diff --git a/frontend-js/src/main/js/map/data/Alias.js b/frontend-js/src/main/js/map/data/Alias.js
index a813a5ba24c25ec4300d1ea8d1a5aeabb71fba5f..e1d30f6f0c66dab022ab81fa5fe382b00cac5637 100644
--- a/frontend-js/src/main/js/map/data/Alias.js
+++ b/frontend-js/src/main/js/map/data/Alias.js
@@ -2,6 +2,7 @@
var BioEntity = require("./BioEntity");
+// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
/**
@@ -26,7 +27,7 @@ function Alias(javaObject) {
}
if (this._modelId === undefined) {
- throw new Error("ModelId is not defined for alias", javaObject);
+ throw new Error("ModelId is not defined for alias");
}
if (javaObject.name === undefined) {
diff --git a/frontend-js/src/main/js/map/marker/AliasMarker.js b/frontend-js/src/main/js/map/marker/AliasMarker.js
index 2b6c66c608c0770241c06a2e7d822462e787033b..a74a1a7bac3e04a3d78c6bf2297b60ace970ee48 100644
--- a/frontend-js/src/main/js/map/marker/AliasMarker.js
+++ b/frontend-js/src/main/js/map/marker/AliasMarker.js
@@ -40,8 +40,8 @@ AliasMarker.prototype.setAliasData = function (data) {
* @returns {google.maps.Point} - coordinates where marker is pointing
*/
AliasMarker.prototype.getCoordinates = function () {
- return new google.maps.Point(this._aliasData.x + this._aliasData.width / 2, this._aliasData.y
- + this._aliasData.height / 2);
+ var alias = this.getAliasData();
+ return new google.maps.Point(alias.getX() + alias.getWidth() / 2, alias.getY() + alias.getHeight() / 2);
};
AliasMarker.prototype.init = function () {
diff --git a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
index d657fd6bceeb294d0f01cd2440652bce567ba8d7..a161dca5d6494cb96bfaa3a38014e807f9d32a2f 100644
--- a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
+++ b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
@@ -8,7 +8,7 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
* Class representing abstract overlay element on the map relevant for a
* specific layout.
*/
-function AbstractOverlayElement(params) {
+function AbstractSurfaceElement(params) {
var self = this;
// call super constructor
ObjectWithListeners.call(this);
@@ -31,16 +31,16 @@ function AbstractOverlayElement(params) {
}
}
-AbstractOverlayElement.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractOverlayElement.prototype.constructor = AbstractOverlayElement;
+AbstractSurfaceElement.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractSurfaceElement.prototype.constructor = AbstractSurfaceElement;
-AbstractOverlayElement.prototype.setMap = function(map) {
+AbstractSurfaceElement.prototype.setMap = function (map) {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
this.getGoogleMapObjects()[i].setMap(map);
}
};
-AbstractOverlayElement.prototype.getBounds = function() {
+AbstractSurfaceElement.prototype.getBounds = function () {
var bounds = new google.maps.LatLngBounds();
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
bounds.extend(this.getGoogleMapObjects()[i].getBounds().getSouthWest());
@@ -49,7 +49,7 @@ AbstractOverlayElement.prototype.getBounds = function() {
return bounds;
};
-AbstractOverlayElement.prototype.isShown = function() {
+AbstractSurfaceElement.prototype.isShown = function () {
var result = false;
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
var map = this.getGoogleMapObjects()[i].getMap();
@@ -61,7 +61,7 @@ AbstractOverlayElement.prototype.isShown = function() {
return result;
};
-AbstractOverlayElement.prototype.show = function() {
+AbstractSurfaceElement.prototype.show = function () {
if (this.isShown()) {
logger.warn("Surface already shown");
return;
@@ -69,51 +69,60 @@ AbstractOverlayElement.prototype.show = function() {
this.setMap(this.getCustomMap().getGoogleMap());
};
-AbstractOverlayElement.prototype.hide = function() {
+AbstractSurfaceElement.prototype.hide = function () {
this.setMap(null);
};
-AbstractOverlayElement.prototype.onClickHandler = function() {
+AbstractSurfaceElement.prototype.onClickHandler = function () {
return this.callListeners("onClick");
};
-AbstractOverlayElement.prototype.getGoogleMarker = function() {
