Merge 4f76584 into ea9df81

client/apollo/css/webapollo_track_styles.css

@@ -321,6 +321,13 @@ div.annot-sequence  {
     top: 10%;
 }
 
+.black-80pct,
+.plus-black-80pct,
+.minus-black-80pct  {
+    background-color: #222;
+    height: 80%;
+    top: 10%;
+}
 
 .brightgreen-80pct, 
 .plus-brightgreen-80pct, 

client/apollo/js/SequenceOntologyUtils.js

@@ -22,6 +22,7 @@ SequenceOntologyUtils.neverHasCDS = {
     alignment: true, 
     repeat: true,
     repeat_region: true,
+    terminator: true,
     transposable_element: true
 };
 
@@ -40,6 +41,7 @@ SequenceOntologyUtils.neverHasExons = {
     alignment: true, 
     repeat: true,
     repeat_region: true,
+    terminator: true,
     transposable_element: true
 };
 

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

@@ -1276,6 +1276,15 @@ var draggableTrack = declare( HTMLFeatureTrack,
                 atrack.createGenericOneLevelAnnotations(selFeats, "repeat_region", true);
             })
         }));
+        createAnnotationMenu.addChild(new dijitMenuItem( {
+            label: "terminator",
+            onClick: dojo.hitch(this, function() {
+                var selection = this.selectionManager.getSelection();
+                var selFeats = this.selectionManager.getSelectedFeatures();
+                this.selectionManager.clearSelection();
+                atrack.createGenericOneLevelAnnotations(selFeats, "terminator", true);
+            })
+        }));
         createAnnotationMenu.addChild(new dijitMenuItem( {
             label: "transposable_element",
             onClick: dojo.hitch(this, function() {

client/apollo/js/View/Track/WebApolloCanvasFeatures.js

@@ -112,6 +112,13 @@ return declare( CanvasFeaturesTrack,
                      atrack.createGenericOneLevelAnnotations([this.feature], "repeat_region", true);
                    }
                 },
+                {
+                  "label" : "terminator",
+                  "action" : function() {
+                      var atrack=thisB.webapollo.getAnnotTrack();
+                      atrack.createGenericOneLevelAnnotations([this.feature], "terminator", true);
+                  }
+                },
                 {
                   "label" : "transposable element",
                   "action" : function() {

client/apollo/json/annot.json

@@ -22,6 +22,10 @@
             },
             "arrowheadClass" : "annot-arrowhead",
             "alternateClasses" : {
+               "terminator" : {
+                  "renderClassName" : "black-80pct annot-apollo",
+                  "className" : "black-80pct"
+               },
                "transposable_element" : {
                   "renderClassName" : "blue-ibeam-render annot-apollo",
                   "className" : "blue-ibeam"

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

@@ -314,6 +314,8 @@ class AnnotatorController {
                         break
                     case "repeat_region": viewableTypes.add(RepeatRegion.class.canonicalName)
                         break
+                    case "terminator": viewableTypes.add(Terminator.class.canonicalName)
+                        break
                     case "transposable_element": viewableTypes.add(TransposableElement.class.canonicalName)
                         break
                     case "sequence_alteration": viewableTypes.add(SequenceAlteration.class.canonicalName)

grails-app/domain/org/bbop/apollo/Terminator.groovy

@@ -0,0 +1,9 @@
+package org.bbop.apollo
+
+class Terminator extends BiologicalRegion{
+    static constraints = {
+    }
+    static String cvTerm  = "Terminator"
+    static String ontologyId = "SO:0000141"
+    static String alternateCvTerm = "terminator"
+}

grails-app/services/org/bbop/apollo/ChadoHandlerService.groovy

@@ -36,7 +36,7 @@ class ChadoHandlerService {
     private static final String SEQUENCE_ONTOLOGY = "sequence"
     private static final String RELATIONSHIP_ONTOLOGY = "relationship"
     private static final String FEATURE_PROPERTY = "feature_property"
-    private static final def topLevelFeatureTypes = [Gene.cvTerm, Pseudogene.cvTerm, TransposableElement.cvTerm, RepeatRegion.cvTerm,
+    private static final def topLevelFeatureTypes = [Gene.cvTerm, Pseudogene.cvTerm, Terminator.cvTerm, TransposableElement.cvTerm, RepeatRegion.cvTerm,
                                                      InsertionArtifact.cvTerm, DeletionArtifact.cvTerm, SubstitutionArtifact.cvTerm]
     private static final ontologyDb = ["SO", "GO", "RO"]
     Map<String, org.gmod.chado.Organism> chadoOrganismsMap = new HashMap<String, org.gmod.chado.Organism>()

grails-app/services/org/bbop/apollo/FeatureService.groovy

@@ -36,7 +36,7 @@ class FeatureService {
     public static final String MANUALLY_DISSOCIATE_TRANSCRIPT_FROM_GENE = "Manually dissociate transcript from gene"
     public static final
     def rnaFeatureTypes = [MRNA.cvTerm, MiRNA.cvTerm, NcRNA.cvTerm, RRNA.cvTerm, SnRNA.cvTerm, SnoRNA.cvTerm, TRNA.cvTerm, Transcript.cvTerm]
-    public static final def singletonFeatureTypes = [RepeatRegion.cvTerm, TransposableElement.cvTerm]
+    public static final def singletonFeatureTypes = [RepeatRegion.cvTerm, TransposableElement.cvTerm,Terminator.cvTerm]
 
