chise - npm Package Compare versions

Comparing version 1.0.2 to 1.1.0

package.json

 {
   "name": "chise",
-  "version": "1.0.2",
+  "version": "1.1.0",
   "description": "SBGNPD editing library",
@@ -5,0 +5,0 @@ "main": "src/index.js",

README.md

@@ -30,2 +30,6 @@ # ChiSE version 1
         },
+        // Whether to infer nesting on load 
+        inferNestingOnLoad: function () {
+          return false;
+        },
         // percentage used to calculate compound paddings
@@ -92,31 +96,43 @@ compoundPadding: function () {
 
-`chise.addNode(x, y , nodeclass, id, parent, visibility)`
+`chise.register(options)`
+Register with libraries before creating instances
+
+`var instance = chise(options)`
+Creates an extension instance with the given options
+
+`instance.getSbgnvizInstance()`
+Get the Sbgnviz.js instance created for this Chise.js instance.
+
+`instance.getCy()`
+Get the Cytoscape.js instance created for this Chise.js instance.
+
+`instance.addNode(x, y , nodeclass, id, parent, visibility)`
 Adds a new node with the given class and at the given coordinates. Optionally you can set the id, parent and visibility of the node. Considers undoable option.
 
-`chise.addEdge(source, target , edgeclass, id, visibility)`
+`instance.addEdge(source, target , edgeclass, id, visibility)`
 Adds a new edge with the given class and having the given source and target ids. Optionally you can set the id and visibility of the node. Considers undoable option.
 
-`chise.addProcessWithConvenientEdges(source, target , processType)`
+`instance.addProcessWithConvenientEdges(source, target , processType)`
 Adds a process with convenient edges. For more information please see 'https://github.com/iVis-at-Bilkent/newt/issues/9'. Considers undoable option.
 
-`chise.cloneElements(eles)`
+`instance.cloneElements(eles)`
 Clone given elements. Considers undoable option. Requires cytoscape-clipboard extension.
 
-`chise.copyElements(eles)`
+`instance.copyElements(eles)`
 Copy given elements to clipboard. Requires cytoscape-clipboard extension.
 
-`chise.pasteElements(eles)`
+`instance.pasteElements(eles)`
 Paste the elements copied to clipboard. Considers undoable option. Requires cytoscape-clipboard extension.
 
-`chise.align(nodes, horizontal, vertical, alignTo)`
+`instance.align(nodes, horizontal, vertical, alignTo)`
 Aligns given nodes in given horizontal and vertical order. Horizontal and vertical parameters may be 'none' or undefined.<br>
 `alignTo`: indicates the leading node. Requires cytoscape-grid-guide extension and considers undoable option.
 
-`chise.createCompoundForGivenNodes(nodes, compoundType)`
+`instance.createCompoundForGivenNodes(nodes, compoundType)`
 Create compound for given nodes. compoundType may be 'complex' or 'compartment'. This method considers undoable option.
 
-`chise.changeParent(nodes, newParent, posDiffX, posDiffY)`
+`instance.changeParent(nodes, newParent, posDiffX, posDiffY)`
 Move the nodes to a new parent and change their position if possDiff params are set. Considers undoable option and checks if the operation is valid.
 
-`chise.createTemplateReaction(templateType, macromoleculeList, complexName, processPosition, tilingPaddingVertical, tilingPaddingHorizontal, edgeLength)`
+`instance.createTemplateReaction(templateType, macromoleculeList, complexName, processPosition, tilingPaddingVertical, tilingPaddingHorizontal, edgeLength)`
 Creates a template reaction with given parameters. Requires cose-bilkent layout to tile the free macromolecules included in the complex.
@@ -132,12 +148,12 @@ Considers undoable option. Parameters are explained below.<br>
 
-`chise.resizeNodes(nodes, newParent, posDiffX, posDiffY)`
+`instance.resizeNodes(nodes, newParent, posDiffX, posDiffY)`
 Resize given nodes if `useAspectRatio` is truthy one of width or height should not be set. Considers undoable option.
 
-`chise.changeNodeLabel(nodes, label)`
+`instance.changeNodeLabel(nodes, label)`
 Changes the label of the given nodes to the given label. Considers undoable option.
 
-`chise.changeFontProperties(nodes, data)`
+`instance.changeFontProperties(nodes, data)`
 Change font properties for given nodes use the given font data. Considers undoable option.
 
