minor docs

README.md

@@ -123,8 +123,8 @@ Heta compiler has been written in NodeJS environment and can be used as a packag
 ```javascript
 const { Container } = require('heta-compiler');
 
-// platform code in Queue format
-let queue = [
+// platform code in Q-array format
+let qArr = [
     { class: 'Compartment', id: 'comp1', assignments: {start_: '1'} },
     { class: 'Species', id: 's1', compartment: 'comp1', assignments: {start_: '10'} },
     { class: 'Reaction', id: 'r1', actors: 's1 =>', assignments: {ode_: 'k1*s1*comp1'} },
@@ -134,7 +134,7 @@ let queue = [
 
 // compilation
 let c = (new Container)
-    .loadMany(queue)
+    .loadMany(qArr)
     .knitMany();
 // get export element
 let output = c.exportStorage[0]

classes.uxf

@@ -0,0 +1,77 @@
+<diagram program="umletino" version="14.4.0-SNAPSHOT"><zoom_level>10</zoom_level><help_text>Space for diagram notes
+</help_text><element><id>UMLClass</id><coordinates><x>10</x><y>370</y><w>280</w><h>350</h></coordinates><panel_attributes>Container
+{}
+--
+- classes: Object.&lt;String,Constructor&gt;
+- logger: Logger
+- defaultLogs: Array.&lt;object&gt;
+- exportStorage: Map.&lt;string, _Export&gt;
+- unitDefStorage: Map.&lt;string, UnitDef&gt;
+- namespaceStorage: Map.&lt;string, Namespace&gt;
+- _componentClasses: &lt;String,Constructor&gt;
+- _exportClasses: &lt;String,Constructor&gt;
+
+--
+
+#export()
+#defineUnit()
+#insert()
+#update()
+#upsert()
+#delete()
+#import()
+#setNS()
+#importNS()
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>UMLClass</id><coordinates><x>360</x><y>520</y><w>210</w><h>110</h></coordinates><panel_attributes>Namespace extends Map
+{}
+--
+- _spaceName: String
+- container: Container
+- isAbstract: Boolean = false
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>Relation</id><coordinates><x>280</x><y>480</y><w>210</w><h>60</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>10;10;190;10;190;40</additional_attributes></element><element><id>UMLClass</id><coordinates><x>580</x><y>0</y><w>210</w><h>220</h></coordinates><panel_attributes>Top (Element)
+{}
+--
+- isCore: Boolean
+- _id: String
+- isRandomId: Boolean = false
+- _container: Container
+
+--
+
+#id
+#index
+#className
+#toQ()
+#toFlat()
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>UMLClass</id><coordinates><x>610</x><y>570</y><w>210</w><h>360</h></coordinates><panel_attributes>Component
+{}
+--
+- _id: String
+- namespace: Namespace
+- _isCore: Boolean = false
+- tags: Array.&lt;String&gt;
+- aux: Object
+- title: String
+- notes: String
+
+--
+
+#id
+#space
+#index
+#className
+#indexObj
+#notesHTML
+#clone()
+#updateReferences()
+#bind()
+#toQ()
+#toFlat()
+
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>Relation</id><coordinates><x>560</x><y>530</y><w>110</w><h>60</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>10;10;90;10;90;40</additional_attributes></element><element><id>UMLClass</id><coordinates><x>340</x><y>280</y><w>160</w><h>70</h></coordinates><panel_attributes>_Export
+{}
+--
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>UMLClass</id><coordinates><x>450</x><y>360</y><w>160</w><h>70</h></coordinates><panel_attributes>UnitDef
+{}
+--
+</panel_attributes><additional_attributes></additional_attributes></element><element><id>Relation</id><coordinates><x>280</x><y>340</y><w>150</w><h>130</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>10;110;130;110;130;10</additional_attributes></element><element><id>Relation</id><coordinates><x>280</x><y>420</y><w>270</w><h>70</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;&lt;-</panel_attributes><additional_attributes>10;50;250;50;250;10</additional_attributes></element><element><id>Relation</id><coordinates><x>410</x><y>210</y><w>280</w><h>90</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;-</panel_attributes><additional_attributes>260;10;260;40;10;40;10;70</additional_attributes></element><element><id>Relation</id><coordinates><x>520</x><y>210</y><w>210</w><h>170</h></coordinates><panel_attributes>lt=&lt;&lt;&lt;-</panel_attributes><additional_attributes>190;10;190;50;10;50;10;150</additional_attributes></element></diagram>

src/builder/index.js

@@ -114,10 +114,10 @@ class Builder {
         this.logger.info(`Meta file was saved to ${absPath}`);
       });
     }
-    let queue = ms.integrate();
+    let qArr = ms.integrate();
 
     // 3. Translation
-    this.container.loadMany(queue, false);
+    this.container.loadMany(qArr, false);
     //console.log([...this.container.unitDefStorage]); // XXX: debugging
 
     // 4. Binding

src/container/actions.js

@@ -534,7 +534,7 @@ Container.prototype.select = function(q = {}){
  * Calculates string formatted index.