     @Timed
     @Transactional
@@ -1527,6 +1527,7 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
             case Pseudogene.ontologyId: return new Pseudogene()
             case Transcript.ontologyId: return new Transcript()
             case TransposableElement.ontologyId: return new TransposableElement()
+            case Terminator.ontologyId: return new Terminator()
             case RepeatRegion.ontologyId: return new RepeatRegion()
             case InsertionArtifact.ontologyId: return new InsertionArtifact()
             case DeletionArtifact.ontologyId: return new DeletionArtifact()
@@ -1570,6 +1571,8 @@ public void setTranslationEnd(Transcript transcript, int translationEnd) {
                 case Pseudogene.cvTerm.toUpperCase(): return Pseudogene.ontologyId
                 case TransposableElement.alternateCvTerm.toUpperCase():
                 case TransposableElement.cvTerm.toUpperCase(): return TransposableElement.ontologyId
+                case Terminator.alternateCvTerm.toUpperCase():
+                case Terminator.cvTerm.toUpperCase(): return Terminator.ontologyId
                 case RepeatRegion.alternateCvTerm.toUpperCase():
                 case RepeatRegion.cvTerm.toUpperCase(): return RepeatRegion.ontologyId
                 case InsertionArtifact.cvTerm.toUpperCase(): return InsertionArtifact.ontologyId

grails-app/services/org/bbop/apollo/FeatureTypeService.groovy

@@ -1,7 +1,6 @@
 package org.bbop.apollo
 
 import grails.transaction.Transactional
-import org.bbop.apollo.gwt.shared.FeatureStringEnum
 
 @Transactional
 class FeatureTypeService {
@@ -29,6 +28,8 @@ class FeatureTypeService {
         createFeatureTypeForFeature(NcRNA.class,NcRNA.cvTerm)
         createFeatureTypeForFeature(RRNA.class,RRNA.cvTerm)
         createFeatureTypeForFeature(RepeatRegion.class,RepeatRegion.cvTerm)
+        createFeatureTypeForFeature(Terminator.class,Terminator.alternateCvTerm)
         createFeatureTypeForFeature(TransposableElement.class,TransposableElement.cvTerm)
+        return true
     }
 }

grails-app/services/org/bbop/apollo/RequestHandlingService.groovy

@@ -46,6 +46,7 @@ class RequestHandlingService {
 
     public static final List<String> viewableAnnotationFeatureList = [
             RepeatRegion.class.name,
+            Terminator.class.name,
             TransposableElement.class.name
     ]
     public static final List<String> viewableAnnotationTranscriptParentList = [
@@ -2339,7 +2340,7 @@ class RequestHandlingService {
         User user = permissionService.getCurrentUser(inputObject)
         JSONObject featureContainer = createJSONFeatureContainer()
 
-        def singletonFeatureTypes = [RepeatRegion.cvTerm, TransposableElement.cvTerm]
+        def singletonFeatureTypes = [RepeatRegion.cvTerm, TransposableElement.cvTerm, Terminator.cvTerm]
         def rnaFeatureTypes = [MRNA.cvTerm, MiRNA.cvTerm, NcRNA.cvTerm, RRNA.cvTerm, SnRNA.cvTerm, SnoRNA.cvTerm, TRNA.cvTerm, Transcript.cvTerm]
 
         for (int i = 0; i < features.length(); i++) {

src/gwt/org/bbop/apollo/gwt/client/AnnotatorPanel.java

@@ -428,6 +428,7 @@ private void initializeTypes() {
         typeList.addItem("Gene");
         typeList.addItem("Pseudogene");
         typeList.addItem("Transposable Element", "transposable_element");
+        typeList.addItem("Terminator", "terminator");
         typeList.addItem("Repeat Region", "repeat_region");
         typeList.addItem("Variant", "sequence_alteration");
     }
@@ -481,6 +482,7 @@ private static void updateAnnotationInfo(AnnotationInfo annotationInfo) {
                 tabPanel.getTabWidget(3).getParent().setVisible(false);
                 tabPanel.getTabWidget(4).getParent().setVisible(false);
                 break;
+            case "terminator":
             case "transposable_element":
             case "repeat_region":
                 repeatRegionDetailPanel.updateData(annotationInfo);
@@ -606,6 +608,8 @@ public String getValue(AnnotationInfo annotationInfo) {
 
                 String type = annotationInfo.getType();
                 switch (type) {
+                    case "terminator":
+                        return "term elem";
                     case "repeat_region":
                         return "repeat rgn";
                     case "transposable_element":
@@ -764,7 +768,7 @@ public void displayTranscript(int geneIndex, String uniqueName) {
     public void displayFeature(int featureIndex) {
         AnnotationInfo annotationInfo = dataGrid.getVisibleItem(Math.abs(dataGrid.getVisibleRange().getStart() - featureIndex));
         String type = annotationInfo.getType();
-        if (type.equals("transposable_element") || type.equals("repeat_region")) {
+        if (type.equals("transposable_element") || type.equals("repeat_region") || type.equals("terminator")) {
             // do nothing
         } else {
             exonDetailPanel.updateData(annotationInfo);