+AbstractSurfaceElement.prototype.getGoogleMarker = function () {
return this.getGoogleMapObjects()[0];
};
-AbstractOverlayElement.prototype.getGoogleMapObjects = function() {
+AbstractSurfaceElement.prototype.getGoogleMapObjects = function () {
return this._googleMapObjects;
};
-AbstractOverlayElement.prototype.addGoogleMapObject = function(googleObject) {
+AbstractSurfaceElement.prototype.addGoogleMapObject = function (googleObject) {
this._googleMapObjects.push(googleObject);
var self = this;
- var onclick = function() {
+ var onclick = function () {
return self.onClickHandler();
};
google.maps.event.addListener(googleObject, 'click', onclick);
};
-AbstractOverlayElement.prototype.getIdentifiedElement = function() {
+AbstractSurfaceElement.prototype.getIdentifiedElement = function () {
return this._identifiedElement;
};
-AbstractOverlayElement.prototype.getModelId = function() {
+AbstractSurfaceElement.prototype.setIdentifiedElement = function (identifiedElement) {
+ this._identifiedElement = identifiedElement;
+};
+
+AbstractSurfaceElement.prototype.getBioEntity = function () {
+ return this._bioEntity;
+};
+
+AbstractSurfaceElement.prototype.setBioEntity = function (bioEntity) {
+ this._bioEntity = bioEntity;
+};
+
+
+AbstractSurfaceElement.prototype.getModelId = function () {
return this.getIdentifiedElement().getModelId();
};
-AbstractOverlayElement.prototype.updateIdentifiedElement = function(identifiedElement) {
+AbstractSurfaceElement.prototype.updateIdentifiedElement = function (identifiedElement) {
if (identifiedElement.getColor() !== undefined) {
this.setColor(identifiedElement.getColor());
}
};
-AbstractOverlayElement.prototype.setIdentifiedElement = function(identifiedElement) {
- this._identifiedElement = identifiedElement;
-};
-
-AbstractOverlayElement.prototype.getBounds = function() {
+AbstractSurfaceElement.prototype.getBounds = function () {
var self = this;
var bounds = new google.maps.LatLngBounds();
for (var i = 0; i < self.getGoogleMapObjects().length; i++) {
@@ -127,15 +136,15 @@ AbstractOverlayElement.prototype.getBounds = function() {
/**
* Returns {@link AbstractCustomMap} where surface is located.
- *
- * @returns {@link AbstractCustomMap} where surface is located
+ *
+ * @returns {AbstractCustomMap} where surface is located
*/
-AbstractOverlayElement.prototype.getCustomMap = function() {
+AbstractSurfaceElement.prototype.getCustomMap = function () {
return this._customMap;
};
-AbstractOverlayElement.prototype.setCustomMap = function(customMap) {
+AbstractSurfaceElement.prototype.setCustomMap = function (customMap) {
this._customMap = customMap;
};
-module.exports = AbstractOverlayElement;
+module.exports = AbstractSurfaceElement;
diff --git a/frontend-js/src/main/js/map/surface/AliasSurface.js b/frontend-js/src/main/js/map/surface/AliasSurface.js
index 58c38c691eafad16972d0090a2449c600e16e007..f062657fdc63d1f28a7a33d37da61bcb6cdbead4 100644
--- a/frontend-js/src/main/js/map/surface/AliasSurface.js
+++ b/frontend-js/src/main/js/map/surface/AliasSurface.js
@@ -2,6 +2,7 @@
/* exported logger */
+// noinspection JSUnusedLocalSymbols
var logger = require('../../logger');
var functions = require('../../Functions');
@@ -20,18 +21,18 @@ function AliasSurface(params) {
this.addGoogleMapObject(params.gmapObj);
// original data
- this.aliasData = params.alias;
+ this.setBioEntity(params.alias);
}
AliasSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
AliasSurface.prototype.constructor = AliasSurface;
-AliasSurface.prototype.setColor = function(color) {
+AliasSurface.prototype.setColor = function (color) {
this._color = color;
var googleMapObjects = this.getGoogleMapObjects();
for (var i = 0; i < googleMapObjects.length; i++) {
googleMapObjects[i].setOptions({
- strokeColor : color,
+ strokeColor: color
});
}
};
@@ -40,16 +41,16 @@ AliasSurface.prototype.setColor = function(color) {
* Function used to recalculate boundaries of the {@link AliasSurface}.
* Boundaries define how big part of original alias is taken by this layout
* visualization.