-`chise.changeStateOrInfoBox(nodes, index, value, type)`
+`instance.changeStateOrInfoBox(nodes, index, value, type)`
 Change state value or unit of information box of given nodes with given index. Considers undoable option.<br>
@@ -148,25 +164,25 @@ `type` indicates whether to change value or variable, it is valid if the box at the given index is a state variable.<br>
 
-`chise.addStateOrInfoBox(nodes, obj)`
+`instance.addStateOrInfoBox(nodes, obj)`
 Add a new state or info box to given `nodes`. The box is represented by the parameter `obj`. Considers undoable option.
 
-`chise.removeStateOrInfoBox(nodes, index)`
+`instance.removeStateOrInfoBox(nodes, index)`
 Remove the state or info boxes of the given `nodes` at given `index`. Considers undoable option.
 
-`chise.setMultimerStatus(nodes, status)`
+`instance.setMultimerStatus(nodes, status)`
 Set multimer status of the given `nodes` to the given `status`. Considers undoable option.
 
-`chise.setCloneMarkerStatus(nodes, status)`
+`instance.setCloneMarkerStatus(nodes, status)`
 Set clone marker status of given `nodes` to the given `status`. Considers undoable option.
 
-`chise.changeCss(eles, name, value)`
+`instance.changeCss(eles, name, value)`
 Change style/css of given `eles` by setting given property `name` to the given `value/values (Note that `value` parameter may be a single string or an id to value map). Considers undoable option. (From cytoscape.js documentation: 'You should use this function very sparingly, because it overrides the style of an element, despite the state and classes that it has.')
 
-`chise.changeData(eles, name, value)`
+`instance.changeData(eles, name, value)`
 Change data of given `eles` by setting given property `name` to the given value/values (Note that `value` parameter may be a single string or an id to value map). Considers undoable option.
 
-`chise.showAndPerformLayout(eles, layoutparam)`
-Unhide given `eles` and perform given layout afterward. `layoutparam` parameter may be layout options or a function to call. 
+`instance.showAndPerformLayout(eles, layoutparam)`
+Unhide given `eles` and perform given layout afterward. `layoutparam` parameter may be layout options or a function to call.
 Requires `viewUtilities` extension and considers undoable option.
 
-`chise.elementUtilities`
+`instance.elementUtilities`
 General and sbgn specific utilities for cytoscape elements. Extends `sbgnviz.elementUtilities`, you can find the ChiSE extensions for `sbgnviz.elementUtilities` below.
@@ -185,8 +201,8 @@
     'border-color': The default border color
- * `addNode(x, y, sbgnclass, id, parent, visibility)` Similar to `chise.addNode()` but do not considers undoable option.
- * `addEdge(source, target, sbgnclass, id, visibility)` Similar to `chise.addEdge()` but do not considers undoable option.
- * `addProcessWithConvenientEdges(source, target, processType)` Similar to `chise.addProcessWithConvenientEdges()` but do not considers undoable option.
- * `createCompoundForGivenNodes(nodesToMakeCompound, compoundType)` Similar to `chise.createCompoundForGivenNodes()` but do not considers undoable option.
- * `changeParent(nodes, newParent, posDiffX, posDiffY)` Similar to `chise.changeParent()` but do not considers undoable option.
- * `resizeNodes(nodes, width, height, useAspectRatio)` Similar to `chise.resizeNodes()` but do not considers undoable option.
+ * `addNode(x, y, sbgnclass, id, parent, visibility)` Similar to `instance.addNode()` but do not considers undoable option.
+ * `addEdge(source, target, sbgnclass, id, visibility)` Similar to `instance.addEdge()` but do not considers undoable option.
+ * `addProcessWithConvenientEdges(source, target, processType)` Similar to `instance.addProcessWithConvenientEdges()` but do not considers undoable option.
+ * `createCompoundForGivenNodes(nodesToMakeCompound, compoundType)` Similar to `instance.createCompoundForGivenNodes()` but do not considers undoable option.
+ * `changeParent(nodes, newParent, posDiffX, posDiffY)` Similar to `instance.changeParent()` but do not considers undoable option.
+ * `resizeNodes(nodes, width, height, useAspectRatio)` Similar to `instance.resizeNodes()` but do not considers undoable option.
  * `isValidParent(nodeClass, parentClass)` Returns if the elements with the given parent class can be parent of the elements with the given node class.
@@ -210,16 +226,16 @@ * `getCommonProperty(nodes, width, height, useAspectRatio)` Get common properties of given elements. Returns null if the given element list is empty or the property is not common for all elements.
  * `relocateStateAndInfos(ele)` Relocates the state and info boxes of the given node.
- * `changeStateOrInfoBox(nodes, index, value, type)` Similar to `chise.changeStateOrInfoBox()` but do not considers undoable option.
- * `addStateOrInfoBox(nodes, obj)` Similar to `chise.addStateOrInfoBox()` but do not considers undoable option.
- * `removeStateOrInfoBox(nodes, index)` Similar to `chise.removeStateOrInfoBox()` but do not considers undoable option.
- * `setMultimerStatus(nodes, status)` Similar to `chise.setMultimerStatus()` but do not considers undoable option.
- * `setCloneMarkerStatus(nodes, status)` Similar to `chise.setCloneMarkerStatus()` but do not considers undoable option.
- * `changeFontProperties(nodes, data)` Similar to `chise.changeFontProperties()` but do not considers undoable option.
+ * `changeStateOrInfoBox(nodes, index, value, type)` Similar to `instance.changeStateOrInfoBox()` but do not considers undoable option.
+ * `addStateOrInfoBox(nodes, obj)` Similar to `instance.addStateOrInfoBox()` but do not considers undoable option.
+ * `removeStateOrInfoBox(nodes, index)` Similar to `instance.removeStateOrInfoBox()` but do not considers undoable option.
+ * `setMultimerStatus(nodes, status)` Similar to `instance.setMultimerStatus()` but do not considers undoable option.
+ * `setCloneMarkerStatus(nodes, status)` Similar to `instance.setCloneMarkerStatus()` but do not considers undoable option.
+ * `changeFontProperties(nodes, data)` Similar to `instance.changeFontProperties()` but do not considers undoable option.
  * `validateArrowEnds(edge, source, target)`  This function gets an edge, and ends of that edge (Optionally it may take just the classes of these elements as well) as parameters.
     It may return 'valid' (that ends is valid for that edge), 'reverse' (that ends is not valid for that edge but they would be valid 
     if you reverse the source and target), 'invalid' (that ends are totally invalid for that edge).
- * `showAndPerformLayout(eles, layoutparam)` Similar to `chise.showAndPerformLayout()` but do not considers undoable option.
+ * `showAndPerformLayout(eles, layoutparam)` Similar to `instance.showAndPerformLayout()` but do not considers undoable option.
 
