Added styling for genomikon parts and fixed SequenceDNA.asNewSequenceDNA

Synbiota · Nov 20, 2013 · 6ae8c93 · 6ae8c93
1 parent 465a25f
commit 6ae8c93
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Showing 4 changed files with 15 additions and 2 deletions.
diff --git a/data/data.js b/data/data.js
@@ -452,7 +452,7 @@ var cd = { // Common data, filled by loadBaseData()
    	"feature_types" : { //colours determined in main.css, .feat_misc
 		'misc' : 			{ 'category':'General',					'annotation_row_offset':0 , 'name':'Misc' } ,
 		'note' : 			{ 'category':'General', 				'annotation_row_offset':0 , 'name':'Note' } ,
-		'genomicon_part' :	{ 'category':'General', 'is_main_type':1 ,	'annotation_row_offset':0 , 'name':'Genomikon Part' } ,
+		'genomikon_part' :	{ 'category':'General', 'is_main_type':1 ,	'annotation_row_offset':0 , 'name':'Genomikon Part' } ,
 
 		'alu_element' : 	{ 'category':'DNA', 'is_main_type':1 , 	'annotation_row_offset':1 , 'name':'Alu element' },
 		'cds' : 			{ 'category':'DNA', 'is_main_type':1 , 	'annotation_row_offset':1 , 'name':'Coding sequence' },

diff --git a/public/main.css b/public/main.css
@@ -94,6 +94,12 @@
   background-color:black;
   color:white;
 }
+.designer_row_feature_genomikon_part {
+  height:34px;
+  background-color:#FFFBD0;
+  color:#9C2A99;
+}
+
 
 
 
@@ -449,6 +455,11 @@ h1 {
   left:55px;
 }
 
+.feat_genomikon_part {
+  background-color:#FF4848;
+  left: 35px;
+}
+
 .feat_cds {
   background-color:#FF4848;
   left:75px;

diff --git a/util/sequence/sequences.js b/util/sequence/sequences.js
@@ -122,7 +122,8 @@ SequenceDNA.prototype.insert = function ( base , text , skip_feature_adjustment
 
 SequenceDNA.prototype.asNewSequenceDNA = function ( start , stop ) {
 	var me = this ;
-	var ret = new SequenceDNA ( me.name , me.seq.substr ( start , stop-start+1 ) ) ;
+	//var ret = new SequenceDNA ( me.name , me.seq.substr ( start , stop-start+1 ) ) ; ALEX
+	var ret = new SequenceDNA ( me.name , me.seq.substr ( start-1 , stop-start+1 ) ) ;
 	$.each ( (me.features||[]) , function ( k , v ) {
 		if ( v['_range'][0].from > stop ) return ;
 		if ( v['_range'][v['_range'].length-1].to < start ) return ;

diff --git a/util/topDisplay/top_display.js b/util/topDisplay/top_display.js
@@ -67,6 +67,7 @@ TopDisplayDNA.prototype.get_feature_div = function ( v ) {
 	else if ( v['_type'].match(/^gene$/i) ) cl = 'gene' ;
 	else if ( v['_type'].match(/^CDS$/i) ) cl = 'cds' ;
 	else if ( v['_type'].match(/^note$/i) ) cl = 'note' ;
+	else if ( v['_type'].match(/^genomikon/i) ) cl = 'genomikon_part' ;
 
 	// Name
 	var name = '' ;