diff --git a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
index 38d38419447956b808f8cfd8f4dc7108ab2c7672..4b3c3d2a124e6b5914054439155c7d1d54084b6b 100644
--- a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
@@ -136,9 +136,9 @@ GraphicsExportPanel.prototype._createDownloadButton = function () {
var identifier = null;
var defaultOverlayName = "Network";
for (var i = 0; i < self.getProject().getDataOverlays().length; i++) {
- var layout = self.getProject().getDataOverlays()[i];
- if (identifier === null || layout.getName() === defaultOverlayName) {
- identifier = layout.getId();
+ var overlay = self.getProject().getDataOverlays()[i];
+ if (identifier === null || overlay.getName() === defaultOverlayName) {
+ identifier = overlay.getId();
}
}
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index ff7a66e80fd7a01599e106ce57a04ff8fdc4c121..2150be2c13c952084102f242a4d3b859e699d1dc 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -37,9 +37,9 @@ function AbstractCustomMap(model, options) {
this.setModel(model);
- // this array contains elements that are presented on a specific layout (set
+ // this array contains elements that are presented on a specific overlay (set
// of google map object representing lines/areas that are associated with
- // layout)
+ // overlay)
this.selectedLayoutOverlays = [];
// following fields are used in conversion between x,y coordinates and lat,lng
@@ -90,8 +90,8 @@ AbstractCustomMap.prototype.getMarkerSurfaceCollection = function () {
return this._markerSurfaceCollection;
};
/**
- * Assigns layouts with images to the google map (which set of images should be
- * used by google maps api for which layout).
+ * Assigns overlays with images to the google map (which set of images should be
+ * used by google maps api for which overlay).
*
*/
AbstractCustomMap.prototype.setupLayouts = function () {
@@ -157,10 +157,10 @@ AbstractCustomMap.prototype.createMapOptions = function () {
};
/**
- * Create google maps configuration options object for a specific layout.
+ * Create google maps configuration options object for a specific overlay.
*
* @param param
- * object with information about layout
+ * object with information about overlay
*/
AbstractCustomMap.prototype.createTypeOptions = function (param) {
var self = this;
@@ -556,22 +556,22 @@ AbstractCustomMap.prototype.getTopMap = function () {
};
/**
- * Method that should be called when number of layouts to visualize changed to
- * modify boundaries of the elements to visualize. When few layouts are
+ * Method that should be called when number of overlays to visualize changed to
+ * modify boundaries of the elements to visualize. When few overlays are
* visualized at the same time then index contains information where this new
- * layout is placed in the list (starting from 0) and length contains
- * information how many layouts we visualize in total.
+ * overlay is placed in the list (starting from 0) and length contains
+ * information how many overlays we visualize in total.
*
- * @param layoutId
- * identifier of a layout
+ * @param overlayId
+ * identifier of a overlay
* @param index
- * when visualizing more than one layout at the same time index
- * contains information at which position in the list this layout is
+ * when visualizing more than one overlay at the same time index
+ * contains information at which position in the list this overlay is
* placed
* @param length
- * number of layouts that are currently visualized
+ * number of overlays that are currently visualized
*/
-AbstractCustomMap.prototype._resizeSelectedDataOverlay = function (layoutId, index, length) {
+AbstractCustomMap.prototype._resizeSelectedDataOverlay = function (overlayId, index, length) {
var self = this;
return new Promise(function (resolve) {
// if map is not initialized then don't perform this operation
@@ -579,35 +579,35 @@ AbstractCustomMap.prototype._resizeSelectedDataOverlay = function (layoutId, ind
logger.debug("Model " + self.getId() + " not initialized");
resolve();
}
- logger.debug("Resize layout: " + layoutId);
+ logger.debug("Resize overlay: " + overlayId);
// start ratio
var startX = index * (1.0 / length);
// end ratio
var endX = (index + 1) * (1.0 / length);
- for (var i = 0; i < self.selectedLayoutOverlays[layoutId].length; i++) {
- self.selectedLayoutOverlays[layoutId][i].setBoundsForAlias(startX, endX);
+ for (var i = 0; i < self.selectedLayoutOverlays[overlayId].length; i++) {
+ self.selectedLayoutOverlays[overlayId][i].setBoundsForAlias(startX, endX);
}
resolve();
});
};
/**
- * Shows all elements from a given layout. When few layouts are visualized at
- * the same time then index contains information where this new layout is placed
+ * Shows all elements from a given overlay. When few overlays are visualized at
+ * the same time then index contains information where this new overlay is placed
* in the list (starting from 0) and length contains information how many
- * layouts we visualize in total.
