update terminator type - 1990 (#1997)

* fixed width calculation

* small fixes and disabled portions of the drop-down menu

* fixed counting errors

* added the initial associated transcript type

* added the appropriate hooks

* some minor fix type things

* reverted unnecessary changes

* added a basic start to an image

* removed unused code

* some minor fixes, but still not adaquetyly drawing

* testing readthedocs webhook

* added

* adding a semi-sange default

* started to add the strand types

* is properly adding strand

* gotthe styling correct

README.md

@@ -81,3 +81,4 @@ Thanks to YourKit for providing us the use of their YourKit Java Profiler. Your
 
 [![Waffle.io - Columns and their card count](https://badge.waffle.io/GMOD/Apollo.svg?columns=all)](https://waffle.io/GMOD/Apollo)
 
+

client/apollo/css/webapollo_track_styles.css

@@ -829,6 +829,35 @@ div.track_webapollo_view_track_annotsequencetrack div.track-label .track-close-b
  background-color: magenta;
 }
 
+
+.jbrowse .terminator {
+ position: absolute;
+ height: 16px;
+ z-index: 100;
+ /*background-color: black;*/
+ background-repeat: no-repeat;
+ background-size: 9px 15px;
+
+
+ /* TODO: remove when we have another strand type */
+ background-image: url('../img/plus-terminator.png');
+ background-position: bottom center; /* center image vertically */
+}
+
+.jbrowse .terminator-render {
+ position: absolute;
+ height: 10px;
+ z-index: 100;
+ background-color: black;
+}
+
+
+.jbrowse .minus-terminator {
+}
+
+.jbrowse .plus-terminator {
+}
+
 .jbrowse .transposable_element,
 .jbrowse .plus-transposable_element,
 .jbrowse .minus-transposable_element {

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

@@ -1147,9 +1147,11 @@ define([
  var biotype ;
 
  // TODO: pull from the server at some point
+ // TODO: this list is duplicated
  var recognizedBioType = [
- 'transcript' ,'tRNA','snRNA','snoRNA','ncRNA','rRNA','mRNA','miRNA','repeat_region','transposable_element'
+ 'transcript' ,'tRNA','snRNA','snoRNA','ncRNA','rRNA','mRNA','miRNA','repeat_region','transposable_element','terminator'
  ];
+ var strandedOneLevelTypes = ['terminator'];
 
  if(force_type) {
  biotype = featureToAdd.get('type');
@@ -1175,7 +1177,7 @@ define([
  target_track.createGenericAnnotations([featureToAdd], biotype, null , 'gene');
  }
  else {
- target_track.createGenericOneLevelAnnotations([featureToAdd], biotype , true );
+ target_track.createGenericOneLevelAnnotations([featureToAdd], biotype , strandedOneLevelTypes.indexOf(biotype)<0);
  }
 
  var postData = {
@@ -1495,14 +1497,12 @@ define([
  track.executeUpdateOperation(postData);
  }
  else if (feature.afeature.parent_id) {
- var feats = [feature];
  this.createGenericAnnotations([feature], feature.get("type"), feature.get("subfeatures")[0].get("type"), feature.afeature.parent_type.name);
  }
  else {
  if (!feature.get("name")) {
  feature.set("name", feature.afeature.name);
  }
- var feats = [feature];
  this.createGenericOneLevelAnnotations([feature], feature.get("type"), feature.get("strand") == 0);
  }
  }
@@ -4275,7 +4275,6 @@ define([
  var nameField = new dijitTextBox({'class': "annotation_editor_field"});
  var nameLabelss = "Follow GenBank or UniProt-SwissProt guidelines for gene, protein, and CDS nomenclature.";
  dojo.place(nameField.domNode, nameDiv);
- // var nameField = new dojo.create("input", { type: "text" }, nameDiv);
 
  new Tooltip({
  connectId: nameDiv,
@@ -4456,8 +4455,6 @@ define([
  dojo.attr(deleteGoIdButton, "disabled", true);
  dojo.attr(addCommentButton, "disabled", true);
  dojo.attr(deleteCommentButton, "disabled", true);
- //dojo.attr(addreplacementButton, "disabled", true);
- //dojo.attr(deletereplacementButton, "disabled", true);
  }
 
  var pubmedIdDb = "PMID";
@@ -4497,7 +4494,6 @@ define([
  initSymbol(feature);
  initDescription(feature);
  initDates(feature);
- // initStatus(feature, config);
  initStatus(feature);
  initDbxrefs(feature, config);
  initAttributes(feature, config);
@@ -4606,7 +4602,7 @@ define([
  var statusRadio = new dijitRadioButton({
  value: status[i],
  name: "status_" + uniqueName,
- checked: status[i] == feature.status ? true : false
+ checked: status[i] == feature.status
  });
  if (!hasWritePermission) {
  statusRadio.set("disabled", true);
@@ -4643,6 +4639,7 @@ define([
  }
  };
 
