Adding StabilityZ3 back into server and CLI tools (#7)

* Adding StabilityZ3 back into server and CLI tools
* Removing Any CPU build definitions
* Updating copyright notices

.github/workflows/build-cli.yml

@@ -27,6 +27,14 @@ jobs:
     - name: Test CRN
       run: vstest.console.exe .\CRNEngine\CRNEngineTests\bin\Release\netcoreapp3.1\CRNEngineTests.dll /Platform:x64
     
+    - name: Restore StabilityZ3 dependencies
+      run: dotnet restore StabilityZ3/StabilityZ3.sln
+    - name: Build StabilityZ3
+      shell: cmd
+      run: msbuild StabilityZ3/StabilityZ3.sln /p:Configuration=Release /p:Platform=x64
+    - name: Test StabilityZ3
+      run: vstest.console.exe .\StabilityZ3\Tests\bin\Release\netcoreapp3.1\StabilityTests.dll /Platform:x64
+    
     - name: Restore GEC dependencies
       run: dotnet restore ClassicGEC/ClassicGECCli.sln
     - name: Build GEC

CRNEngine/CRNEngineCli.sln

@@ -40,6 +40,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CRNEngineCloudLib", "CRNEng
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CRNEngineRunAllExamples", "CRNEngineRunAllExamples\CRNEngineRunAllExamples.fsproj", "{0298CF1C-4A9B-48A6-B60A-9B3D42BB2502}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "StabilityZ3", "..\StabilityZ3\StabilityZ3\StabilityZ3.fsproj", "{D51E7B2F-86CC-473E-8251-C80792725E15}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|x64 = Debug|x64

CRNEngine/CRNEngineServer.sln

@@ -62,6 +62,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CRNIntegrationTestLib", "CR
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CRNEngineCloudLib", "CRNEngineCloudLib\CRNEngineCloudLib.fsproj", "{2F834887-65D5-4294-A7A5-4BDCCF08C88F}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "StabilityZ3", "..\StabilityZ3\StabilityZ3\StabilityZ3.fsproj", "{0B810A30-9C35-466E-AA5B-FF8045EE23C8}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|x64 = Debug|x64
@@ -163,6 +165,10 @@ Global
 		{2F834887-65D5-4294-A7A5-4BDCCF08C88F}.Debug|x64.Build.0 = Debug|Any CPU
 		{2F834887-65D5-4294-A7A5-4BDCCF08C88F}.Release|x64.ActiveCfg = Release|Any CPU
 		{2F834887-65D5-4294-A7A5-4BDCCF08C88F}.Release|x64.Build.0 = Release|Any CPU
+		{0B810A30-9C35-466E-AA5B-FF8045EE23C8}.Debug|x64.ActiveCfg = Debug|Any CPU
+		{0B810A30-9C35-466E-AA5B-FF8045EE23C8}.Debug|x64.Build.0 = Debug|Any CPU
+		{0B810A30-9C35-466E-AA5B-FF8045EE23C8}.Release|x64.ActiveCfg = Release|Any CPU
+		{0B810A30-9C35-466E-AA5B-FF8045EE23C8}.Release|x64.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

CRNEngine/CRNEngineServerLib/CRNEngineServerLib.fsproj

@@ -16,6 +16,7 @@
     <Compile Include="Inference.fs" />
     <Compile Include="Simulation.fs" />
     <Compile Include="StateSpace.fs" />
+    <Compile Include="Synthesis.fs" />
     <Compile Include="Server.fs" />
     <None Include="paket.references" />
   </ItemGroup>

CRNEngine/CRNEngineServerLib/Server.fs

@@ -260,14 +260,12 @@ let defaultProcessRequest (webSocket:WebSocket) (mtype:string) (json:string) (ca
             let getProbabilities = WebSharper.Json.Deserialize<Messages.Request_GetProbabilityMap> json
             let map = JSAPI.getProbabilityMap getProbabilities.probabilities getProbabilities.species getProbabilities.lowerBound
             sendObject webSocket { mtype = "probabilitymap" ; map = map }
-        (*
         | "synthesis" ->
             let synthesis = WebSharper.Json.Deserialize<Messages.Request_Synthesis> json
             Synthesis.processSynthesisRequest synthesis.model synthesis.nodeId synthesis.crnId webSocket
         | "bistability" ->
             let bistability = WebSharper.Json.Deserialize<Messages.Request_Bistability> json
             Synthesis.processGetBistabilityPlot bistability.crn bistability.solution bistability.spX bistability.spY bistability.numPoints webSocket
-        *)
         | "getcloudcapabilities" ->
             sendObject webSocket { mtype= "pools" ; account = Azure.batchAccountName ; pools = Azure.getPoolNames() |> Seq.toArray };
         | "getjobs" ->

CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 //These interfaces are code generated from F#, any changes to this file will be lost.
 export namespace WebSharperGeneratedInterfaces {
 
@@ -936,4 +939,4 @@ export namespace WebSharperGeneratedInterfaces {
         (crn: string): Microsoft.Research.CRNEngine.JSAPI.table_array<Microsoft.Research.CRNEngine.Point>
     }
 
-}
+}

CRNEngine/CliLibrary/CliLibrary.fsproj

@@ -11,6 +11,7 @@
     <Compile Include="simulation.fs" />
     <Compile Include="export.fs" />
     <Compile Include="inference.fs" />
+    <Compile Include="synthesis.fs" />
     <Compile Include="program.fs" />
     <Compile Include="testing.fs" />
     <None Include="paket.references" />
@@ -18,6 +19,7 @@
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\..\MomentClosure\MomentClosure\MomentClosure.fsproj" />
+    <ProjectReference Include="..\..\StabilityZ3\StabilityZ3\StabilityZ3.fsproj" />
     <ProjectReference Include="..\CRNEngineCloudLib\CRNEngineCloudLib.fsproj" />
     <ProjectReference Include="..\CRNEngineDotNet\CRNEngineDotNet.fsproj" />
   </ItemGroup>

CRNEngine/CliLibrary/program.fs

@@ -307,11 +307,21 @@ let run parser (programName:string) (parser_results:ParseResults<CliArguments>)
                 let baseName = match copy with None -> baseName | Some copy -> (baseName+"_"+(string copy))
                 let results = Inference.do_inference inf_options model (Path.Combine [|baseName + "_inference" ;model.top.name|]) copy programCode
                 results.to_summary()
-            ) |> ignore
+            ) |> ignore                
                 
+        // Synthesis
+        if synthesize
+        then
+          updated_igraph 
+          |> InferenceSiteGraph.iterNodes (fun _ model ->
+            Synthesis.run model
+          )
+        
         // Output CRN (useful when the CRN comes from DSD for example)
         if text
           then printf "%s" (ig.to_string ())
+
+         
     done
 