- *
+ *
* @param startX
* value between 0..1 defining where should be the start on OX axis
* @param endX
* value between 0..1 defining where should be the end on OX axis
*/
-AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
- var pointA = new google.maps.Point(this.aliasData.x + startX * this.aliasData.width, this.aliasData.y);
- var pointB = new google.maps.Point(this.aliasData.x + endX * this.aliasData.width, this.aliasData.y
- + this.aliasData.height);
+AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
+ var alias = this.getBioEntity();
+ var pointA = new google.maps.Point(alias.x + startX * alias.width, alias.y);
+ var pointB = new google.maps.Point(alias.x + endX * alias.width, alias.y + alias.height);
var latLngA = this.getCustomMap().fromPointToLatLng(pointA);
var latLngB = this.getCustomMap().fromPointToLatLng(pointB);
@@ -61,7 +62,7 @@ AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
/**
* Creates {@link AliasSurface}.
- *
+ *
* @param params
* dict containing set of information required for surface creation:
* <li>overlayAlias - {@link LayoutAlias} for which overlay is created
@@ -79,7 +80,7 @@ AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
* starting point of the overlay
* @returns {AliasSurface}
*/
-AliasSurface.create = function(params) {
+AliasSurface.create = function (params) {
var overlayAlias = params.overlayAlias;
var alias = params.alias;
var map = params.map;
@@ -95,32 +96,32 @@ AliasSurface.create = function(params) {
bounds.extend(latLngA);
bounds.extend(latLngB);
var rectangle = new google.maps.Rectangle({
- fillOpacity : 0.8,
- strokeWeight : 1,
- map : map.getGoogleMap(),
- bounds : bounds
+ fillOpacity: 0.8,
+ strokeWeight: 1,
+ map: map.getGoogleMap(),
+ bounds: bounds
});
- return functions.overlayToColor(overlayAlias).then(function(color) {
+ return functions.overlayToColor(overlayAlias).then(function (color) {
rectangle.setOptions({
- fillColor : color,
+ fillColor: color
});
var result = new AliasSurface({
- map : map,
- gmapObj : rectangle,
- alias : alias,
- onClick : params.onClick
+ map: map,
+ gmapObj: rectangle,
+ alias: alias,
+ onClick: params.onClick
});
result.setIdentifiedElement(new IdentifiedElement(alias));
return result;
});
};
-AliasSurface.createFromIdentifiedElement = function(params) {
+AliasSurface.createFromIdentifiedElement = function (params) {
var element = params.element;
var map = params.map;
var model = map.getModel().getSubmodelById(element.getModelId());
- return model.getByIdentifiedElement(element).then(function(alias) {
+ return model.getByIdentifiedElement(element).then(function (alias) {
var pointA = new google.maps.Point(alias.getX(), alias.getY());
var pointB = new google.maps.Point(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
var latLngA = map.fromPointToLatLng(pointA);
@@ -152,21 +153,21 @@ AliasSurface.createFromIdentifiedElement = function(params) {
}
var rectangle = new google.maps.Rectangle({
- map : map.getGoogleMap(),
- bounds : bounds,
-
- fillOpacity : fillOpacity,
- fillColor : color,
- strokeColor : strokeColor,
- strokeOpacity : strokeOpacity,
- strokeWeight : strokeWeight,
+ map: map.getGoogleMap(),
+ bounds: bounds,
+
+ fillOpacity: fillOpacity,
+ fillColor: color,
+ strokeColor: strokeColor,
+ strokeOpacity: strokeOpacity,
+ strokeWeight: strokeWeight
});
var result = new AliasSurface({
- gmapObj : rectangle,
- map : map,
- onClick : params.onClick,
- alias : alias,
+ gmapObj: rectangle,
+ map: map,
+ onClick: params.onClick,
+ alias: alias
});
result.setIdentifiedElement(element);
return result;
diff --git a/frontend-js/src/main/js/map/surface/ReactionSurface.js b/frontend-js/src/main/js/map/surface/ReactionSurface.js
index e57d7d8086c3026fc8cfca5ff9ac513d142f45ed..58748537d193ee03bb53accf1092483d5653f6a2 100644
--- a/frontend-js/src/main/js/map/surface/ReactionSurface.js
+++ b/frontend-js/src/main/js/map/surface/ReactionSurface.js
@@ -1,5 +1,7 @@
"use strict";
+var Promise = require("bluebird");
+
/* exported logger */
var functions = require('../../Functions');
@@ -29,7 +31,7 @@ function ReactionSurface(params) {
AbstractSurfaceElement.call(this, params);
var overlayData = params.layoutReaction;
- this.setReactionData(params.reaction);
+ this.setBioEntity(params.reaction);
var color = params.color;
this.width = 5.0;
@@ -46,7 +48,7 @@ function ReactionSurface(params) {
this.setColor(color);
this.setCustomized(params.customized);
- this.setIdentifiedElement(new IdentifiedElement(this.getReactionData()));
+ this.setIdentifiedElement(new IdentifiedElement(this.getBioEntity()));
this.init();
}
@@ -89,7 +91,7 @@ ReactionSurface.prototype.setColor = function (color) {
var gmapObjects = this.getGoogleMapObjects();
for (var i = 0; i < gmapObjects.length; i++) {
gmapObjects[i].setOptions({
- strokeColor: color,
+ strokeColor: color
});
}
this.customized = true;
@@ -165,7 +167,7 @@ ReactionSurface.prototype.changedToDefault = function () {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
this.getGoogleMapObjects()[i].setOptions({
strokeColor: "#0000FF",
- strokeWeight: 5,
+ strokeWeight: 5
});
}
this.customized = false;
@@ -175,11 +177,11 @@ ReactionSurface.prototype.changedToDefault = function () {
* Changes visualization of the ReactionSurface to customized mode where we mark
* reaction as highlighted with customized reaction layout data.
