Provided API for 'iVis-at-Bilkent/newt#9'

README.md

@@ -79,19 +79,15 @@ edge.data('bendPointPositions'); // Bend point positions of an edge. Includes x
 ## API
 ChiSE.js is built at the top of SBGNViz.js and any method exposed by SBGNViz.js is exposed in ChiSE.js as well ([SBGNViz.js API](https://github.com/iVis-at-Bilkent/sbgnviz.js#api)). Other ChiSE.js API is presented below.
 
-`chise.startSpinner(classname)`
-Starts a spinner at the middle of network container element. You can specify a css class that the 
-spinner will have. The default classname is 'default-class'. Requires 'fontawesome.css'.
-
-`chise.endSpinner(classname)`
-Ends any spinner having a css class with the given name. Requires 'fontawesome.css'.
-
 `chise.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)`
 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)`
+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)`
 Clone given elements. Considers undoable option. Requires cytoscape-clipboard extension.
 
@@ -168,6 +164,7 @@ General and sbgn specific utilities for cytoscape elements. Extends `sbgnviz.ele
  * `defaultProperties` Access the default properties for elements by their classes using this map. These properties are considered in addNode() and addEdge().
  * `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.
  * `removeCompound(compoundToRemove)` Similar to `chise.removeCompound()` but do not considers undoable option.
  * `changeParent(nodes, newParent, posDiffX, posDiffY)` Similar to `chise.changeParent()` but do not considers undoable option.
@@ -205,7 +202,7 @@ Functions to be utilized in defining new actions for `cytoscape.js-undo-redo` ex
 an extension library of chise. Extends `sbgnviz.undoRedoActionFunctions`, you can find the ChiSE extensions for `sbgnviz.undoRedoActionFunctions` below.
 
  * `addNode(param)` Do/Redo function for 'addNode' undo redo command.
- * `addEdge(param)` Do/Redo function for 'addEdge' undo redo command.
+ * `addProcessWithConvenientEdges(param)` Do/Redo function for 'addProcessWithConvenientEdges' undo redo command.
  * `createCompoundForGivenNodes(param)` Do/Redo function for 'createCompoundForGivenNodes' undo redo command.
  * `removeCompound(param)` Undo function for 'createCompoundForGivenNodes' undo redo command.
  * `createTemplateReaction(param)` Do/Redo function for 'createTemplateReaction' undo redo command.

src/utilities/element-utilities.js

@@ -204,6 +204,32 @@ elementUtilities.addEdge = function (source, target, sbgnclass, id, visibility)
   return newEdge;
 };
 
+elementUtilities.addProcessWithConvenientEdges = function(_source, _target, processType) {
+  // If source and target IDs are given get the elements by IDs
+  var source = typeof _source === 'string' ? cy.getElementById(_source) : _source;
+  var target = typeof _target === 'string' ? cy.getElementById(_target) : _target;
+
+  // Process parent should be the closest common ancestor of the source and target nodes
+  var processParent = cy.collection([source[0], target[0]]).commonAncestors().first();
+
+  // Process should be at the middle of the source and target nodes
+  var x = ( source.position('x') + target.position('x') ) / 2;
+  var y = ( source.position('y') + target.position('y') ) / 2;
+
+  // Create the process with given/calculated variables
+  var process = elementUtilities.addNode(x, y, processType, undefined, processParent.id());
+
+  // Create the edges one is between the process and the source node (which should be a consumption), 
+  // the other one is between the process and the target node (which should be a production).
+  // For more information please refer to SBGN-PD reference card.
+  var edgeBtwSrc = elementUtilities.addEdge(source.id(), process.id(), 'consumption');
+  var edgeBtwTgt = elementUtilities.addEdge(process.id(), target.id(), 'production');
+
+  // Create a collection including the elements and to be returned
+  var collection = cy.collection([process[0], edgeBtwSrc[0], edgeBtwTgt[0]]);
+  return collection;
+};
+
 /*
  * This method assumes that param.nodesToMakeCompound contains at least one node
  * and all of the nodes including in it have the same parent. It creates a compound fot the given nodes an having the given type.

src/utilities/main-utilities.js

@@ -67,6 +67,34 @@ mainUtilities.addEdge = function(source, target , edgeclass, id, visibility) {
   }
 };
 
+/*
+ * Adds a process with convenient edges. For more information please see 'https://github.com/iVis-at-Bilkent/newt/issues/9'.
+ * Considers undoable option.
+ */
+mainUtilities.addProcessWithConvenientEdges = function(_source, _target, processType) {
+  // If source and target IDs are given get the elements by IDs
+  var source = typeof _source === 'string' ? cy.getElementById(_source) : _source;
+  var target = typeof _target === 'string' ? cy.getElementById(_target) : _target;
+
+  // If source or target does not have an EPN class the operation is not valid
+  if (!elementUtilities.isEPNClass(source) || !elementUtilities.isEPNClass(target)) {
+    return;
+  }
+
+  if (!options.undoable) {
+    return elementUtilities.addProcessWithConvenientEdges(_source, _target, processType);
+  }
+  else {
+    var param = {
+      source: _source,
+      target: _target,
+      processType: processType
+    };
+
+    cy.undoRedo().do("addProcessWithConvenientEdges", param);
+  }
+};
+
 /*
  * Clone given elements. Considers undoable option. Requires cytoscape-clipboard extension.
  */

src/utilities/register-undo-redo-actions.js

@@ -12,6 +12,7 @@ var registerUndoRedoActions = function (undoableDrag) {
   ur.action("addNode", undoRedoActionFunctions.addNode, undoRedoActionFunctions.deleteElesSimple);
   ur.action("deleteElesSimple", undoRedoActionFunctions.deleteElesSimple, undoRedoActionFunctions.restoreEles);
   ur.action("addEdge", undoRedoActionFunctions.addEdge, undoRedoActionFunctions.deleteElesSimple);
+  ur.action("addProcessWithConvenientEdges", undoRedoActionFunctions.addProcessWithConvenientEdges, undoRedoActionFunctions.deleteElesSimple);
   ur.action("deleteElesSmart", undoRedoActionFunctions.deleteElesSmart, undoRedoActionFunctions.restoreEles);
   ur.action("createCompoundForGivenNodes", undoRedoActionFunctions.createCompoundForGivenNodes, undoRedoActionFunctions.removeCompound);
 

src/utilities/undo-redo-action-functions.js

@@ -37,6 +37,20 @@ undoRedoActionFunctions.addEdge = function (param) {
   };
 };
 
+undoRedoActionFunctions.addProcessWithConvenientEdges = function(param) {
+  var result;
+  if (param.firstTime) {
+    result = elementUtilities.addProcessWithConvenientEdges(param.source, param.target, param.processType);
+  }
+  else {
+    result = elementUtilities.restoreEles(param);
+  }
+
+  return {
+    eles: result
+  };
+};
+
 undoRedoActionFunctions.createCompoundForGivenNodes = function (param) {
   var nodesToMakeCompound = param.nodesToMakeCompound;
   var newCompound;