 

CRNEngine/CliLibrary/synthesis.fs

@@ -0,0 +1,39 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+module Microsoft.Research.CliLibrary.Synthesis
+
+open Microsoft.Research.CRNEngine
+open Microsoft.Research.Biology.StabilityZ3
+
+let run (model:Model) = 
+  model.top :: model.systems
+  |> List.iter (fun crn ->
+    let dyn = Dynamical.fromCRN crn
+    let timeout = crn.settings.synthesis.timeout
+    let solver = 
+      match crn.settings.synthesis.solver with
+      | Z3Solver.NLSat -> match timeout with Some t -> Solver.NlsatTO ((uint32 t)*1000u) | None -> Solver.Nlsat
+      | Z3Solver.Portfolio -> match timeout with Some t -> Solver.PortfolioTO ((uint32 t)*1000u) | None -> Solver.Portfolio
+    let res = 
+      match crn.settings.synthesis.mode with
+      | Synthesis_mode.Multistability ->
+        printfn "Synthesizing parameters for multistability..."
+        dyn |> Solver.CheckBistability true solver false crn.settings.synthesis.seed
+      | Synthesis_mode.Turing ->
+        printfn "Synthesizing parameters for Turing instability..."
+        let turingSettings = TuringSymbolic.TuringAnalysisSettings.Default
+        dyn |> Solver.CheckTuring true solver { turingSettings with print_status = false; seed = crn.settings.synthesis.seed }
+    match res.solution with
+    | AnalysisResult.UNSAT _ -> printfn "Unsatisfiable"
+    | AnalysisResult.UNKNOWN b -> printfn "No solution found after %1.1f seconds" b.time
+    | AnalysisResult.FAILED _  -> printfn "Synthesis procedure failed"
+    | AnalysisResult.INCOMPLETE _ -> printfn "Synthesis procedure did not complete"
+    | AnalysisResult.SAT (p, b) -> 
+        printfn "Solution found after %1.1f seconds" b.time
+        printfn "\n================"
+        printfn "Variable | Value"
+        printfn "----------------"
+        Map.iter (printfn "%8s | %1.1f") p
+        printfn "----------------"
+  )

ClassicDSD/ClassicDSDServer.sln

@@ -185,6 +185,10 @@ Global
 		{04B49866-5D5F-44DA-801D-69276362230F}.Debug|x64.Build.0 = Debug|Any CPU
 		{04B49866-5D5F-44DA-801D-69276362230F}.Release|x64.ActiveCfg = Release|Any CPU
 		{04B49866-5D5F-44DA-801D-69276362230F}.Release|x64.Build.0 = Release|Any CPU
+		{D6C2B8E2-573C-42BC-A8AD-111785F864D9}.Debug|x64.ActiveCfg = Debug|Any CPU
+		{D6C2B8E2-573C-42BC-A8AD-111785F864D9}.Debug|x64.Build.0 = Debug|Any CPU
+		{D6C2B8E2-573C-42BC-A8AD-111785F864D9}.Release|x64.ActiveCfg = Release|Any CPU
+		{D6C2B8E2-573C-42BC-A8AD-111785F864D9}.Release|x64.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

ClassicDSD/ClassicDSDTSWrapper/Scripts/WebSharperGeneratedInterfaces.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 //These interfaces are code generated from F#, any changes to this file will be lost.
 export namespace WebSharperGeneratedInterfaces {
 
@@ -741,4 +744,4 @@ export namespace WebSharperGeneratedInterfaces {
         (bundle: Microsoft.Research.DNA.Dsd.bundle): boolean
     }
 
-}
+}

ClassicGEC/ClassicGECServer.sln

@@ -63,6 +63,8 @@ Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "CRNEngineCloudLib", "..\CRN
 EndProject
 Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "RulesDSD", "..\RulesDSD\RulesDSD\RulesDSD.fsproj", "{30177D74-4775-4629-BB08-CA533C6EB294}"
 EndProject
+Project("{6EC3EE1D-3C4E-46DD-8F32-0CC8E7565705}") = "StabilityZ3", "..\StabilityZ3\StabilityZ3\StabilityZ3.fsproj", "{A7F6C30E-8925-4A2F-BC4C-7C2560809609}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|x64 = Debug|x64
@@ -173,6 +175,14 @@ Global
 		{66A501F9-427B-4DB8-9C72-9A844D917D2A}.Debug|x64.Build.0 = Debug|Any CPU
 		{66A501F9-427B-4DB8-9C72-9A844D917D2A}.Release|x64.ActiveCfg = Release|Any CPU
 		{66A501F9-427B-4DB8-9C72-9A844D917D2A}.Release|x64.Build.0 = Release|Any CPU
+		{30177D74-4775-4629-BB08-CA533C6EB294}.Debug|x64.ActiveCfg = Debug|x64
+		{30177D74-4775-4629-BB08-CA533C6EB294}.Debug|x64.Build.0 = Debug|x64
+		{30177D74-4775-4629-BB08-CA533C6EB294}.Release|x64.ActiveCfg = Release|x64
+		{30177D74-4775-4629-BB08-CA533C6EB294}.Release|x64.Build.0 = Release|x64
+		{A7F6C30E-8925-4A2F-BC4C-7C2560809609}.Debug|x64.ActiveCfg = Debug|Any CPU
+		{A7F6C30E-8925-4A2F-BC4C-7C2560809609}.Debug|x64.Build.0 = Debug|Any CPU
+		{A7F6C30E-8925-4A2F-BC4C-7C2560809609}.Release|x64.ActiveCfg = Release|Any CPU
+		{A7F6C30E-8925-4A2F-BC4C-7C2560809609}.Release|x64.Build.0 = Release|Any CPU
 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE

ClassicGEC/ClassicGECTSWrapper/Scripts/WebSharperGeneratedInterfaces.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 import { rSBOLDocument } from "./Interfaces"
 
 //These interfaces are code generated from F#, any changes to this file will be lost.
@@ -446,4 +449,4 @@ export namespace WebSharperGeneratedInterfaces {
         (so: Microsoft.Research.GEC.JSAPI.solve_result, i: number): Microsoft.Research.GEC.JSAPI.solution_result
     }
 
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/CRNSelector.ts

@@ -1,4 +1,7 @@
-import * as CRN from './crnVM';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as CRN from './crnVM';
 import * as ko from 'knockout';
 
 class ModelsVM {
@@ -57,4 +60,4 @@ class CRNSelector {
     public SelectedNodeID: KnockoutComputed<string> = ko.pureComputed(() => this.SelectedNode().NodeID());
 }
 
