New: mark up structure with linked positions of proteins not in struc…

…ture.

proxl_web_app/front_end/src/js/page_js/data_pages/project_search_ids_driven_pages/structure_page/structure-markup-handler.js

@@ -0,0 +1,155 @@
+"use strict";
+
+export class StructureMarkupHandler {
+
+    constructor() {
+        this._proteinsMarkedOnStructure = { };
+        this._lastInsertId = 0;
+    }
+
+    /**
+     * Get the next id to use
+     *
+     * @returns {number}
+     */
+    getNewId() {
+        this._lastInsertId++;
+        return this._lastInsertId;
+    }
+
+    /**
+     * Delete the protein annotation data with the given id
+     *
+     * @param id
+     */
+    deleteStructureProteinMarkup({id}) {
+        delete this._proteinsMarkedOnStructure[id];
+    }
+
+    /**
+     * Add the given protein annotation data
+     *
+     * @param proteinId
+     * @param start
+     * @param end
+     * @param color
+     */
+    addProteinColorAnnotation({proteinId, start, end, color}) {
+        const newId = this.getNewId();
+        const structureMarkupObject = {
+            "proteinId" : proteinId,
+            "start" : start,
+            "end" : end,
+            "color" : color,
+            "id" : newId
+        }
+
+        this._proteinsMarkedOnStructure[newId] = structureMarkupObject;
+
+        console.log(this);
+    }
+
+    /**
+     * Replace the protein annotation with the given id with the given data
+     * @param id
+     * @param proteinId
+     * @param start
+     * @param end
+     * @param color
+     */
+    updateProteinColorAnnotation({id, proteinId, start, end, color}) {
+        const structureMarkupObject = {
+            "proteinId" : proteinId,
+            "start" : start,
+            "end" : end,
+            "color" : color,
+            "id" : id
+        }
+
+        this._proteinsMarkedOnStructure[id] = structureMarkupObject;
+    }
+
+    /**
+     * Get all the protein color anotation objects in order of id
+     *
+     * @returns {[]}
+     */
+    getOrderedProteinColorAnnotations() {
+
+        const sortedIds = this.getSortedIds();
+
+        let objects = [];
+
+        for (const id of sortedIds) {
+            objects.push(this._proteinsMarkedOnStructure[id]);
+        }
+
+        return objects;
+    }
+
+    /**
+     * Get all the ids sorted from smallest to largest
+     *
+     * @returns {this}
+     */
+    getSortedIds() {
+        let ids = [];
+
+        for (const id of Object.keys(this._proteinsMarkedOnStructure)) {
+            ids.push(id);
+        }
+
+        ids = ids.sort();
+        return ids;
+    }
+
+    /**
+     * Get the data structure to use for storing the state of this object in the URL hash
+     *
+     * @returns {[]}
+     */
+    getDataStructureForHash() {
+        let ds = [];
+
+        for(const markup of this.getOrderedProteinColorAnnotations()) {
+            let item = "";
+            item += markup.proteinId + "-";
+            item += markup.start + "-";
+            item += markup.end + "-";
+            item += markup.color;
+
+            ds.push(item);
+        }
+
+        return ds;
+    }
+
+    /**
+     * Populate this object with data passed in via the dataObject, expected format is
+     * ["proteinid-start-end-color", "proteinid-start-end-color", ...]
+     * @param dataObject
+     */
+    initializeFromJSON(dataObject) {
+
+        console.log('dataObject', dataObject);
+
+        if(!dataObject) { return; }
+
+        for(const stringifiedData of dataObject) {
+            const fields = stringifiedData.split('-');
+
+            const proteinId = fields[0];
+            const start = parseInt(fields[1]);
+            const end = parseInt(fields[2]);
+            const color = fields[3];
+
+            this.addProteinColorAnnotation({
+                proteinId:proteinId,
+                start:start,
+                end:end,
+                color:color
+            });
+        }
+    }
+
+}