+ * overlays we visualize in total.
*
- * @param layoutId
- * identifier of a layout
+ * @param overlayId
+ * identifier of a overlay
* @param index
- * when visualizing more than one layout at the same time index
- * contains information at which position in the list this layout is
+ * when visualizing more than one overlay at the same time index
+ * contains information at which position in the list this overlay is
* placed
* @param length
- * number of layouts that are currently visualized
+ * number of overlays that are currently visualized
*/
-AbstractCustomMap.prototype._showSelectedDataOverlay = function (layoutId, index, length) {
+AbstractCustomMap.prototype._showSelectedDataOverlay = function (overlayId, index, length) {
var self = this;
// if map is not initialized then don't perform this operation
return new Promise(function (resolve, reject) {
@@ -619,43 +619,43 @@ AbstractCustomMap.prototype._showSelectedDataOverlay = function (layoutId, index
logger.debug("Showing model " + self.getId());
}
- self.selectedLayoutOverlays[layoutId] = [];
+ self.selectedLayoutOverlays[overlayId] = [];
// start ratio
var startX = index * (1.0 / length);
// end ratio
var endX = (index + 1) * (1.0 / length);
- var layoutAliases;
- var layoutReactions;
+ var overlayAliases;
+ var overlayReactions;
- return self.getProject().getDataOverlayById(layoutId).then(function (layout) {
- layoutAliases = layout.getAliases();
- layoutReactions = layout.getReactions();
+ return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
+ overlayAliases = overlay.getAliases();
+ overlayReactions = overlay.getReactions();
var identifiedElements = [];
var i;
- for (i = 0; i < layoutAliases.length; i++) {
- if (layoutAliases[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(layoutAliases[i]));
+ for (i = 0; i < overlayAliases.length; i++) {
+ if (overlayAliases[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(overlayAliases[i]));
}
}
var reactionIds = [];
- for (i = 0; i < layoutReactions.length; i++) {
- if (layoutReactions[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(layoutReactions[i]));
+ for (i = 0; i < overlayReactions.length; i++) {
+ if (overlayReactions[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(overlayReactions[i]));
}
}
return self.getModel().getByIdentifiedElements(identifiedElements, false);
}).then(function () {
- return Promise.each(layoutAliases, function (layoutAlias) {
- if (layoutAlias.getModelId() === self.getId()) {
+ return Promise.each(overlayAliases, function (overlayAlias) {
+ if (overlayAlias.getModelId() === self.getId()) {
var surface;
var element;
- return self.getModel().getAliasById(layoutAlias.getId()).then(function (aliasData) {
+ return self.getModel().getAliasById(overlayAlias.getId()).then(function (aliasData) {
element = new IdentifiedElement(aliasData);
return AliasSurface.create({
- overlayAlias: layoutAlias,
+ overlayAlias: overlayAlias,
alias: aliasData,
map: self,
startX: startX,
@@ -668,18 +668,18 @@ AbstractCustomMap.prototype._showSelectedDataOverlay = function (layoutId, index
});
}).then(function (result) {
surface = result;
- self.selectedLayoutOverlays[layoutId].push(surface);
+ self.selectedLayoutOverlays[overlayId].push(surface);
});
}
});
}).then(function () {
- return Promise.each(layoutReactions, function (layoutReaction) {
- if (layoutReaction.getModelId() === self.getId()) {
- return self.getModel().getReactionById(layoutReaction.getId()).then(function (reactionData) {
+ return Promise.each(overlayReactions, function (overlayReaction) {
+ if (overlayReaction.getModelId() === self.getId()) {
+ return self.getModel().getReactionById(overlayReaction.getId()).then(function (reactionData) {
var surface;
var element = new IdentifiedElement(reactionData);
return ReactionSurface.create({
- layoutReaction: layoutReaction,
+ layoutReaction: overlayReaction,
reaction: reactionData,
map: self,
onClick: [function () {
@@ -690,7 +690,7 @@ AbstractCustomMap.prototype._showSelectedDataOverlay = function (layoutId, index
customized: (length === 1)
}).then(function (result) {
surface = result;
- self.selectedLayoutOverlays[layoutId].push(surface);
+ self.selectedLayoutOverlays[overlayId].push(surface);
surface.show();
});
});
@@ -703,21 +703,21 @@ AbstractCustomMap.prototype._showSelectedDataOverlay = function (layoutId, index
};
/**
- * Hides all elements from layout.
+ * Hides all elements from overlay.