-export default CRNSelector
+export default CRNSelector

HTML5SharedGUI/CRNComponent/Scripts/DataSetStorage.ts

@@ -1,4 +1,7 @@
-import { IDataSet, IDataSetStorage } from './crnDataSets'
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import { IDataSet, IDataSetStorage } from './crnDataSets'
 
 // (FP) This file contains several implementations of the IDataSetStorage interface, i.e. several different ways to store a set of
 // observation data points.
@@ -179,4 +182,4 @@ export class LocalStorageDataSetStorage implements IDataSetStorage {
         if (!this.instance) this.instance = new LocalStorageDataSetStorage();
         return this.instance;
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/ModificationMonitor.ts

@@ -1,4 +1,7 @@
-import * as CrnVM from "./crnVM";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as CrnVM from "./crnVM";
 import * as rx from 'rx';
 import * as ko from 'knockout';
 
@@ -54,4 +57,4 @@ export class JsonSnapshotMonitor implements IModificationMonitor {
     }
 
     public Modified: rx.Observable<void> = this.subject;
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/SortableFileNamesList.ts

@@ -1,4 +1,7 @@
-import * as $ from 'jquery';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as $ from 'jquery';
 import * as ko from 'knockout';
 import * as CRNvm from './crnVM';
 import * as CRNsettings from './crnSettings';
@@ -82,4 +85,4 @@ export class SortableFilenamesList {
         ko.cleanNode(div);
         ko.applyBindings(this.viewModel, div);
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/Utils.ts

@@ -1,4 +1,7 @@
-// Copy the element tree to the SVG tree. Assigning the element directly does not work.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// Copy the element tree to the SVG tree. Assigning the element directly does not work.
 export function copyTree(source: any, dest: Element) {
     if (source.tagName === undefined) {
         // It's a text node. Copy it.
@@ -18,4 +21,4 @@ export function copyTree(source: any, dest: Element) {
         }
         dest.appendChild(el);
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnDataSets.ts

@@ -1,4 +1,7 @@
-// (FP) This file contains code that handles observation data sets for inference.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// (FP) This file contains code that handles observation data sets for inference.
 
 import "../../KnockoutGrid/knockoutgrid";
 import * as Papa from "papaparse";
@@ -331,4 +334,4 @@ export class KnockoutGridDataSetViewer {
     Show(data: IDataSet) {
         this.dataSet.Show(data);
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnExport.ts

@@ -1,4 +1,7 @@
-// (FP) This file contains the code for the export viewer component, which is just a tabbed view of several text areas.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// (FP) This file contains the code for the export viewer component, which is just a tabbed view of several text areas.
 
 import * as $ from "jquery";
 import * as ko from "knockout";
@@ -436,4 +439,4 @@ export class CRNExportViewer {
     public clear() {
         this.exportVM.clear();
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnGraphViewer.ts

@@ -1,4 +1,7 @@
-// Implements a reaction graph viewer that has a MSAGL/JS graph plus some controls to operate on it.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// Implements a reaction graph viewer that has a MSAGL/JS graph plus some controls to operate on it.
 
 import * as $ from 'jquery';
 import * as CRNvm from './crnVM';
@@ -460,4 +463,4 @@ export class CRNGraphViewer {
         // Begin layout.
         this.graphInLayout.beginLayoutGraph();
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnKO.ts

@@ -1,4 +1,7 @@
-import "../../KnockoutGrid/knockoutgrid";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import "../../KnockoutGrid/knockoutgrid";
 import * as $ from 'jquery';
 import * as ko from 'knockout';
 import * as CRNSettings from './crnSettings';
@@ -253,4 +256,4 @@ export function bindStateSpace(div: HTMLElement, crnSS: StateSpaceGraph.StateSpa
     (<any>ko.utils.domNodeDisposal).cleanExternalData = function () { };
     ko.cleanNode(div);
     ko.applyBindings(crnSS, div);
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnSettings.ts

@@ -1,4 +1,7 @@
-import * as ko from 'knockout';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ko from 'knockout';
 import { WebSharperGeneratedInterfaces as WGI } from "./../../../CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces";
 // https://github.com/Microsoft/TypeScript/issues/5711
 import * as Serializable from '../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
@@ -742,4 +745,4 @@ export class CRNSettingsVM {
     DeleteVariable = () => {
         this.FocusedSweep().Assignments.remove(this.FocusedAssignments());
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnStateSpaceViewer.ts

@@ -1,4 +1,7 @@
-import * as MSAGL from '../../../HTML5SharedGUI/MSAGL_JS/Scripts/msagl';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as MSAGL from '../../../HTML5SharedGUI/MSAGL_JS/Scripts/msagl';
 import { WebSharperGeneratedInterfaces as WGI } from "../../../CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces"; // https://github.com/Microsoft/TypeScript/issues/5711
 import * as Interfaces from '../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as CRN from './crnVM';
@@ -406,4 +409,4 @@ export class StateSpaceViewer {
         // Begin layout.
         this.graphInLayout.beginLayoutGraph();
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/crnVM.ts

@@ -1,4 +1,7 @@
-// Data structures that represent a CRN that comes from Crn.gui.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// Data structures that represent a CRN that comes from Crn.gui.
 import * as $ from 'jquery';
 import * as ko from 'knockout';
 import * as CRNSettings from './crnSettings';
@@ -742,4 +745,4 @@ export class InferenceGraph {
         this.speciesShowGraphic(true);
         this.speciesShowStructural(true);
     }
-}
+}

HTML5SharedGUI/CRNComponent/Scripts/inferenceGraphViewer.ts

@@ -1,4 +1,7 @@
-// Implements an inference graph viewer that has a MSAGL/JS graph plus some controls to operate on it.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// Implements an inference graph viewer that has a MSAGL/JS graph plus some controls to operate on it.
 
 import "./../../GenericComponents/Styles/shared.css";
 import "./../Styles/crn.css";
@@ -237,4 +240,4 @@ export class InferenceGraphViewer {
         // Begin layout.
         this.graphInLayout.beginLayoutGraph();
     }
-}
+}

HTML5SharedGUI/CRNComponent/Tests/Config.ts

@@ -1 +1,4 @@
-export var Timeout = 300000;
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+export var Timeout = 300000;

HTML5SharedGUI/CRNComponent/Tests/SpeciesSampleTests.ts

@@ -1,4 +1,7 @@
-/// <reference path="../Scripts/typings/jasmine/jasmine.d.ts" />
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+/// <reference path="../Scripts/typings/jasmine/jasmine.d.ts" />
 /// <reference path="../Scripts/typings/requirejs/require.d.ts" />
 
 import Config = require('./Config');
@@ -33,4 +36,4 @@ describe("CRN Component sample code", () => {
             done();
         });
     }, Config.Timeout);    
-});
+});