*/
-ReactionSurface.prototype.changedToCustomized = function() {
+ReactionSurface.prototype.changedToCustomized = function () {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
this.getGoogleMapObjects()[i].setOptions({
strokeColor: this.getColor(),
- strokeWeight: this.getWidth(),
+ strokeWeight: this.getWidth()
});
}
this.customized = true;
@@ -215,15 +217,6 @@ ReactionSurface.createLine = function (line, color, width, map) {
return googleLine;
};
-/**
- * Returns {@link Reaction} data for this marker.
- *
- * @returns {@link Reaction} data for this marker
- */
-ReactionSurface.prototype.getReactionData = function () {
- return this.reactionData;
-};
-
ReactionSurface.prototype.getId = function () {
return this._id;
};
@@ -232,11 +225,11 @@ ReactionSurface.prototype.setId = function (id) {
this._id = id;
};
-ReactionSurface.prototype.setReactionData = function (value) {
+ReactionSurface.prototype.setBioEntity = function (value) {
if (value === undefined || value === null) {
throw new Error("Reaction must be defined");
}
- this.reactionData = value;
+ AbstractSurfaceElement.prototype.setBioEntity.call(this, value);
this.setId(value.getId());
};
@@ -245,21 +238,22 @@ ReactionSurface.prototype.isCustomized = function () {
};
ReactionSurface.prototype.init = function () {
+ var reaction = this.getBioEntity();
var i;
var line;
var googleLine;
- for (i = 0; i < this.reactionData.startLines.length; i++) {
- line = this.reactionData.startLines[i];
+ for (i = 0; i < reaction.startLines.length; i++) {
+ line = reaction.startLines[i];
googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
this.addGoogleMapObject(googleLine);
}
- for (i = 0; i < this.reactionData.endLines.length; i++) {
- line = this.reactionData.endLines[i];
+ for (i = 0; i < reaction.endLines.length; i++) {
+ line = reaction.endLines[i];
googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
this.addGoogleMapObject(googleLine);
}
- for (i = 0; i < this.reactionData.midLines.length; i++) {
- line = this.reactionData.midLines[i];
+ for (i = 0; i < reaction.midLines.length; i++) {
+ line = reaction.midLines[i];
googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
this.addGoogleMapObject(googleLine);
}
diff --git a/frontend-js/src/test/js/map/data/Alias-test.js b/frontend-js/src/test/js/map/data/Alias-test.js
index 2444f2ac02ebf0abfe95595a16d9aff32f775a6a..9c72fb22fdcf754cc7560e22fe60cd07f7347975 100644
--- a/frontend-js/src/test/js/map/data/Alias-test.js
+++ b/frontend-js/src/test/js/map/data/Alias-test.js
@@ -61,70 +61,91 @@ describe('Alias', function () {
});
- it("Alias update method", function () {
- var javaObject = {
- bounds: {
- x: 190,
- y: 44,
- width: 80,
- height: 40
- },
- modelId: 57,
- idObject: 18554
- };
- var alias = new Alias(javaObject);
- var javaObject2 = {
- notes: "",
- type: "Protein",
- name: "s1",
- synonyms: [],
- formerSymbols: [],
- references: [],
- other: [],
- bounds: {
- x: 59,
- y: 73,
- width: 80,
- height: 40
- },
- modelId: 54,
- idObject: 18552
- };
- alias.update(javaObject2);
- assert.ok(alias.isComplete());
- assert.equal('s1', alias.name);
- });
+ describe("update", function () {
+ describe("from json", function () {
+ it("full update", function () {
+ var javaObject = {
+ bounds: {
+ x: 190,
+ y: 44,
+ width: 80,
+ height: 40
+ },
+ modelId: 57,
+ idObject: 18554
+ };
+ var alias = new Alias(javaObject);
+ var javaObject2 = {
+ notes: "",
+ type: "Protein",
+ name: "s1",