  * Exampel: `{id: 'k1', space: 'one'}` => `'one::k1'`
  * 
- * @param {object} q Heta's element in queue format.
+ * @param {object} q Heta's element in Q-object format.
  * @returns {string} Get index of a component.
  */
 function getIndexFromQ(q = {}){

src/container/main.js

@@ -32,7 +32,7 @@ const TopoSort = require('@insysbio/topo-sort');
  * 
  * @property {object} classes Map-like storage for all element constructors that can be created inside platform.
  *    For example the element of the type `UnitsDef` can be created as follows:
- *    ```let new_unit = new c.UnitDef({id: 'new', units: 'g/litre'})```
+ *    ```let new_unit = new c.classes.UnitDef({id: 'new', units: 'g/litre'})```
  *    The `new_unit` element will be automatically bound to the container and pushed to `unitDefStorage`.
  * @property {Logger} logger object providing transport of errors, warnings and info messages on Heta platform level.
  * @property {object[]} defaultLogs Default storage of errors which will be used for diagnostics.
@@ -42,7 +42,8 @@ const TopoSort = require('@insysbio/topo-sort');
  * @property {Map<string,Namespace>} namespaceStorage Storage for `Namespace` instances. Key is a string identifier.
  *    There is a default namespace with identifier `nameless` which will be used as a default namespace 
  *    for all components where namespace name is not set.
- * @property {object} _componentClasses map-like structure for storing all available classes describing `Component`s.
+ * @property {object} _componentClasses map-like structure for storing all available constructors for `Component`s.
+ * @property {object} _exportClasses map-like structure for storing all available constructors describing `_Export`s.
  */
 class Container {
   /* constructor can be run many times */
@@ -105,7 +106,7 @@ class Container {
    * If `q.action` is not set than apply "upsert".
    * An "action" name should be set as a name of the `Container` method. 
    * 
-   * This is the main method to convert from elements of "queue" into platform elements.
+   * This is the main method to convert from Q-object into platform elements.
    * 
    * @param {object} q Simple object with the same structure as Heta plain format.
    * @param {boolean} isCore Set element as a "core" which means you cannot rewrite or delete it.
@@ -129,7 +130,7 @@ class Container {
   /**
    * Runs {@link Container#load} method many times for each element of `qArr` vector sequentially.
    * 
-   * @param {object[]} qArr Array of "queue" formatted elements.
+   * @param {object[]} qArr Q-array.
    * @param {boolean} isCore Set element as a "core" which means you cannot rewrite or delete it.
    * 
    * @returns {Container} This function returns the container.

src/core/top.js

@@ -39,73 +39,73 @@ const schema = {
 
 */
 class Top { // or const Top = class {...}
-    /*
-    new Top({id: 'ttt1'});
-    */
-    constructor(q = {}, isCore = false){
-        let logger = this._container.logger;
-        let valid = Top.isValid(q, logger);
-        if (!valid) { this.errored = true; return; }
+  /*
+  new Top({id: 'ttt1'});
+  */
+  constructor(q = {}, isCore = false){
+    let logger = this._container.logger;
+    let valid = Top.isValid(q, logger);
+    if (!valid) { this.errored = true; return; }
 
-        if (isCore) this.isCore = true;
-        if (typeof q.id !== 'undefined') {
-          this._id = q.id;
-          this.isRandomId = false;
-        } else {
-          this._id = 'rand_' + randomId(lengthRandom, patternRandom);
-          this.isRandomId = true;
-        }
+    if (isCore) this.isCore = true;
+    if (typeof q.id !== 'undefined') {
+      this._id = q.id;
+      this.isRandomId = false;
+    } else {
+      this._id = 'rand_' + randomId(lengthRandom, patternRandom);
+      this.isRandomId = true;
     }
-    get id(){
-        return this._id;
-    }
-    get index(){
-        return this._id;
-    }
-    get className(){
-      return 'Top';
-    }
-    static get validate(){
-      return ajv.compile(schema);
-    }
-    static isValid(q, logger){
-      let valid = this.validate(q);
-      if (!valid) {
-        let msg = `${q.id} Some of properties do not satisfy requirements for class "${this.name}"\n`
-          + this.validate.errors.map((x, i) => `    ${i+1}. ${x.dataPath} ${x.message}`)
-            .join('\n');
-        logger.error(msg, {type: 'ValidationError', space: q.space});
-      }
-
-      return valid;
+  }
+  get id(){
+    return this._id;
+  }
+  get index(){
+    return this._id;
+  }
+  get className(){
+    return 'Top';
+  }
+  static get validate(){
+    return ajv.compile(schema);
+  }
+  static isValid(q, logger){
+    let valid = this.validate(q);
+    if (!valid) {