HTML5SharedGUI/CRNComponent/Tests/modificationMonitorTests.ts

@@ -1,4 +1,7 @@
-/// <reference path="../Scripts/typings/jasmine/jasmine.d.ts" />
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+/// <reference path="../Scripts/typings/jasmine/jasmine.d.ts" />
 /// <reference path="../Scripts/typings/requirejs/require.d.ts" />
 
 import CrnVM = require('../Scripts/src/Scripts/crnVM');
@@ -70,4 +73,4 @@ describe("CRN vm JSON snapshot based modification monitor", () => {
 
         crn.reactions()[0].rate("20")
     }, Config.Timeout);
-});
+});

HTML5SharedGUI/CRNComponent/declarations.d.ts

@@ -1,4 +1,7 @@
-declare module "*.html"
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare module "*.html"
 declare module "idd" {
     var InteractiveDataDisplay: any;
     export = InteractiveDataDisplay;
@@ -10,4 +13,4 @@ declare module "worker-loader*" {
     }
 
     export default WebpackWorker;
-}
+}

HTML5SharedGUI/CRNComponent_Samples/Export/App.ts

@@ -1,4 +1,7 @@
-import * as ko from 'knockout';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ko from 'knockout';
 import * as CRN from './../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as CRNExport from "./../../CRNComponent/Scripts/crnExport";
 import "../samples.css";
@@ -39,4 +42,4 @@ function getExportContent(id: string): JQueryPromise<{ content: string[], save_c
 var crnExport = new CRNExport.CRNExportViewer(getExportContent);
 crnExport.Bind(document.getElementById("crnexport"));
 for (let exportDef of data)
-    crnExport.showExport(exportDef);
+    crnExport.showExport(exportDef);

HTML5SharedGUI/CRNComponent_Samples/Graph/App.ts

@@ -1,4 +1,7 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import * as crnGraph from "../../CRNComponent/Scripts/crnGraphViewer";
 import "../samples.css";
@@ -12,4 +15,4 @@ $(window).on('load', function () {
     var graphVM = new crnGraph.CRNGraphVM(vm);
 
     crnKO.bindGraph(<HTMLDivElement>document.getElementById("graph"), graphVM);
-});
+});

HTML5SharedGUI/CRNComponent_Samples/InferenceGraph/App.ts

@@ -1,4 +1,7 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import * as InferenceGraphViewer from "../../CRNComponent/Scripts/inferenceGraphViewer";
 import CRNSelector from "../../CRNComponent/Scripts/CRNSelector";
@@ -54,4 +57,4 @@ $(window).on('load', function () {
     var selector = document.getElementById('CRNSelector');
     var crnSelector = new CRNSelector(sampleCRN);
     crnSelector.Bind(selector);
-});
+});

HTML5SharedGUI/CRNComponent_Samples/Parameters/App.ts

@@ -1,6 +1,9 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import sampleCRN from "../SampleCRN";
 import "../samples.css";
 
-crnKO.bind(<HTMLDivElement>document.getElementById("crnParameters"), sampleCRN);
+crnKO.bind(<HTMLDivElement>document.getElementById("crnParameters"), sampleCRN);

HTML5SharedGUI/CRNComponent_Samples/Reactions/App.ts

@@ -1,4 +1,7 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import sampleCRN from "../SampleCRN";
 import "../samples.css";
@@ -17,4 +20,4 @@ graph.setDefaultOptions();
 crnKO.bind(<HTMLDivElement>document.getElementById("reactions"), graph);
 
 for (var i = 0; i < crn.initials().length; i++)
-    crn.initials()[i].svg(svgs[i]);
+    crn.initials()[i].svg(svgs[i]);

HTML5SharedGUI/CRNComponent_Samples/SampleCRN.ts

@@ -1,4 +1,7 @@
-import * as crnVM from "../CRNComponent/Scripts/crnVM";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnVM from "../CRNComponent/Scripts/crnVM";
 import * as CRNSettings from '../CRNComponent/Scripts/crnSettings';
 import { WebSharperGeneratedInterfaces as WGI } from '../../CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces';
 
@@ -192,4 +195,4 @@ let graph = new crnVM.InferenceGraph(null);
 graph.Nodes([model]);
 graph.SelectedNode(model);
 
-export default graph
+export default graph

HTML5SharedGUI/CRNComponent_Samples/Settings/App.ts

@@ -1,4 +1,7 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import sampleCRN from "../SampleCRN";
 import * as ko from "knockout";
@@ -21,4 +24,4 @@ var crn = sampleCRN.SelectedCRN();
 var externalSetting = new MyExternalSetting(crn);
 crn.externalSettings.push(externalSetting);
 
-crnKO.bind(<HTMLDivElement>document.getElementById("crnsettings"), sampleCRN);
+crnKO.bind(<HTMLDivElement>document.getElementById("crnsettings"), sampleCRN);

HTML5SharedGUI/CRNComponent_Samples/Species/App.ts

@@ -1,6 +1,9 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import sampleCRN from "../SampleCRN";
 import "../samples.css";
 
-crnKO.bind(<HTMLDivElement>document.getElementById("species"), sampleCRN);
+crnKO.bind(<HTMLDivElement>document.getElementById("species"), sampleCRN);

HTML5SharedGUI/CRNComponent_Samples/StateSpace/App.ts

@@ -1,4 +1,7 @@
-import * as crnKO from "../../CRNComponent/Scripts/crnKO";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as crnKO from "../../CRNComponent/Scripts/crnKO";
 import * as crnVM from "../../CRNComponent/Scripts/crnVM";
 import sampleCRN from "../SampleCRN";
 import * as crnStateSpace from "../../CRNComponent/Scripts/crnStateSpaceViewer";
@@ -22,4 +25,4 @@ let crn = sampleCRN.SelectedCRN();
 var graphVM = new crnStateSpace.StateSpaceGraphVM(crn);
 graphVM.stateSpace(stateSpace);
 
-crnKO.bindStateSpace(<HTMLDivElement>document.getElementById("graph"), graphVM);
+crnKO.bindStateSpace(<HTMLDivElement>document.getElementById("graph"), graphVM);

HTML5SharedGUI/CRNComponent_Samples/declarations.d.ts

@@ -1,4 +1,7 @@
-declare module "*.html"
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare module "*.html"
 declare module "idd" {
     var InteractiveDataDisplay: any;
     export = InteractiveDataDisplay;
@@ -10,4 +13,4 @@ declare module "worker-loader*" {
     }
 
     export default WebpackWorker;
-}
+}

HTML5SharedGUI/CRNComponent_Samples/webpack.config.js

@@ -1,4 +1,7 @@
-/// <binding AfterBuild='Run - Development' />
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+/// <binding AfterBuild='Run - Development' />
 "use strict";
 var webpack = require('webpack');
 var HtmlWebpackPlugin = require('html-webpack-plugin');
@@ -112,4 +115,4 @@ module.exports = [{
             filename: './StateSpace.html'
         })
     ]
-}];
+}];