*
- * @param layoutId
- * identifier of a layout
+ * @param overlayId
+ * identifier of a overlay
*/
-AbstractCustomMap.prototype._hideSelectedLayout = function (layoutId) {
+AbstractCustomMap.prototype._hideSelectedLayout = function (overlayId) {
// if map is not initialized then don't perform this operation
if (!this.initialized) {
logger.debug("Model " + this.getId() + " not initialized");
return;
}
- for (var i = 0; i < this.selectedLayoutOverlays[layoutId].length; i++) {
- this.selectedLayoutOverlays[layoutId][i].setMap(null);
+ for (var i = 0; i < this.selectedLayoutOverlays[overlayId].length; i++) {
+ this.selectedLayoutOverlays[overlayId][i].setMap(null);
}
- this.selectedLayoutOverlays[layoutId] = [];
+ this.selectedLayoutOverlays[overlayId] = [];
};
/**
@@ -749,20 +749,20 @@ AbstractCustomMap.prototype._openInfoWindowForAlias = function (alias, googleMar
/**
* Returns promise of a list of {@link LayoutAlias} information for a given
- * {@link Alias} in all currently visualized layouts.
+ * {@link Alias} in all currently visualized overlays.
*
* @param aliasId
* identifier of the {@link Alias}
* @returns promise of an {Array} with list of {@link LayoutAlias} information
- * for a given {@link Alias} in all currently visualized layouts
+ * for a given {@link Alias} in all currently visualized overlays
*/
AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function (aliasId) {
var self = this;
return self.getTopMap().getVisibleDataOverlays().then(function (visibleDataOverlays) {
var result = [];
for (var i = 0; i < visibleDataOverlays.length; i++) {
- var layout = visibleDataOverlays[i];
- result.push(layout.getFullAliasById(aliasId));
+ var overlay = visibleDataOverlays[i];
+ result.push(overlay.getFullAliasById(aliasId));
}
return Promise.all(result);
});
@@ -987,13 +987,13 @@ AbstractCustomMap.prototype.getPictureSize = function () {
};
/**
- * Returns array containing elements that are presented on a specific layout
+ * Returns array containing elements that are presented on a specific overlay
* (set of google map objects representing lines/areas that are associated with
- * layout).
+ * overlay).
*
* @returns {Array} containing elements that are presented on a specific
- * layout (set of google map objects representing lines/areas that are
- * associated with layout).
+ * overlay (set of google map objects representing lines/areas that are
+ * associated with overlay).
*/
AbstractCustomMap.prototype.getSelectedLayoutOverlays = function () {
return this.selectedLayoutOverlays;
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 66a7fa93f2bddba5982dd6b141959fb29bfdb4dc..86759aabadc7a88a0b3830a13c8bf36c4bbd41b2 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -415,20 +415,20 @@ CustomMap.prototype.openSubmap = function (id) {
// we have to perform it on top map, because on submaps id is different
return this.openDataOverlay(self.getGoogleMap().getMapTypeId()).then(function () {
if (!wasInitialized) {
- // now we have to visualize layouts
- var layouts = [];
+ // now we have to visualize overlays
+ var overlayIds = [];
- // get list of layouts
+ // get list of overlays
for (var key in self._selectedOverlays) {
if (self._selectedOverlays.hasOwnProperty(key) && self._selectedOverlays[key] === true) {
- layouts.push(key);
+ overlayIds.push(key);
}
}
- // show layouts that should be visualized (resize or show them)
- for (var i = 0; i < layouts.length; i++) {
- var layoutId = layouts[i];
- submap._showSelectedDataOverlay(layoutId, i, layouts.length);
+ // show overlays that should be visualized (resize or show them)
+ for (var i = 0; i < overlayIds.length; i++) {
+ var overlayId = overlayIds[i];
+ submap._showSelectedDataOverlay(overlayId, i, overlayIds.length);
}
return self.refreshMarkers(true);
}
@@ -482,7 +482,7 @@ CustomMap.prototype.createMapChangedCallbacks = function () {
var self = this;
var sessionData = ServerConnector.getSessionData(self.getProject());
- // listener for changing type of layout
+ // listener for changing type of background overlay
google.maps.event.addListener(self.getGoogleMap(), 'maptypeid_changed', function () {
sessionData.setSelectedBackgroundOverlay(self.getGoogleMap().getMapTypeId());
});
@@ -520,15 +520,15 @@ CustomMap.prototype.removeSelection = function () {
};
/**
- * Removes layout from visualization.
+ * Removes overlay from visualization.