+ synonyms: [],
+ formerSymbols: [],
+ references: [],
+ other: [],
+ bounds: {
+ x: 59,
+ y: 73,
+ width: 80,
+ height: 40
+ },
+ modelId: 54,
+ idObject: 18552
+ };
+ alias.update(javaObject2);
+ assert.ok(alias.isComplete());
+ assert.equal('s1', alias.getName());
+ });
+
+ it("partial update", function () {
+ var javaObject = {
+ bounds: {
+ x: 190,
+ y: 44,
+ width: 80,
+ height: 40
+ },
+ modelId: 57,
+ idObject: 18554
+ };
+ var alias = new Alias(javaObject);
+ var javaObject2 = {
+ notes: "",
+ type: "Protein",
+ synonyms: [],
+ formerSymbols: [],
+ references: [],
+ other: [],
+ bounds: {
+ x: 59,
+ y: 73,
+ width: 80,
+ height: 40
+ },
+ modelId: 54,
+ idObject: 18552
+ };
+ alias.update(javaObject2);
+ assert.equal(alias.isComplete(), false);
+ });
+ });
- it("Alias update method 2", function () {
- var javaObject = {
- bounds: {
- x: 190,
- y: 44,
- width: 80,
- height: 40
- },
- modelId: 57,
- idObject: 18554
- };
- var alias = new Alias(javaObject);
- var javaObject2 = {
- notes: "",
- type: "Protein",
- synonyms: [],
- formerSymbols: [],
- references: [],
- other: [],
- bounds: {
- x: 59,
- y: 73,
- width: 80,
- height: 40
- },
- modelId: 54,
- idObject: 18552
- };
- alias.update(javaObject2);
- assert.equal(alias.isComplete(), false);
+ it("from Alias", function () {
+ var javaObject = {
+ bounds: {
+ x: 190,
+ y: 44,
+ width: 80,
+ height: 40
+ },
+ modelId: 57,
+ idObject: 18554
+ };
+ var alias = new Alias(javaObject);
+ var alias2 = new Alias(javaObject);
+ alias.update(alias2);
+ assert.equal(alias.isComplete(), false);
+ });
});
});
diff --git a/frontend-js/src/test/js/map/data/MapModel-test.js b/frontend-js/src/test/js/map/data/MapModel-test.js
index 5bad0d3b69968bb7314a452a5e4d9bfd90a8b6b7..77ae8c60cab9c8b203023875539d4c44de2b9aed 100644
--- a/frontend-js/src/test/js/map/data/MapModel-test.js
+++ b/frontend-js/src/test/js/map/data/MapModel-test.js
@@ -7,6 +7,7 @@ var LayoutData = require('../../../../main/js/map/data/LayoutData');
var MapModel = require('../../../../main/js/map/data/MapModel');
var NetworkError = require('../../../../main/js/NetworkError');
var PointData = require('../../../../main/js/map/data/PointData');
+var ServerConnector = require('../../ServerConnector-mock');
var assert = require('chai').assert;
diff --git a/frontend-js/src/test/js/map/surface/ReactionSurface-test.js b/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
index c8a81162dc4e1244185126d171bd98cbe1c36224..babf8bf7fdc4c2097910502dab9fd1e232947ba2 100644
--- a/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
+++ b/frontend-js/src/test/js/map/surface/ReactionSurface-test.js
@@ -23,7 +23,7 @@ describe('ReactionSurface', function () {
assert.ok(reactionOverlay.getColor());
assert.ok(reactionOverlay.getWidth());
assert.ok(reactionOverlay.getBounds());
- assert.ok(reactionOverlay.getReactionData());
+ assert.ok(reactionOverlay.getBioEntity());
assert.ok(reactionOverlay.getCustomMap());
assert.ok(reactionOverlay.getId());
assert.ok(typeof reactionOverlay.getColor() === "string");
@@ -44,7 +44,7 @@ describe('ReactionSurface', function () {
assert.ok(reactionOverlay.getColor());
assert.ok(reactionOverlay.getWidth());
assert.ok(reactionOverlay.getBounds());
- assert.ok(reactionOverlay.getReactionData());
+ assert.ok(reactionOverlay.getBioEntity());
assert.ok(reactionOverlay.getCustomMap());
assert.ok(reactionOverlay.getId());
assert.ok(typeof reactionOverlay.getColor() === "string");