HTML5SharedGUI/CodeEditor/Scripts/CodeEditor.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 ///<reference path="./Interfaces.ts"/>
 
 // (FP) The code in this file represents the bare editor, by which I mean the text box alone. This has its own KO component, called code-editor-widget. The full editor, which is in CodePad.ts, makes use of it.
@@ -194,4 +197,4 @@ export class Editor {
 }
 
 if (!ko.components.isRegistered("code-editor-widget"))
-    ko.components.register("code-editor-widget", new EditorViewerConfig());
+    ko.components.register("code-editor-widget", new EditorViewerConfig());

HTML5SharedGUI/CodeEditor/Scripts/CodeExamples.ts

@@ -1,4 +1,7 @@
-///<reference path="./Interfaces.ts"/>
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+///<reference path="./Interfaces.ts"/>
 
 // (FP) The code in this file handles the logic related to examples (i.e. the files you can load via the drop-down menu).
 
@@ -84,4 +87,4 @@ class ExamplesViewerConfig implements KnockoutComponentTypes.Config {
 }
 
 if (!ko.components.isRegistered("code-examples"))
-    ko.components.register("code-examples", new ExamplesViewerConfig());
+    ko.components.register("code-examples", new ExamplesViewerConfig());

HTML5SharedGUI/CodeEditor/Scripts/CodePad.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 ///<reference path="./Interfaces.ts"/>
 
 // (FP) This file contains the logic for the full-fledged editor (i.e. including buttons and stuff).
@@ -211,4 +214,4 @@ monaco.editor.defineTheme('crn', {
     colors: {}
 });
 
-export default CodePad;
+export default CodePad;

HTML5SharedGUI/CodeEditor/Scripts/Interfaces.ts

@@ -1,4 +1,7 @@
-// This file is only for type checking. (FP) These are the types for examples.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// This file is only for type checking. (FP) These are the types for examples.
 interface ExamplesGroup {
     Name: string;
     Correspondence: { [key: string]: string };

HTML5SharedGUI/CodeEditor/declarations.d.ts

@@ -1,5 +1,8 @@
-declare module "*.html"
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare module "*.html"
 declare module "monaco-editor" {
     var monaco: any;
     export = monaco;
-}
+}

HTML5SharedGUI/CodeEditor_Samples/CRNEditor.ts

@@ -1,4 +1,7 @@
-import CodePad from "../CodeEditor/Scripts/CodePad";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CodePad from "../CodeEditor/Scripts/CodePad";
 import language from "./crnlang";
 
 class CRNEditor extends CodePad {
@@ -25,4 +28,4 @@ class CRNEditor extends CodePad {
     }
 }
 
-export default CRNEditor;
+export default CRNEditor;

HTML5SharedGUI/CodeEditor_Samples/CRNEditorApp.ts

@@ -1,6 +1,9 @@
-import CRNEditor from "./CRNEditor";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CRNEditor from "./CRNEditor";
 import * as ko from "knockout";
 import "../CodeEditor/Styles/Codepad.css";
 
 var editor = new CRNEditor();
-ko.applyBindings();
+ko.applyBindings();

HTML5SharedGUI/CodeEditor_Samples/CRNEditorErrorsApp.ts

@@ -1,4 +1,7 @@
-import CRNEditor from "./CRNEditor";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CRNEditor from "./CRNEditor";
 import * as ko from "knockout";
 import "../CodeEditor/Styles/Codepad.css";
 
@@ -15,4 +18,4 @@ class TestVM {
 }
 
 var editor = new CRNEditor();
-ko.applyBindings(new TestVM());
+ko.applyBindings(new TestVM());

HTML5SharedGUI/CodeEditor_Samples/crnlang.ts

@@ -1,4 +1,7 @@
-var crnLanguage = {
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+var crnLanguage = {
     displayName: 'CRN',       // start by writing your language name here
     name: 'crn',
     mimeTypes: ['text/x-crn'],
@@ -169,4 +172,4 @@
     },
 };
 
-export default crnLanguage;
+export default crnLanguage;

HTML5SharedGUI/CodeEditor_Samples/declarations.d.ts

@@ -1,5 +1,8 @@
-declare module "*.html"
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare module "*.html"
 declare module "monaco-editor" {
     var monaco: any;
     export = monaco;
-}
+}

HTML5SharedGUI/CodeEditor_Samples/webpack.config.js

@@ -1,4 +1,7 @@
-/// <binding AfterBuild='Run - Development' />
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+/// <binding AfterBuild='Run - Development' />
 "use strict";
 var webpack = require('webpack');
 var HtmlWebpackPlugin = require('html-webpack-plugin');
@@ -76,4 +79,4 @@ module.exports = [{
             filename: './CRNEditorErrors.html'
         })
     ]
-}];
+}];

HTML5SharedGUI/GenericComponents/Scripts/Dropdown.ts

@@ -1,4 +1,7 @@
-import * as ko from 'knockout';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ko from 'knockout';
 import * as template from 'raw-loader!../Templates/dropdown.html';
 
 var allowCloseTypes = ["button", "checkbox", "hidden", "radio", "reset", "search", "submit"];
@@ -42,4 +45,4 @@ ko.components.register("dropdown", {
             return context === null ? {} : context.$data;
         }
     }
-});
+});

HTML5SharedGUI/GenericComponents/Scripts/HintScreen.ts

@@ -1,4 +1,7 @@
-import * as I from "./Interfaces";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as I from "./Interfaces";
 import * as ko from 'knockout';
 
 class HintScreenVM {
@@ -33,4 +36,4 @@ export class HintScreen implements I.IUIBindable {
     public Bind(elem: HTMLElement) {
         ko.applyBindings(this.vm, elem);
     }
-}
+}

HTML5SharedGUI/GenericComponents/Scripts/IDDTabs.ts

@@ -1,4 +1,7 @@
-// This module uses jQuery's tab functionality to set up any element with the j-has-tabs class as a set of tabs. It also ensures that any IDD content is properly resized when the tab size changes.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// This module uses jQuery's tab functionality to set up any element with the j-has-tabs class as a set of tabs. It also ensures that any IDD content is properly resized when the tab size changes.
 import * as $ from "jquery"
 import "idd";
 declare var InteractiveDataDisplay: any;
@@ -49,4 +52,4 @@ var refreshTabs = function () {
 $(window).resize(refreshTabs);
 refreshTabs();
 
-export default setup;
+export default setup;