*
* @param identifier
- * identifier of layout to remove
+ * identifier of overlay to remove
*
*/
CustomMap.prototype.hideDataOverlay = function (identifier) {
var self = this;
- logger.debug("Removing layout: " + identifier);
+ logger.debug("Hiding overlay: " + identifier);
if (this._selectedOverlays[identifier] !== true) {
logger.warn("Overlay " + identifier + " is not selected");
@@ -553,7 +553,7 @@ CustomMap.prototype.hideDataOverlay = function (identifier) {
};
/**
- * Refresh visualization of selected layouts.
+ * Redrawing selected overlays.
*/
CustomMap.prototype.redrawSelectedDataOverlays = function () {
logger.debug("Redrawing overlays");
@@ -585,81 +585,81 @@ CustomMap.prototype.redrawSelectedDataOverlays = function () {
};
/**
- * Hides layout from the map and all submaps
+ * Hides overlay on the map and all submaps
*
- * @param layoutId
- * identifier of a layout to hide
+ * @param overlayId
+ * identifier of a overlay to hide
*/
-CustomMap.prototype.hideSelectedLayout = function (layoutId) {
- this._hideSelectedLayout(layoutId);
+CustomMap.prototype.hideSelectedLayout = function (overlayId) {
+ this._hideSelectedLayout(overlayId);
for (var i = 0; i < this.submaps.length; i++) {
- this.submaps[i]._hideSelectedLayout(layoutId);
+ this.submaps[i]._hideSelectedLayout(overlayId);
}
};
/**
- * Resize(refresh) layout on the map and all submaps. Resizing should be called
- * when number of layouts to visualize change.
+ * Resize(refresh) overlay on the map and all submaps. Resizing should be called
+ * when number of overlays to visualize change.
*
- * @param layoutId
- * identifier of layout to refresh
+ * @param overlayId
+ * identifier of overlay to refresh
* @param index
- * position of the layout in list of layouts that we visualize
+ * position of the overlay in list of overlays that we visualize
* @param length
- * number of layouts that we currently visualize
+ * number of overlays that we currently visualize
*/
-CustomMap.prototype.resizeSelectedDataOverlay = function (layoutId, index, length) {
- logger.debug("Resize layout: " + layoutId);
+CustomMap.prototype.resizeSelectedDataOverlay = function (overlayId, index, length) {
+ logger.debug("Resize overlay: " + overlayId);
var promises = [];
- promises.push(this._resizeSelectedDataOverlay(layoutId, index, length));
+ promises.push(this._resizeSelectedDataOverlay(overlayId, index, length));
for (var i = 0; i < this.submaps.length; i++) {
- promises.push(this.submaps[i]._resizeSelectedDataOverlay(layoutId, index, length));
+ promises.push(this.submaps[i]._resizeSelectedDataOverlay(overlayId, index, length));
}
return Promise.all(promises);
};
/**
- * Show layout on the map and all submaps.
+ * Show overlay on the map and all submaps.
*
- * @param layoutId
- * identifier of layout to show
+ * @param overlayId
+ * identifier of overlay to show
* @param index
- * position of the layout in list of layouts that we visualize
+ * position of the overlay in list of overlays that we visualize
* @param length
- * number of layouts that we currently visualize
+ * number of overlays that we currently visualize
*/
-CustomMap.prototype.showSelectedDataOverlay = function (layoutId, index, length) {
- logger.debug("Resize layout: " + layoutId);
+CustomMap.prototype.showSelectedDataOverlay = function (overlayId, index, length) {
+ logger.debug("Show overlay: " + overlayId);
var promises = [];
- promises.push(this._showSelectedDataOverlay(layoutId, index, length));
+ promises.push(this._showSelectedDataOverlay(overlayId, index, length));
for (var i = 0; i < this.submaps.length; i++) {
- promises.push(this.submaps[i]._showSelectedDataOverlay(layoutId, index, length));
+ promises.push(this.submaps[i]._showSelectedDataOverlay(overlayId, index, length));
}
return Promise.all(promises);
};
/**
- * This method checks if the layout contains any overlays (like AliasSurface or
+ * This method checks if the overlay contains any overlays (like AliasSurface or
* ReactionSurface) that is currently visible on the map.