-`chise.undoRedoActionFunctions`
+`instance.undoRedoActionFunctions`
 Functions to be utilized in defining new actions for `cytoscape.js-undo-redo` extension. These are exposed for the users who builds
-an extension library of chise. Extends `sbgnviz.undoRedoActionFunctions`, you can find the ChiSE extensions for `sbgnviz.undoRedoActionFunctions` below.
+an extension library of chise. Extends `sbgnvizInstance.undoRedoActionFunctions`, you can find the ChiSE extensions for `sbgnvizInstance.undoRedoActionFunctions` below.
 
@@ -244,9 +260,9 @@ * `addNode(param)` Do/Redo function for 'addNode' undo redo command.
 ## Events
-`$(document).on('sbgnvizLoadSample', function(event, filename) { ... });` Triggered when a sample is being loaded
+`$(document).on('sbgnvizLoadSample', function(event, filename, cy) { ... });` Triggered when a sample is being loaded
 
-`$(document).on('sbgnvizLoadFile', function(event, filename) { ... });` Triggered when an external sbgnml file is being loaded
+`$(document).on('sbgnvizLoadFile', function(event, filename, cy) { ... });` Triggered when an external sbgnml file is being loaded
 
-`$(document).on('updateGraphStart', function(event) { ... });` Triggered when the graph update is just started
+`$(document).on('updateGraphStart', function(event, cy) { ... });` Triggered when the graph update is just started
 
-`$(document).on('updateGraphEnd', function(event) { ... });` Triggered when the graph update is ended
+`$(document).on('updateGraphEnd', function(event, cy) { ... });` Triggered when the graph update is ended
 
