fixes #2129 (#2609)

* fixes #2129 * updated menu * fixed linting error * updated * reformatted and synced the apis * removed redundant method * updated javadoc * everything seems to be working now * cleaned up
GMOD · Apr 15, 2021 · 2f54601 · 2f54601
1 parent 1728c28
commit 2f54601
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diff --git a/ChangeLog.md b/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
 

diff --git a/client/apollo/js/View/Track/AnnotTrack.js b/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();

diff --git a/grails-app/controllers/org/bbop/apollo/AnnotationEditorController.groovy b/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}"