*
- * @param layoutId
- * identifier of the layout
- * @returns {Boolean}: <code>true</code> if the layout contains overlays to
+ * @param overlayId
+ * identifier of the overlay
+ * @returns {Boolean}: <code>true</code> if the overlay contains overlays to
* visualize, <code>false</code> otherwise
*/
-CustomMap.prototype.layoutContainsOverlays = function (layoutId) {
+CustomMap.prototype.layoutContainsOverlays = function (overlayId) {
// first, check top map
- if (this.selectedLayoutOverlays.hasOwnProperty(layoutId) && this.selectedLayoutOverlays[layoutId].length > 0) {
+ if (this.selectedLayoutOverlays.hasOwnProperty(overlayId) && this.selectedLayoutOverlays[overlayId].length > 0) {
return true;
}
// now check all submaps
for (var i = 0; i < this.submaps.length; i++) {
if (this.submaps[i].initialized) {
- if (this.submaps[i].selectedLayoutOverlays.hasOwnProperty(layoutId)
- && this.submaps[i].selectedLayoutOverlays[layoutId].length > 0) {
+ if (this.submaps[i].selectedLayoutOverlays.hasOwnProperty(overlayId)
+ && this.submaps[i].selectedLayoutOverlays[overlayId].length > 0) {
return true;
}
}
diff --git a/frontend-js/src/main/js/map/data/DataOverlay.js b/frontend-js/src/main/js/map/data/DataOverlay.js
index 3231fc430dbb0c520ef019ff3108a5a0c4d2c7fb..a859fe054c2e50dd300201a31b05280bcecc4803 100644
--- a/frontend-js/src/main/js/map/data/DataOverlay.js
+++ b/frontend-js/src/main/js/map/data/DataOverlay.js
@@ -8,14 +8,14 @@ var LayoutReaction = require('./LayoutReaction');
var logger = require('../../logger');
/**
- * Class representing data in a specific layout.
+ * Class representing data in a specific overlay.
*/
-function DataOverlay(layoutId, name) {
+function DataOverlay(overlayId, name) {
this.setInitialized(false);
if (name === undefined) {
// from json structure
- var object = layoutId;
+ var object = overlayId;
this.setId(object.idObject);
this.setOrder(object.order);
this.setName(object.name);
@@ -33,7 +33,7 @@ function DataOverlay(layoutId, name) {
}
} else {
// default two param call
- this.setId(layoutId);
+ this.setId(overlayId);
this.setName(name);
}
this.aliases = [];
@@ -44,22 +44,22 @@ function DataOverlay(layoutId, name) {
/**
* Adds alias to the {@link DataOverlay}
*
- * @param layoutAlias
- * information about alias in a layout
+ * @param overlayAlias
+ * information about alias in the overlay
*/
-DataOverlay.prototype.addAlias = function (layoutAlias) {
- this.aliases.push(layoutAlias);
- this.aliasById[layoutAlias.getId()] = layoutAlias;
+DataOverlay.prototype.addAlias = function (overlayAlias) {
+ this.aliases.push(overlayAlias);
+ this.aliasById[overlayAlias.getId()] = overlayAlias;
};
/**
* Adds reaction to the {@link DataOverlay}
*
- * @param layoutReaction
- * information about reaction in a layout
+ * @param overlayReaction
+ * information about reaction in the overlay
*/
-DataOverlay.prototype.addReaction = function (layoutReaction) {
- this.reactions.push(layoutReaction);
+DataOverlay.prototype.addReaction = function (overlayReaction) {
+ this.reactions.push(overlayReaction);
};
DataOverlay.prototype.getId = function () {
@@ -126,11 +126,11 @@ DataOverlay.prototype.setImagesDirectory = function (imagesDirectory) {
this._imagesDirectory = imagesDirectory;
};
-DataOverlay.prototype.updateAlias = function (layoutAlias) {
- if (this.aliasById[layoutAlias.getId()] === undefined) {
- logger.warn("Cannot update alias, it doesn't exist. Alias: ", layoutAlias.getId());
+DataOverlay.prototype.updateAlias = function (overlayAlias) {
+ if (this.aliasById[overlayAlias.getId()] === undefined) {
+ logger.warn("Cannot update alias, it doesn't exist. Alias: ", overlayAlias.getId());
} else {
- this.aliasById[layoutAlias.getId()].update(layoutAlias);
+ this.aliasById[overlayAlias.getId()].update(overlayAlias);
}
};
diff --git a/frontend-js/src/main/js/map/data/LayoutAlias.js b/frontend-js/src/main/js/map/data/LayoutAlias.js
index 7527d6ec9543f81478cd64890e107fedf260c307..d41d52b7bc5f173f05a86fd859876b6fafb04646 100644
--- a/frontend-js/src/main/js/map/data/LayoutAlias.js
+++ b/frontend-js/src/main/js/map/data/LayoutAlias.js
@@ -3,8 +3,8 @@
var GeneVariant = require('./GeneVariant');
/**
- * Class representing alias visualized in a layout.