HTML5SharedGUI/GenericComponents/Scripts/Interfaces.ts

@@ -1,4 +1,7 @@
-//bind to specific DOM element and occupy it
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+//bind to specific DOM element and occupy it
 export interface IUIBindable {
     Bind(elem: HTMLElement): void;
 }

HTML5SharedGUI/GenericComponents/Scripts/KOBindings.ts

@@ -1,4 +1,7 @@
-// This file contains general-purpose additional KO bindings.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// This file contains general-purpose additional KO bindings.
 
 import * as ko from 'knockout';
 

HTML5SharedGUI/GenericComponents/Scripts/ModificationIndicators.ts

@@ -1,4 +1,7 @@
-import * as $ from 'jquery';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as $ from 'jquery';
 
 export interface IModificationIndicator {
     SetModified(): void;
@@ -37,4 +40,4 @@ export class TabSuffixIndicator implements IModificationIndicator {
         });
         this.isSet = false;
     }
-}
+}

HTML5SharedGUI/GenericComponents/Scripts/MultiFilter.ts

@@ -1,4 +1,7 @@
-// This file implements a control that allows selecting traces. Traces are organised in a hierarchical structure of Model(CRN), Settings, Instance and Species. In this control, all such objects with the same name are collapsed in a single VM, which the user can select. For example, if we have two instances A and B each of which has species S1 and S2, then there will only be two species VMs, rather than 4. This means that the relationship between VMs and traces is many-to-many (i.e. an instance VM can be connected to multiple instances with the same name, and any given trace will be connected to a species, an instance, a settings and a model).
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// This file implements a control that allows selecting traces. Traces are organised in a hierarchical structure of Model(CRN), Settings, Instance and Species. In this control, all such objects with the same name are collapsed in a single VM, which the user can select. For example, if we have two instances A and B each of which has species S1 and S2, then there will only be two species VMs, rather than 4. This means that the relationship between VMs and traces is many-to-many (i.e. an instance VM can be connected to multiple instances with the same name, and any given trace will be connected to a species, an instance, a settings and a model).
 
 import * as ko from "knockout";
 import * as $ from "jquery";
@@ -418,4 +421,4 @@ export class View implements I.ITracesFilter {
     public ResetNames() {
         this.vm.Species([]);
     }
-}
+}

HTML5SharedGUI/GenericComponents/Scripts/Options.ts

@@ -1,4 +1,7 @@
-import CRNEngine from '../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CRNEngine from '../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import "./Dropdown";
 
 class Options {
@@ -32,4 +35,4 @@ class Options {
     }
 }
 
-export default Options;
+export default Options;

HTML5SharedGUI/GenericComponents/Scripts/PaletteEditor.ts

@@ -1,4 +1,7 @@
-import * as tinycolor from "tinycolor2";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as tinycolor from "tinycolor2";
 import * as ko from 'knockout';
 import * as template from 'raw-loader!../Templates/paletteeditor.html';
 import "idd";
@@ -44,4 +47,4 @@ class PaletteEditor {
     }
 }
 
-export default PaletteEditor;
+export default PaletteEditor;

HTML5SharedGUI/GenericComponents/Scripts/SVGExporter.ts

@@ -1,4 +1,7 @@
-declare var SVG: any;
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare var SVG: any;
 import "svg";
 import "idd";
 declare var InteractiveDataDisplay: any;
@@ -46,4 +49,4 @@ function GetExporter(name: string, container: HTMLElement, generator?: (containe
     }
 }
 
-export default GetExporter
+export default GetExporter

HTML5SharedGUI/GenericComponents/Scripts/SingleFilter.ts

@@ -1,4 +1,7 @@
-// (FP) This file implements a control that allows selection of a species from a list of species.
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+// (FP) This file implements a control that allows selection of a species from a list of species.
 
 import * as ko from "knockout";
 import * as I from "./Interfaces";
@@ -113,4 +116,4 @@ export class View implements I.ITracesFilter {
                     maxSpecies = svm;
         vm.Species.push(new SpeciesVM(data.Instance, maxSpecies == null ? 0 : maxSpecies.Species + 1, data.Name));
     }
-}
+}

HTML5SharedGUI/GenericComponents/Scripts/TraceColourEditor.ts

@@ -1,4 +1,7 @@
-import * as tinycolor from "tinycolor2";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as tinycolor from "tinycolor2";
 import * as ko from 'knockout';
 import * as template from 'raw-loader!../Templates/tracecoloureditor.html';
 
@@ -41,4 +44,4 @@ class TraceColourEditor {
     }
 }
 
-export default TraceColourEditor;
+export default TraceColourEditor;

HTML5SharedGUI/GenericComponents/Scripts/ZoomSlider.ts

@@ -1,4 +1,7 @@
-import * as ko from 'knockout';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ko from 'knockout';
 import * as template from 'raw-loader!../Templates/zoomslider.html';
 
 ko.components.register("zoomslider", {
@@ -51,4 +54,4 @@ class ZoomSlider {
     public StepSize: KnockoutObservable<number> = ko.observable(1.1);
 }
 
-export default ZoomSlider
+export default ZoomSlider

HTML5SharedGUI/GenericComponents/declarations.d.ts

@@ -1,4 +1,7 @@
-declare module "*.html";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+declare module "*.html";
 declare module "raw-loader*"
 declare module "idd" {
     var InteractiveDataDisplay: any;
@@ -17,4 +20,4 @@ declare module "worker-loader*" {
         constructor();
     }
     export default WebpackWorker;
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/CRNGraphAdapter.ts

@@ -1,4 +1,7 @@
-import * as ParseOperation from '../Operations/ParseCodeFillCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ParseOperation from '../Operations/ParseCodeFillCRN';
 import * as serialization from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as ReactionGraphViewer from "../../../../HTML5SharedGUI/CRNComponent/Scripts/crnGraphViewer";
 import * as CRN from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
@@ -23,4 +26,4 @@ class CRNGraphAdapter<TCustomSettings> implements ParseOperation.IModelViewer<TC
     }
 }
 
-export default CRNGraphAdapter
+export default CRNGraphAdapter

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/CodeEditorCodeSource.ts

@@ -1,3 +1,6 @@
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import * as ModificationIndicator from '../../../GenericComponents/Scripts/ModificationIndicators';
 import * as GenericParseOperation from '../Operations/GenericCodeParsing';
@@ -70,4 +73,4 @@ export abstract class CodeEditorBasedCodeSource<TOptions> implements GenericPars
 
     //Features.IUIAutoBindable implementation
     public abstract AutoBind(): void;
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/CodeEditorStorageDecorator.ts

