Rename source and sink to empty set

iVis-at-Bilkent/newt#658
iVis-at-Bilkent · Jun 1, 2021 · ed33cfc · ed33cfc
1 parent deada2c
commit ed33cfc
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diff --git a/README.md b/README.md
@@ -405,7 +405,7 @@ library of sbgnviz. Most users will not need to use this. It includes the follow
 * `getSbgnClass(ele)`  Returns sbgnclass of the given element. If the parameter is a string return it by assuming that it is the sbgnclass itself. 
 * `getPureSbgnClass(ele)` Returns sbgn class omitting the multimer information.
 * `canHaveUnitOfInformation(ele)` Returns whether the give element have unit of information.
-* `isEmptySetClass(ele)` Returns wether the given element or string is of the special empty set/source and sink class.
+* `isEmptySetClass(ele)` Returns wether the given element or string is of the special empty set class.
 * `isModulationArcClass(ele)` Returns whether the class of given element is a modulation arc as defined in PD specs.
 * `convertToRenderedPosition(modelPos, pan, zoom)` Returns rendered position of a given model position.
 * `getArrayLineStyle(ele)` Returns whether the line style is dashed or solid.

diff --git a/sbgnviz.js b/sbgnviz.js
diff --git a/src/sbgn-extensions/sbgn-cy-renderer.js b/src/sbgn-extensions/sbgn-cy-renderer.js
@@ -136,7 +136,7 @@ module.exports = function () {
   };
 
   var sbgnShapes = $$.sbgn.sbgnShapes = {
-    'source and sink': true,
+    'empty set': true,
     'nucleic acid feature': true,
     'complex': true,
     'macromolecule': true,
@@ -470,7 +470,7 @@ module.exports = function () {
   };
 
   cyStyleProperties.types.nodeShape.enums.push(
-    'source and sink', 'nucleic acid feature', 'complex', 'macromolecule',
+    'empty set', 'nucleic acid feature', 'complex', 'macromolecule',
     'simple chemical', 'biological activity', 'compartment'
   );
 
@@ -606,7 +606,7 @@ module.exports = function () {
     }
 
     var shapeNames = [ "simple chemical", "macromolecule", "complex",
-      "nucleic acid feature", "source and sink", "biological activity",
+      "nucleic acid feature", "empty set", "biological activity",
       "compartment", "oldCompartment"
     ];
 
@@ -695,17 +695,17 @@ module.exports = function () {
     "macromolecule": $$.sbgn.drawRoundRectangle,
     "complex": $$.sbgn.drawComplex,
     "nucleic acid feature": $$.sbgn.drawBottomRoundRectangle,
-    "source and sink": $$.sbgn.drawEllipse,
+    "empty set": $$.sbgn.drawEllipse,
     "biological activity": $$.sbgn.drawBiologicalActivity,
     "compartment": $$.sbgn.drawBarrel,
     "oldCompartment": $$.sbgn.drawRoundRectangle
   };
 
   // To define an extra drawing for the node that is rendered at the very end,
   // even after the node background image is drawn.
-  // E.g. cross lines of "source and sink" nodes.
+  // E.g. cross lines of "empty set" nodes.
   $$.sbgn.extraDraw = {
-    "source and sink": $$.sbgn.drawCrossLine
+    "empty set": $$.sbgn.drawCrossLine
   };
 
   $$.sbgn.plainIntersectLine = {
@@ -727,7 +727,7 @@ module.exports = function () {
     "nucleic acid feature": function( centerX, centerY, width, height, x, y, padding ) {
       return cyBaseNodeShapes["bottomroundrectangle"].intersectLine( centerX, centerY, width, height, x, y, padding );
     },
-    "source and sink": function( centerX, centerY, width, height, x, y, padding ) {
+    "empty set": function( centerX, centerY, width, height, x, y, padding ) {
       return cyBaseNodeShapes["ellipse"].intersectLine( centerX, centerY, width, height, x, y, padding );
     },
     "biological activity": function( centerX, centerY, width, height, x, y, padding ) {
@@ -822,7 +822,7 @@ module.exports = function () {
     "nucleic acid feature": function( x, y, padding, width, height, centerX, centerY ) {
       return cyBaseNodeShapes["bottomroundrectangle"].checkPoint( x, y, padding, width, height, centerX, centerY );
     },
-    "source and sink": function( x, y, padding, width, height, centerX, centerY ) {
+    "empty set": function( x, y, padding, width, height, centerX, centerY ) {
       return cyBaseNodeShapes["ellipse"].checkPoint( x, y, padding, width, height, centerX, centerY );
     },
     "biological activity": function( x, y, padding, width, height, centerX, centerY ) {