+
  var initDbxrefs = function (feature, config) {
  if (config.hasDbxrefs) {
  var oldDb;
@@ -6610,6 +6607,10 @@ define([
  },
 
  initAnnotContextMenu: function () {
+
+ // TODO: this list is duplicated
+ var topTypes = ['repeat_region','transposable_element','gene','pseudogene', 'SNV', 'SNP', 'MNV', 'MNP', 'indel', 'insertion', 'deletion','terminator'];
+
  var thisB = this;
  contextMenuItems = new Array();
  annot_context_menu = new dijit.Menu({});
@@ -6650,7 +6651,6 @@ define([
  var selected = thisB.selectionManager.getSelection();
  var selectedFeature = selected[0].feature;
  var selectedFeatureDetails = selectedFeature.afeature;
- var topTypes = ['repeat_region','transposable_element','gene','pseudogene', 'SNV', 'SNP', 'MNV', 'MNP', 'indel', 'insertion', 'deletion'];
  while(selectedFeature ){
  if(topTypes.indexOf(selectedFeatureDetails.type.name)>=0){
  thisB.getApollo().viewInAnnotationPanel(selectedFeatureDetails.name);
@@ -6741,13 +6741,28 @@ define([
  thisB.changeAnnotationType("miRNA");
  }
  }));
+ changeAnnotationMenu.addChild(new dijitMenuItem( {
+ label: "terminator",
+ onclick: function(event) {
+ var selected = thisB.selectionManager.getSelection();
+ var selectedFeatureType = selected[0].feature.afeature.type.name === "exon" ?
+ selected[0].feature.afeature.parent_type.name : selected[0].feature.afeature.type.name;
+ if (selectedFeatureType != "transposable_element" && selectedFeatureType != "repeat_region") {
+ var message = "Warning: You will not be able to revert back to " + selectedFeatureType + " via 'Change annotation type' menu option, use 'Undo' instead. Do you want to proceed?";
+ thisB.confirmChangeAnnotationType(thisB, [selected], "terminator", message);
+ }
+ else {
+ thisB.changeAnnotationType("terminator");
+ }
+ }
+ }));
  changeAnnotationMenu.addChild(new dijitMenuItem( {
  label: "repeat_region",
  onClick: function(event) {
  var selected = thisB.selectionManager.getSelection();
  var selectedFeatureType = selected[0].feature.afeature.type.name === "exon" ?
  selected[0].feature.afeature.parent_type.name : selected[0].feature.afeature.type.name;
- if (selectedFeatureType != "transposable_element") {
+ if (selectedFeatureType != "transposable_element" && selectedFeatureType != "terminator" ) {
  var message = "Warning: You will not be able to revert back to " + selectedFeatureType + " via 'Change annotation type' menu option, use 'Undo' instead. Do you want to proceed?";
  thisB.confirmChangeAnnotationType(thisB, [selected], "repeat_region", message);
  }
@@ -6762,7 +6777,7 @@ define([
  var selected = thisB.selectionManager.getSelection();
  var selectedFeatureType = selected[0].feature.afeature.type.name === "exon" ?
  selected[0].feature.afeature.parent_type.name : selected[0].feature.afeature.type.name;
- if (selectedFeatureType != "repeat_region") {
+ if (selectedFeatureType != "repeat_region" && selectedFeatureType != "terminator") {
  var message = "Warning: You will not be able to revert back to " + selectedFeatureType + " via 'Change annotation type' menu option, use 'Undo' instead. Do you want to proceed?";
  thisB.confirmChangeAnnotationType(thisB, [selected], "transposable_element", message);
  }

client/apollo/js/View/Track/DraggableHTMLFeatures.js

@@ -1282,7 +1282,7 @@ var draggableTrack = declare( HTMLFeatureTrack,
  var selection = this.selectionManager.getSelection();
  var selFeats = this.selectionManager.getSelectedFeatures();
  this.selectionManager.clearSelection();
- atrack.createGenericOneLevelAnnotations(selFeats, "terminator", true);
+ atrack.createGenericOneLevelAnnotations(selFeats, "terminator", false);
  })
  }));
  createAnnotationMenu.addChild(new dijitMenuItem( {

client/apollo/json/annot.json

@@ -24,8 +24,8 @@
  "arrowheadClass" : "annot-arrowhead",
  "alternateClasses" : {
  "terminator" : {
- "renderClassName" : "black-80pct annot-apollo",
- "className" : "black-80pct"
+ "renderClassName" : "terminator-render annot-apollo",
+ "className" : "terminator"
  },
  "transposable_element" : {
  "renderClassName" : "blue-ibeam-render annot-apollo",

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

@@ -24,7 +24,7 @@ import org.springframework.http.HttpStatus
 /**
  * This is server-side code supporting the high-level functionality of the GWT AnnotatorPanel class.
  */
-@RestApi(name = "Application Services", description = "Methods for running the annotation engine")
+@RestApi(name = "Annotator Engine Services", description = "Methods for running the annotation engine")
 class AnnotatorController {
 
  def featureService