@@ -253,0 +269,0 @@ ## Dependencies

src/index.js

 (function(){
-  var chise = window.chise = function(_options, _libs) {
-    var libs = {};
-    libs.jQuery = _libs.jQuery || jQuery;
-    libs.cytoscape = _libs.cytoscape || cytoscape;
-    libs.sbgnviz = _libs.sbgnviz || sbgnviz;
-    libs.saveAs = _libs.filesaverjs ? _libs.filesaverjs.saveAs : saveAs;
-    
-    libs.sbgnviz(_options, _libs); // Initilize sbgnviz
-    
-    // Set the libraries to access them from any file
-    var libUtilities = require('./utilities/lib-utilities');
-    libUtilities.setLibs(libs);
-    
-    var optionUtilities = require('./utilities/option-utilities');
+  var chise = function(_options) {
+
+    var param = {};
+
+    // Access the libs
+    var libs = require('./utilities/lib-utilities').getLibs();
+
+    var optionUtilities = require('./utilities/option-utilities-factory')();
     var options = optionUtilities.extendOptions(_options); // Extends the default options with the given options
-    
+
+    // Create an sbgnviz instance
+    var sbgnvizInstanceUtilities = require('./utilities/sbgnviz-instance-utilities-factory')();
+    var sbgnvizInstance = sbgnvizInstanceUtilities(options);
+
     // Update style and bind events
-    var cyStyleAndEvents = require('./utilities/cy-style-and-events');
-    cyStyleAndEvents(libs.sbgnviz);
-    
+    var cyStyleAndEvents = require('./utilities/cy-style-and-events-factory')();
+
     // Register undo/redo actions
-    var registerUndoRedoActions = require('./utilities/register-undo-redo-actions');
-    registerUndoRedoActions(options.undoableDrag);
-    
-    var mainUtilities = require('./utilities/main-utilities');
-    var elementUtilities = require('./utilities/element-utilities');
-    var undoRedoActionFunctions = require('./utilities/undo-redo-action-functions');
-    
+    var registerUndoRedoActions = require('./utilities/register-undo-redo-actions-factory')();
+
+    var mainUtilities = require('./utilities/main-utilities-factory')();
+    var elementUtilitiesExtender = require('./utilities/element-utilities-extender-factory')();
+    var undoRedoActionFunctionsExtender = require('./utilities/ur-action-functions-extender-factory')();
+
+    var elementUtilities =  sbgnvizInstance.elementUtilities;
+    var undoRedoActionFunctions = sbgnvizInstance.undoRedoActionFunctions;
+
+    param.sbgnvizInstanceUtilities = sbgnvizInstanceUtilities;
+    param.optionUtilities = optionUtilities;
+    param.elementUtilities = elementUtilities;
+    param.undoRedoActionFunctions = undoRedoActionFunctions;
+
+    undoRedoActionFunctionsExtender(param);
+    elementUtilitiesExtender(param);
+    cyStyleAndEvents(param);
+    registerUndoRedoActions(param);
+    mainUtilities(param);
+
     // Expose the api
-    
+    var api = {};
+
     // Expose the properties inherited from sbgnviz
     // then override some of these properties and expose some new properties
-    for (var prop in libs.sbgnviz) {
-      chise[prop] = libs.sbgnviz[prop];
+    for (var prop in sbgnvizInstance) {
+      api[prop] = sbgnvizInstance[prop];
     }
-    
+
     // Expose each main utility seperately
     for (var prop in mainUtilities) {
-      chise[prop] = mainUtilities[prop];
+      api[prop] = mainUtilities[prop];
     }
-    
+
+    // Expose getSbgnvizInstance()
+    api.getSbgnvizInstance = sbgnvizInstanceUtilities.getInstance;
+
     // Expose elementUtilities and undoRedoActionFunctions as is
-    chise.elementUtilities = elementUtilities;
-    chise.undoRedoActionFunctions = undoRedoActionFunctions;
+    api.elementUtilities = elementUtilities;
+    api.undoRedoActionFunctions = undoRedoActionFunctions;
+
+    return api;
   };
-  
+
+  // Register chise with given libraries
+  chise.register = function (_libs) {
+
+    var libs = {};
+    libs.jQuery = _libs.jQuery || jQuery;
+    libs.cytoscape = _libs.cytoscape || cytoscape;
+    libs.sbgnviz = _libs.sbgnviz || sbgnviz;
+    libs.saveAs = _libs.filesaverjs ? _libs.filesaverjs.saveAs : saveAs;
+
+    libs.sbgnviz.register(_libs); // Register sbgnviz with the given libs
+
+    // Set the libraries to access them from any file
+    var libUtilities = require('./utilities/lib-utilities');
+    libUtilities.setLibs(libs);
+  };
+
   if ( typeof module !== 'undefined' && module.exports ) {
     module.exports = chise;
   }
-})();
+})();

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Improved metrics

Total package byte prevSize

508005

increased by9.27%

Lines of code

7306

increased by3.09%

Number of lines in readme file

325

increased by5.18%

Worsened metrics

Number of medium supply chain risk alerts

3

increased by50%

No dependency changes