- *
+ * Class representing alias visualized in a overlay.
+ *
* @param javaObject
* object de-serialized ajax query to the server side
*/
@@ -21,7 +21,7 @@ function LayoutAlias(javaObject) {
} else if (javaObject.type === LayoutAlias.GENERIC) {
this.setType(LayoutAlias.GENERIC);
} else {
- throw new Error("Unknown type: ", javaObject.type);
+ throw new Error("Unknown type: " + javaObject.type);
}
this.setGeneVariants([]);
@@ -36,55 +36,55 @@ LayoutAlias.LIGHT = "LIGHT";
LayoutAlias.GENETIC_VARIANT = "GENETIC_VARIANT";
LayoutAlias.GENERIC = "GENERIC";
-LayoutAlias.prototype.getId = function() {
+LayoutAlias.prototype.getId = function () {
return this.id;
};
-LayoutAlias.prototype.setId = function(id) {
+LayoutAlias.prototype.setId = function (id) {
this.id = parseInt(id);
};
-LayoutAlias.prototype.getModelId = function() {
+LayoutAlias.prototype.getModelId = function () {
return this._modelId;
};
-LayoutAlias.prototype.setModelId = function(modelId) {
+LayoutAlias.prototype.setModelId = function (modelId) {
this._modelId = parseInt(modelId);
};
-LayoutAlias.prototype.getValue = function() {
+LayoutAlias.prototype.getValue = function () {
return this.value;
};
-LayoutAlias.prototype.getColor = function() {
+LayoutAlias.prototype.getColor = function () {
return this.color;
};
-LayoutAlias.prototype.getType = function() {
+LayoutAlias.prototype.getType = function () {
return this._type;
};
-LayoutAlias.prototype.getGeneVariants = function() {
+LayoutAlias.prototype.getGeneVariants = function () {
return this._geneVariants;
};
-LayoutAlias.prototype.setValue = function(newValue) {
+LayoutAlias.prototype.setValue = function (newValue) {
this.value = newValue;
};
-LayoutAlias.prototype.setColor = function(newColor) {
+LayoutAlias.prototype.setColor = function (newColor) {
this.color = newColor;
};
-LayoutAlias.prototype.setType = function(newType) {
+LayoutAlias.prototype.setType = function (newType) {
this._type = newType;
};
-LayoutAlias.prototype.setGeneVariants = function(newGeneVariants) {
+LayoutAlias.prototype.setGeneVariants = function (newGeneVariants) {
this._geneVariants = newGeneVariants;
};
-LayoutAlias.prototype.update = function(alias) {
+LayoutAlias.prototype.update = function (alias) {
if (!(alias instanceof LayoutAlias)) {
throw new Error("Unknown parameter type: " + alias);
}
@@ -96,15 +96,15 @@ LayoutAlias.prototype.update = function(alias) {
this.setDescription(alias.getDescription());
};
-LayoutAlias.prototype.addGeneVariant = function(geneVariant) {
+LayoutAlias.prototype.addGeneVariant = function (geneVariant) {
this._geneVariants.push(geneVariant);
};
-LayoutAlias.prototype.getDescription = function() {
+LayoutAlias.prototype.getDescription = function () {
return this._description;
};
-LayoutAlias.prototype.setDescription = function(description) {
+LayoutAlias.prototype.setDescription = function (description) {
this._description = description;
};
diff --git a/frontend-js/src/main/js/map/data/LayoutReaction.js b/frontend-js/src/main/js/map/data/LayoutReaction.js
index 58d3dfd3b64e616f84b4b6cc23adee03510c3624..4026262f1371b037036a02890a46d9f2e4d55802 100644
--- a/frontend-js/src/main/js/map/data/LayoutReaction.js
+++ b/frontend-js/src/main/js/map/data/LayoutReaction.js
@@ -1,7 +1,7 @@
"use strict";
/**
- * Class representing reaction visualized in a layout.
+ * Class representing reaction visualized in a overlay.
*
* @param javaObject
* object de-serialized from ajax query to the server side
diff --git a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
index a161dca5d6494cb96bfaa3a38014e807f9d32a2f..fd58a218b009deaeca57dddefcd4e934880baa29 100644
--- a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
+++ b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
@@ -6,7 +6,7 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
/**
* Class representing abstract overlay element on the map relevant for a
- * specific layout.
+ * specific overlay.
