723,22 @@ class FunctionalityTrackingByIseedDataRowsTableSeeder extends Seeder
'required' => 0,
'type' => 'text',
),
+ 169 =>
+ array (
+ 'add' => 1,
+ 'browse' => 1,
+ 'data_type_id' => 28,
+ 'delete' => 1,
+ 'details' => '{"default":"black","options":{"black":"black","red":"red","blue":"blue","magenta":"magenta","green":"green","brown":"brown","blueviolet":"blueviolet","aquamarine":"aquamarine","turquoise":"turquoise","yellow":"yellow","wheat":"wheat","salmon":"salmon","cyan":"cyan","pink":"pink","white":"white"}}',
+ 'display_name' => 'Color',
+ 'edit' => 1,
+ 'field' => 'color',
+ 'id' => 253,
+ 'order' => 6,
+ 'read' => 1,
+ 'required' => 0,
+ 'type' => 'select_dropdown',
+ ),
));
diff --git a/database/seeders/FunctionalityTrackingByIseedDataTypesTableSeeder.php b/database/seeders/FunctionalityTrackingByIseedDataTypesTableSeeder.php
index 9cc29cf2fc0e28074e24edfe86265a812b5b1302..7c7acb0bc6c497b9798c4b219f27267b31aac26d 100755
--- a/database/seeders/FunctionalityTrackingByIseedDataTypesTableSeeder.php
+++ b/database/seeders/FunctionalityTrackingByIseedDataTypesTableSeeder.php
@@ -233,7 +233,7 @@ class FunctionalityTrackingByIseedDataTypesTableSeeder extends Seeder
'policy_name' => NULL,
'server_side' => 0,
'slug' => 'dna-features',
- 'updated_at' => '2021-04-07 08:16:19',
+ 'updated_at' => '2021-04-20 11:26:43',
),
12 =>
array (