@@ -1,4 +1,7 @@
-import * as GenericParseOperation from '../Operations/GenericCodeParsing';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as GenericParseOperation from '../Operations/GenericCodeParsing';
 import * as KOCodeEditor from './KnockoutBasedCodeEditor';
 import * as ko from 'knockout';
 import * as Rx from 'rx';
@@ -28,4 +31,4 @@ export class CodeEditorStorageDecorator<TOptions> implements GenericParseOperati
     }
 
     public EditorLoadEvents: Rx.Observable<string>;
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/GenericCRNParser.ts

@@ -1,4 +1,7 @@
-import * as ParseOperation from '../Operations/GenericCodeParsing';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ParseOperation from '../Operations/GenericCodeParsing';
 import * as CRNParseOperation from '../Operations/ParseCodeFillCRN';
 import * as serialization from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as jQuery from 'jquery';
@@ -72,4 +75,4 @@ export abstract class Parser<TOptions, TCustomSettings> implements ParseOperatio
         dfd.fail((failure: any) => this.failureHandler);
         return dfd;
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/InferenceGraphAdapter.ts

@@ -1,4 +1,7 @@
-import * as ParseOperation from '../Operations/ParseCodeFillCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ParseOperation from '../Operations/ParseCodeFillCRN';
 import * as serialization from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as InferenceGraphViewer from "../../../../HTML5SharedGUI/CRNComponent/Scripts/inferenceGraphViewer";
 import * as CRN from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
@@ -23,4 +26,4 @@ class InferenceGraphAdapter<TCustomSettings> implements ParseOperation.IModelVie
     }
 }
 
-export default InferenceGraphAdapter
+export default InferenceGraphAdapter

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/KnockoutBasedCRNCodeEditor.ts

@@ -1,4 +1,7 @@
-import CRNEditor from '../Components/CRNCodeEditor';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CRNEditor from '../Components/CRNCodeEditor';
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import * as GenericParseOperation from '../Operations/GenericCodeParsing';
 import * as KOCodeEditor from "./KnockoutBasedCodeEditor";
@@ -16,4 +19,4 @@ export class KOCRNCodeEditor extends KOCodeEditor.KOCodeEditor<void> implements
         var codeEditor = new CRNEditor();
         ko.applyBindings(this.vm, document.getElementById('crnCode'));
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/KnockoutBasedCRNExport.ts

@@ -1,4 +1,7 @@
-import * as ParseOperation from '../Operations/ParseCodeFillCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ParseOperation from '../Operations/ParseCodeFillCRN';
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import * as CRN from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import CRNEngine from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine";
@@ -57,4 +60,4 @@ export class CRNExport implements MEExporter.IExportsViewer, I.IUIAutoBindable {
     public Reset(): void {
         this.exportsVM.clear();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/KnockoutBasedCRNViewer.ts

@@ -1,4 +1,7 @@
-import * as ParseOperation from '../Operations/ParseCodeFillCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ParseOperation from '../Operations/ParseCodeFillCRN';
 import * as SimulateOperation from '../Operations/SimulateParsedCRN';
 import * as InferOperation from '../Operations/Inference';
 import * as serialization from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
@@ -105,4 +108,4 @@ export class CRNEditor<TCustomSettings> implements ParseOperation.IModelViewer<T
         var crn = this.modelVM.SelectedCRN();
         return this.customSettingsConverter.convertBack(crn);
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/KnockoutBasedCodeEditor.ts

@@ -1,4 +1,7 @@
-import * as CodeSource from "./CodeEditorCodeSource";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as CodeSource from "./CodeEditorCodeSource";
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import * as GenericParseOperation from '../Operations/GenericCodeParsing';
 import * as ModificationIndicator from "../../../GenericComponents/Scripts/ModificationIndicators";
@@ -21,4 +24,4 @@ export abstract class KOCodeEditor<TOptions> extends CodeSource.CodeEditorBasedC
     }
     
     //other interfaces implemented in the base class
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/KnockoutBasedSSASummaryViewer.ts

@@ -1,4 +1,7 @@
-import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as Operation from '../Operations/StateSpaceAnalysis';
 import * as SummaryViewer from '../Components/SSASummaryViewer';
 import * as ko from 'knockout';
@@ -80,4 +83,4 @@ export class Viewer implements Operation.ISSAViewer {
         this.ssaVM.initialState(states.InitialState);
         this.ssaVM.terminalStates(states.TerminalStates);
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineCRNParser.ts

@@ -1,4 +1,7 @@
-import * as GenericCRNParser from '../Adapters/GenericCRNParser';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as GenericCRNParser from '../Adapters/GenericCRNParser';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as jQuery from 'jquery';
 
@@ -17,4 +20,4 @@ export class Parser extends GenericCRNParser.Parser<void, void> {
         // Coercing format to GenericCRNParser.ICRNStreams.
         return { model: meStreams.model };
     };
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineInferenceRunner.ts

@@ -1,4 +1,7 @@
-import * as InferOperation from '../Operations/Inference';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as InferOperation from '../Operations/Inference';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as IV from '../../../../HTML5SharedGUI/InferenceViewer/Scripts/InferenceViewer';
 import * as MeInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
@@ -305,4 +308,4 @@ export class Adapter implements InferOperation.IInferenceEngine {
     public Abort(): void {
         this.me.Abort();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineSSA.ts

@@ -1,4 +1,7 @@
-import * as SSAOperation from '../Operations/StateSpaceAnalysis';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SSAOperation from '../Operations/StateSpaceAnalysis';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as MeInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as $ from 'jquery';
@@ -32,4 +35,4 @@ export class Adapter implements SSAOperation.ISSAEngine {
     public Abort(): void {
         this.me.Abort();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineSimulationRunner.ts

@@ -1,4 +1,7 @@
-import * as SimulateOperation from '../Operations/SimulateParsedCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimulateOperation from '../Operations/SimulateParsedCRN';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as MeInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as SimViewer from '../../../../HTML5SharedGUI/SimulationViewer/Scripts/SimulationViewerFramework';
@@ -284,4 +287,4 @@ export class SimulationRunner implements
     public Abort() {
         this.me.Abort();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineSpatial1DSimulationRunner.ts

@@ -1,4 +1,7 @@
-import * as SimulateOperation from '../Operations/Spatial1DSimulation';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimulateOperation from '../Operations/Spatial1DSimulation';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as CRNInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as SimViewer from '../../../../HTML5SharedGUI/SimulationViewer/Scripts/SimulationViewerFramework';
@@ -131,4 +134,4 @@ export class SimulationRunner implements
     public Abort() {
         this.me.Abort();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineSpatial2DSimulationRunner.ts