*/
function AbstractSurfaceElement(params) {
var self = this;
diff --git a/frontend-js/src/main/js/map/surface/AliasSurface.js b/frontend-js/src/main/js/map/surface/AliasSurface.js
index 888a7980f139b6afadc2d54b9b07dea8a19c78bf..2aba79b1b4b7c05eb39b9ea80ed4a016b224e08d 100644
--- a/frontend-js/src/main/js/map/surface/AliasSurface.js
+++ b/frontend-js/src/main/js/map/surface/AliasSurface.js
@@ -72,7 +72,7 @@ AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
* <li>map - {@link AbstractCustomMap} where overlay should be placed
* <li> startX - this is the ratio on OX axis that should be use as a
* starting point of the overlay. For instance when there are three
- * layouts to visualize then
+ * overlays to visualize then
* <ul>
* <li>the first layout have startX=0.0; endX=0.33333</li>
* <li>second layout have startX=0.33333; endX=0.66666</li>
diff --git a/frontend-js/src/main/js/map/surface/ReactionSurface.js b/frontend-js/src/main/js/map/surface/ReactionSurface.js
index 58748537d193ee03bb53accf1092483d5653f6a2..1d93d2ec71ea843d916f55e4abb01fd950a84329 100644
--- a/frontend-js/src/main/js/map/surface/ReactionSurface.js
+++ b/frontend-js/src/main/js/map/surface/ReactionSurface.js
@@ -10,22 +10,6 @@ var logger = require('../../logger');
var AbstractSurfaceElement = require('./AbstractSurfaceElement');
var IdentifiedElement = require('../data/IdentifiedElement');
-/**
- * Class representing overlay of the reaction on the map relevant for a specific
- * layout.
- *
- * @param layoutReaction
- * {@link LayoutReaction} for which overlay is created
- * @param reactionData
- * {@link Reaction data} of the reaction
- * @param map
- * {@link AbstractCustomMap} where overlay should be placed
- * @param customized
- * if true then coloring from layoutReaction is taken, if false then
- * default is used. Second option is used when more than one layout is
- * visualized (there is no simple way to visualize few layouts at the
- * same time)
- */
function ReactionSurface(params) {
// call super constructor
AbstractSurfaceElement.call(this, params);
@@ -132,9 +116,9 @@ ReactionSurface.prototype.getWidth = function () {
};
/**
- * This function is used when some layouts are added/removed from visualization.
+ * This function is used when some overlays are added/removed from visualization.
* The syntax is compatible with AliasSurface class so they can be handled in
- * the same way. When visualizing more than one layout startX or endX will be
+ * the same way. When visualizing more than one overlay startX or endX will be
* set to a value between 0..1 (not inclusive). In such case the visualization
* of reaction should turn to some default mode where we know that reaction is
* highlighted, but we have no more information. In this way user will know that
@@ -143,12 +127,12 @@ ReactionSurface.prototype.getWidth = function () {
* @param startX
* see {AliasSurface} class for details, in this implementation the
* only important information is that when there are more than one
- * layout visualized at least one of the two parameters (startX,endX)
+ * overlay visualized at least one of the two parameters (startX,endX)
* will differ from {0.0, 1.0} values
* @param endX
* see {AliasSurface} class for details, in this implementation the
* only important information is that when there are more than one
- * layout visualized at least one of the two parameters (startX,endX)
+ * overlay visualized at least one of the two parameters (startX,endX)
* will differ from {0.0, 1.0} values
*/
ReactionSurface.prototype.setBoundsForAlias = function (startX, endX) {
@@ -161,7 +145,7 @@ ReactionSurface.prototype.setBoundsForAlias = function (startX, endX) {
/**
* Changes visualization of the ReactionSurface to default mode where we mark
- * reaction as highlighted, but we skip customized reaction layout data.
+ * reaction as highlighted, but we skip customized reaction overlay data.
*/
ReactionSurface.prototype.changedToDefault = function () {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
@@ -175,7 +159,7 @@ ReactionSurface.prototype.changedToDefault = function () {
/**
* Changes visualization of the ReactionSurface to customized mode where we mark
- * reaction as highlighted with customized reaction layout data.
+ * reaction as highlighted with customized reaction overlay data.
*/
ReactionSurface.prototype.changedToCustomized = function () {
for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
diff --git a/frontend-js/src/main/js/map/window/AliasInfoWindow.js b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
index 7edbbd32bd8b25d20a6865be01c67e4a975a03e3..bae098392d7fc16b15a8c3b579c855ad86f84dac 100644
--- a/frontend-js/src/main/js/map/window/AliasInfoWindow.js
+++ b/frontend-js/src/main/js/map/window/AliasInfoWindow.js
@@ -68,10 +68,10 @@ AliasInfoWindow.prototype.init = function () {
/**
* Creates and returns chart representing data related to alias on different
- * layouts.