+      let msg = `${q.id} Some of properties do not satisfy requirements for class "${this.name}"\n`
+        + this.validate.errors.map((x, i) => `    ${i+1}. ${x.dataPath} ${x.message}`)
+          .join('\n');
+      logger.error(msg, {type: 'ValidationError', space: q.space});
     }
-    _toQ(options = {}){
-        let q = {};
-        if (!this.isRandomId) q.id = this.id;
+
+    return valid;
+  }
+  _toQ(options = {}){
+    let q = {};
+    if (!this.isRandomId) q.id = this.id;
 
-        return q;
-    }
-    toQ(options = {}){
-        let q = this._toQ(options);
-        q.action = 'defineTop';
+    return q;
+  }
+  toQ(options = {}){
+    let q = this._toQ(options);
+    q.action = 'defineTop';
 
-        return q;
-    } 
-    toFlat(options = {}){
-      // set defaults
-      _.defaults(options, {
-        simplifyModifiers: true,
-        simplifyActors: true,
-        simplifyExpressions: true
-      });
+    return q;
+  } 
+  toFlat(options = {}){
+    // set defaults
+    _.defaults(options, {
+      simplifyModifiers: true,
+      simplifyActors: true,
+      simplifyExpressions: true
+    });
 
-      let q = this.toQ(options);
-      let res = flatten(q);
+    let q = this.toQ(options);
+    let res = flatten(q);
 
-      return res;
-    }
+    return res;
+  }
 }
 
 module.exports = {
-    Top
+  Top
 };

src/module-system/heta-module.js

@@ -27,7 +27,7 @@ _Module.prototype.setHetaModule = function(){
  * 
  * @param {string} filename File to parse. It is used only for log messages.
  * @param  {...any} params Additional parameters passed to `parse()` method.
- * @returns {array} Queue array format.
+ * @returns {array} Module content in Q-array format.
  */
 function _hetaParse(filename, ...params){
   try {

src/module-system/index.js

@@ -110,7 +110,7 @@ class ModuleSystem {
   /**
    * Composes parsed modules into single platform.
    * 
-   * @returns {object[]} integrated queue array.
+   * @returns {object[]} integrated Q-array.
    */
   integrate(){
     this
@@ -141,7 +141,7 @@ class ModuleSystem {
  * @param {object} obj This should be merged.
  * @param {object[]} arr Array to merge.
  * 
- * @returns {object} merged queue array.
+ * @returns {object} merged Q-array.
  */
 function compose(obj, arr){
   let cleanedObj = _.omit(obj, ['action', 'id', 'class', 'source', 'type', 'sheet']);

src/module-system/module.js

@@ -6,7 +6,7 @@ const fs = require('fs');
  * 
  * @class _Module
  * 
- * @property {object[]} parsed Array of queue objects.
+ * @property {object[]} parsed Q-array.
  * @property {string} filename File name (absolute) associated with the module.
  * @property {Logger} logger Object to analyze log events.
  * @property {string} type One of module types: heta, json, yaml, xlsx, sbml
@@ -71,7 +71,7 @@ class _Module {
   }
 
   /**
-   * Select only `#include` actions from the queue array.
+   * Select only `#include` actions from the Q-array.
    * 
    * @returns {object[]} Array of `#include actions`.
    */

src/module-system/sbml-module.js

@@ -4,7 +4,7 @@ const { SBMLParse } = require('./sbml-parse');
 
 /**
  * To initialize a Heta module of the "sbml" type.
- * It includes reading and parsing SBML file and representing it into Heta queue,
+ * It includes reading and parsing SBML file and representing it into Q-object,
  * see [Heta specifications](https://hetalang.github.io/#/specifications/modules?id=sbml-module)
  * 
  * @returns {_Module} Self.

src/namespace.js

@@ -44,12 +44,12 @@ class Namespace extends Map {
     return [...this].map((x) => x[1]);
   }
   /**
-   * Converts namespace into queue array.
+   * Converts namespace into Q-array.
    * 
    * @param {boolean} removeCoreComponents=true 
    * @param {object} options Options passed to {@link Top#toQ} method
    * 
-   * @returns {object[]} Array of JS objects in queue format.
+   * @returns {object[]} Q-array format.
    */
   toQArr(removeCoreComponents = false, options = {}){
     let qArr = this.toArray()
@@ -59,10 +59,10 @@ class Namespace extends Map {
     return qArr;
   }
   /**
-   * Representation of namespace in queue format.
+   * Representation of namespace into Q-object format.
    * 
    * @param {object} options reserved for future versions.
-   * @returns {object} JS object in queue format.
+   * @returns {object} JS object in Q-object format.
    */
   toQ(options = {}){
     let res = {
@@ -75,11 +75,11 @@ class Namespace extends Map {
   }
 
   /**
-   * Representation of namespace in flat queue format.
+   * Representation of namespace in flat Q-object format.
    * 
    * @param {object} options reserved for future versions.
    * 
-   * @returns {object} JS object in flat queue format.
+   * @returns {object} flat Q-object format.
    */
   toFlat(options = {}){
     let q = this.toQ(options);