diff --git a/src/utilities/element-utilities-factory.js b/src/utilities/element-utilities-factory.js
@@ -92,7 +92,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {},   asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true}},
@@ -113,7 +113,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {},   asTarget: {isAllowed: true}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {},   asTarget: {isAllowed: true}},
+      "empty set":            {asSource: {},   asTarget: {isAllowed: true}},
       "perturbing agent":     {asSource: {},   asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {isAllowed: true},    asTarget: {}},
@@ -134,7 +134,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {isAllowed: true},    asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true}},
@@ -155,7 +155,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {isAllowed: true},    asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true}},
@@ -176,7 +176,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {},   asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {},   asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true, maxEdge: 1}},
@@ -197,7 +197,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {isAllowed: true},    asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true}},
@@ -218,7 +218,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {isAllowed: true},    asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {isAllowed: true, maxEdge: 1}},
@@ -239,7 +239,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},    asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {}},
-      "source and sink":      {asSource: {isAllowed: true},    asTarget: {}},
+      "empty set":            {asSource: {isAllowed: true},    asTarget: {}},
       "perturbing agent":     {asSource: {},   asTarget: {}},
       "submap":               {asSource: {},   asTarget: {}},
       "process":              {asSource: {},   asTarget: {}},
@@ -260,7 +260,7 @@ module.exports = function () {
       "nucleic acid feature": {asSource: {isAllowed: true},   asTarget: {}},
       "compartment":          {asSource: {},   asTarget: {}},
       "tag":                  {asSource: {},   asTarget: {isAllowed: true}},
-      "source and sink":      {asSource: {},   asTarget: {}},
+      "empty set":            {asSource: {},   asTarget: {}},
       "perturbing agent":     {asSource: {},   asTarget: {}},
       "submap":               {asSource: {},   asTarget: {isAllowed: true}},
       "process":              {asSource: {},   asTarget: {}},
@@ -464,7 +464,7 @@ module.exports = function () {
     'BA simple chemical', 'BA macromolecule', 'BA nucleic acid feature',
     'BA perturbing agent', 'BA complex'];
   elementUtilities.epnTypes = ['macromolecule', 'nucleic acid feature', 'simple chemical',
-    'source and sink', 'unspecified entity', 'perturbing agent', 'complex', 
+    'empty set', 'unspecified entity', 'perturbing agent', 'complex', 
     'nucleic acid feature multimer', 'macromolecule multimer', 'simple chemical multimer', 'complex multimer'];
   elementUtilities.sifTypes = ['SIF macromolecule', 'SIF simple chemical'];
   elementUtilities.otherNodeTypes = ['compartment', 'tag', 'submap', 'topology group'];
@@ -614,7 +614,7 @@ module.exports = function () {
     var sbgnclass = elementUtilities.getPureSbgnClass( ele );
 
     return sbgnclass != 'and' && sbgnclass != 'or' && sbgnclass != 'not' && sbgnclass != 'delay'
-            && sbgnclass != 'association' && sbgnclass != 'dissociation' && sbgnclass != 'source and sink' && !sbgnclass.endsWith('process');
+            && sbgnclass != 'association' && sbgnclass != 'dissociation' && sbgnclass != 'empty set' && !sbgnclass.endsWith('process');
   };
 
   // Returns whether the give element have unit of information
@@ -656,7 +656,7 @@ module.exports = function () {
   elementUtilities.mustBeSquare = function (ele) {
     var sbgnclass = elementUtilities.getPureSbgnClass( ele );
 
-    return (sbgnclass.indexOf('process') != -1 || sbgnclass == 'source and sink'
+    return (sbgnclass.indexOf('process') != -1 || sbgnclass == 'empty set'
             || sbgnclass == 'and' || sbgnclass == 'or' || sbgnclass == 'not'
             || sbgnclass == 'association' || sbgnclass == 'dissociation' || sbgnclass == 'delay');
   };
@@ -745,10 +745,10 @@ module.exports = function () {
     return inArray( sbgnclass, elementUtilities.processTypes );
   };
 
-  // Returns wether the given element or string is of the special empty set/source and sink class
+  // Returns wether the given element or string is of the special empty set/empty set class
   elementUtilities.isEmptySetClass = function (ele) {
     var sbgnclass = elementUtilities.getPureSbgnClass( ele );
-    return sbgnclass == 'source and sink';
+    return sbgnclass == 'empty set';
   };
 
   // Returns whether the given element is a logical operator
@@ -1068,7 +1068,7 @@ module.exports = function () {
       }
 
       // We need to define new node shapes with their class names for these nodes
-      if (_class == 'source and sink' || _class == 'nucleic acid feature' || _class == 'macromolecule'
+      if (_class == 'empty set' || _class == 'nucleic acid feature' || _class == 'macromolecule'
               || _class == 'simple chemical' || _class == 'complex' || _class == 'biological activity' ) {
           return _class;
       }
@@ -2323,7 +2323,7 @@ module.exports = function () {
       width: 30,
       height: 30
     },
-    'source and sink': {
+    'empty set': {
       width: 22,
       height: 22
     },