+ * overlays.
*
* @returns {String} html string representing chart with data related to alias
- * on different layouts
+ * on different overlays
*/
AliasInfoWindow.prototype.createChartDiv = function () {
var result = document.createElement("div");
@@ -184,9 +184,9 @@ AliasInfoWindow.prototype.createContentDiv = function () {
title.innerHTML = alias.getType() + ": " + alias.getName();
result.appendChild(title);
- var layoutsDiv = document.createElement("div");
+ var overlayDiv = document.createElement("div");
- result.appendChild(layoutsDiv);
+ result.appendChild(overlayDiv);
return self.getCustomMap().getAliasVisibleLayoutsData(alias.getId()).then(function (layoutAliases) {
self.layoutAliases = layoutAliases;
@@ -198,10 +198,10 @@ AliasInfoWindow.prototype.createContentDiv = function () {
}
return self.createChartDiv();
}).then(function (chartDiv) {
- layoutsDiv.appendChild(chartDiv);
+ overlayDiv.appendChild(chartDiv);
return self.createGenomicDiv();
}).then(function (genomicDiv) {
- layoutsDiv.appendChild(genomicDiv);
+ overlayDiv.appendChild(genomicDiv);
return result;
});
} else {
@@ -331,7 +331,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
name: self.layoutNames[iter] + ' - Variants',
options: {
variantHeightByFrequency: true
- },
+ }
});
}
}
diff --git a/frontend-js/src/test/js/minerva-test.js b/frontend-js/src/test/js/minerva-test.js
index 038a8b0a54fd7bd49e74dd0763c18a722d3ac2d2..1a149f451c1750d1d9f43924c1d8f33993f926b7 100644
--- a/frontend-js/src/test/js/minerva-test.js
+++ b/frontend-js/src/test/js/minerva-test.js
@@ -125,8 +125,8 @@ describe('minerva global', function () {
});
});
- it('create with layout', function () {
- var layout, project, plugin, map;
+ it('create with overlay', function () {
+ var overlay, project, plugin, map;
return ServerConnectorMock.getProject().then(function (result) {
project = result;
var options = helper.createCustomMapOptions(project);
@@ -134,9 +134,9 @@ describe('minerva global', function () {
plugin = new ProxyAccessPlugin({});
options.getPlugins().push(plugin);
- layout = project.getDataOverlays()[1];
+ overlay = project.getDataOverlays()[1];
- helper.setUrl("http://test/?layout=" + layout.getName());
+ helper.setUrl("http://test/?layout=" + overlay.getName());
return minerva.create(options);
}).then(function (result) {
@@ -147,7 +147,7 @@ describe('minerva global', function () {
}).then(function (visibleDataOverlays) {
// input file is available so it's not the background file but overlay
assert.equal(visibleDataOverlays.length, 0);
- assert.equal(ServerConnectorMock.getSessionData(project).getSelectedBackgroundOverlay(), layout.getId());
+ assert.equal(ServerConnectorMock.getSessionData(project).getSelectedBackgroundOverlay(), overlay.getId());
assert.equal(logger.getWarnings().length, 0);
return map.destroy();
});
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
index be5c1fe1220fc167f988761be1372ee0f4a965f9..b214a50ab832d9ca984fe23612d4a8fd5b2034d6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
@@ -39,12 +39,12 @@ public enum PrivilegeType {
/**
* User can have custom layouts (access level defines how many).
*/
- CUSTOM_LAYOUTS(BasicPrivilege.class, null, "Custom layouts", true),
+ CUSTOM_LAYOUTS(BasicPrivilege.class, null, "Custom overlays", true),
/**
* User can view non-public layout.
*/
- LAYOUT_VIEW(ObjectPrivilege.class, Layout.class, "View layout"),
+ LAYOUT_VIEW(ObjectPrivilege.class, Layout.class, "View overlay"),
/**
* User can manage configuration.
@@ -54,7 +54,7 @@ public enum PrivilegeType {
/**
* User can manage layouts of all users in the project.
*/
- LAYOUT_MANAGEMENT(ObjectPrivilege.class, Project.class, "Manage layouts"), //
+ LAYOUT_MANAGEMENT(ObjectPrivilege.class, Project.class, "Manage overlays"), //
/**
* User can manage reference genomes.