fixes #2129

ChangeLog.md

@@ -7,6 +7,7 @@ Features
 - Added getAttributions method [2591](https://github.com/GMOD/Apollo/pull/2591) via @mbc32.
 - Make getting track features by location optional to pull unique code [2600](https://github.com/GMOD/Apollo/pull/2600).
 - Added additional websocket authentication support [2598](https://github.com/GMOD/Apollo/pull/2598).
+- Added 'set optimal ORF' function [2129](https://github.com/GMOD/Apollo/pull/2129).
 
 Bug Fix
 

client/apollo/js/View/Track/AnnotTrack.js

@@ -2130,7 +2130,13 @@ define([
  this.setLongestORFForSelectedFeatures(selected);
  },
 
- setLongestORFForSelectedFeatures: function (selection) {
+ setOptimalORF: function () {
+ var selected = this.selectionManager.getSelection();
+ this.selectionManager.clearSelection();
+ this.setLongestORFForSelectedFeatures(selected,false);
+ },
+
+ setLongestORFForSelectedFeatures: function (selection,allowPartials = true) {
  var track = this;
  var features = '"features": [';
  for (var i in selection) {
@@ -2140,19 +2146,16 @@ define([
  // just checking to ensure that all features in selection are from
  // this track
  if (atrack === track) {
- var trackdiv = track.div;
- var trackName = track.getUniqueTrackName();
-
  if (i > 0) {
  features += ',';
  }
- features += ' { "uniquename": "' + uniqueName + '" } ';
+ features += ` { "uniquename": "${uniqueName}" } `;
  }
  }
  features += ']';
  var operation = "set_longest_orf";
  var trackName = track.getUniqueTrackName();
- var postData = '{ "track": "' + trackName + '", ' + features + ', "operation": "' + operation + '" }';
+ var postData = `{ "track": "${trackName}",  ${features} , "operation": "${operation}" , "allow_partials": ${allowPartials} }`;
  track.executeUpdateOperation(postData);
  },
 
@@ -6956,6 +6959,15 @@ define([
  }));
  contextMenuItems["set_longest_orf"] = index++;
 
+
+ annot_context_menu.addChild(new dijit.MenuItem({
+ label: "Set Optimal ORF",
+ onClick: function (event) {
+ thisB.setOptimalORF();
+ }
+ }));
+ contextMenuItems["set_optimal_orf"] = index++;
+
  annot_context_menu.addChild(new dijit.MenuItem({
  label: "Remove CDS",
  onClick: function (event) {
@@ -7271,6 +7283,7 @@ define([
  this.updateSetTranslationStartMenuItem();
  this.updateSetTranslationEndMenuItem();
  this.updateSetLongestOrfMenuItem();
+ this.updateSetOptimalOrfMenuItem();
  this.updateRemoveCDSMenuItem();
  this.updateAssociateTranscriptToGeneItem();
  this.updateDissociateTranscriptFromGeneItem();
@@ -7662,6 +7675,27 @@ define([
  menuItem.set("disabled", false);
  },
 
+ updateSetOptimalOrfMenuItem: function () {
+ var menuItem = this.getMenuItem("set_optimal_orf");
+ var selected = this.selectionManager.getSelection();
+ if (selected.length > 1) {
+ menuItem.set("disabled", true);
+ return;
+ }
+ for (var i = 0; i < selected.length; ++i) {
+ if (!this.isProteinCoding(selected[i].feature)) {
+ menuItem.set("disabled", true);
+ return;
+ }
+ if (!this.canEdit(selected[i].feature)) {
+ menuItem.set("disabled", true);
+ return;
+ }
+ }
+
+ menuItem.set("disabled", false);
+ },
+
  updateSetReadthroughStopCodonMenuItem: function () {
  var menuItem = this.getMenuItem("set_readthrough_stop_codon");
  var selected = this.selectionManager.getSelection();

grails-app/controllers/org/bbop/apollo/AnnotationEditorController.groovy

@@ -429,6 +429,7 @@ class AnnotationEditorController extends AbstractApolloController implements Ann
  , @RestApiParam(name = "sequence", type = "string", paramType = RestApiParamType.QUERY, description = "(optional) Sequence name")
  , @RestApiParam(name = "organism", type = "string", paramType = RestApiParamType.QUERY, description = "(optional) Organism ID or common name")
  , @RestApiParam(name = "features", type = "JSONArray", paramType = RestApiParamType.QUERY, description = "JSONArray containing a single JSONObject feature that contains {'uniquename':'ABCD-1234'}")
+ , @RestApiParam(name = "allow_partials", type = "boolean", paramType = RestApiParamType.QUERY, description = "(optional) Default true. Allow partials when setting longest ORF.")
  ])
  def setLongestOrf() {
  log.debug "setLongestORF ${params}"