@@ -1,4 +1,7 @@
-import * as SimulateOperation from '../Operations/Spatial1DSimulation';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimulateOperation from '../Operations/Spatial1DSimulation';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as CRNInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as SimViewer from '../../../../HTML5SharedGUI/SimulationViewer/Scripts/SimulationViewerFramework';
@@ -134,4 +137,4 @@ export class SimulationRunner implements
     public Abort() {
         this.me.Abort();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ModellingEngineSynthesis.ts

@@ -1,4 +1,7 @@
-import * as SynthesisOperation from '../Operations/Synthesis';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SynthesisOperation from '../Operations/Synthesis';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as MeInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as $ from 'jquery';
@@ -34,4 +37,4 @@ class SynthesisAdapter implements SynthesisOperation.ISynthesisEngine {
     }
 }
 
-export default SynthesisAdapter
+export default SynthesisAdapter

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/MultipleDataSetObsSource.ts

@@ -1,4 +1,7 @@
-//import crn = require("../../CRNEngine/Interfaces");
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+//import crn = require("../../CRNEngine/Interfaces");
 import { WebSharperGeneratedInterfaces as WGI } from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces';
 import { IDataSetStorage, IDataSet } from '../../../../HTML5SharedGUI/CRNComponent/Scripts/crnDataSets';
 import * as InferenceOp from '../Operations/Inference';
@@ -94,4 +97,4 @@ export class ObservationsSource implements InferenceOp.IObservationsSource {
 
         return dfd.promise();
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/ProbabilityMapsAdapter.ts

@@ -1,4 +1,7 @@
-import * as SimulateOperation from '../Operations/SimulateParsedCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimulateOperation from '../Operations/SimulateParsedCRN';
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import CRNEngine from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as MeInterfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
@@ -49,4 +52,4 @@ export class Viewer implements SimulateOperation.ISimulationViewer<ViewerFramewo
     }
 
     private viewer = new PMViewer.ProbabilityMapView(this, this.settings);
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/SSAGraphAdapter.ts

@@ -1,4 +1,7 @@
-import * as StateSpaceViewer from "../../../../HTML5SharedGUI/CRNComponent/Scripts/crnStateSpaceViewer";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as StateSpaceViewer from "../../../../HTML5SharedGUI/CRNComponent/Scripts/crnStateSpaceViewer";
 import * as SSA from "../Operations/StateSpaceAnalysis";
 import * as CRN from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as CRNvm from '../../../../HTML5SharedGUI/CRNComponent/Scripts/crnVM';
@@ -25,4 +28,4 @@ class SSAGraphAdapter implements SSA.ISSAViewer {
     }
 }
 
-export default SSAGraphAdapter
+export default SSAGraphAdapter

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/SimViewerAdapter.ts

@@ -1,4 +1,7 @@
-import * as SimulateOperation from '../Operations/SimulateParsedCRN';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimulateOperation from '../Operations/SimulateParsedCRN';
 import * as I from '../../../GenericComponents/Scripts/Interfaces';
 import * as serialization from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import * as ViewerFramework from '../../../../HTML5SharedGUI/SimulationViewer/Scripts/SimulationViewerFramework';
@@ -39,4 +42,4 @@ export class Viewer implements SimulateOperation.ISimulationViewer<ViewerFramewo
                 }
             });
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Adapters/SumToVum.ts

@@ -1,4 +1,7 @@
-import * as SimRunner from './ModellingEngineSimulationRunner';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as SimRunner from './ModellingEngineSimulationRunner';
 import * as SVF from '../../../../HTML5SharedGUI/SimulationViewer/Scripts/SimulationViewerFramework';
 import * as ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import { WebSharperGeneratedInterfaces as WGI } from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/WebSharperGeneratedInterfaces";
@@ -69,4 +72,4 @@ export function Convert(sum: SimRunner.ISimulationMessage) {
             break;
     }
     return result;
-};
+};

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/CRNCodeEditor.ts

@@ -1,4 +1,7 @@
-import CodePad from "../../../../HTML5SharedGUI/CodeEditor/Scripts/CodePad";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import CodePad from "../../../../HTML5SharedGUI/CodeEditor/Scripts/CodePad";
 import language from "./CrnLang";
 
 var path = "./Examples/CRNModels/";
@@ -91,4 +94,4 @@ class CRNEditor extends CodePad {
     }
 }
 
-export default CRNEditor;
+export default CRNEditor;

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/CRNCompoundViewer.ts

@@ -1,4 +1,7 @@
-import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as Operation from '../Operations/ParseCodeFillCRN';
 import * as serialization from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 
@@ -14,4 +17,4 @@ class Viewer<TCustomSettings> implements Operation.IModelViewer<TCustomSettings>
     }
 }
 
-export default Viewer
+export default Viewer

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/CrnLang.ts

@@ -1,4 +1,7 @@
-var crnLanguage = {
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+var crnLanguage = {
     displayName: 'CRN',       // start by writing your language name here
     name: 'crn',
     mimeTypes: ['text/x-crn'],
@@ -170,4 +173,4 @@
     },
 };
 
-export default crnLanguage;
+export default crnLanguage;

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/SSACompoundViewer.ts

@@ -1,4 +1,7 @@
-import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as Operation from '../Operations/StateSpaceAnalysis';
 
 export class Viewer implements Operation.ISSAViewer {
@@ -13,4 +16,4 @@ export class Viewer implements Operation.ISSAViewer {
             viewer.Show(stateSpace);
         }
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/SSASummaryViewer.ts

@@ -1,4 +1,7 @@
-import * as ko from "knockout";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as ko from "knockout";
 
 export interface ISpecies {
     graphics: string;
@@ -33,4 +36,4 @@ export class SSASummaryViewer {
                 template: ssaSummaryViewerTemplate
             });
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Components/SSATextViewer.ts

@@ -1,4 +1,7 @@
-import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as Interfaces from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
 import * as Operation from '../Operations/StateSpaceAnalysis';
 
 let parser = new DOMParser();
@@ -127,4 +130,4 @@ export class Viewer implements Operation.ISSAViewer {
             this.htmlText = generated;
         }
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/AutoChoiceSimulation.ts

@@ -1,4 +1,7 @@
-import * as HintScreen from "../../../GenericComponents/Scripts/HintScreen";
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as HintScreen from "../../../GenericComponents/Scripts/HintScreen";
 import * as Operations from "./LongOperations";
 import "idd";
 declare var InteractiveDataDisplay: any;
@@ -91,4 +94,4 @@ export class Operation implements Operations.IOperation, HintScreen.IHintRemoveN
     public SubscribeRemoveHint(callback: () => void) {
         this.notificationCallbacks.push(callback);
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/GenericCodeParsing.ts

@@ -1,4 +1,7 @@
-import * as $ from 'jquery';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as $ from 'jquery';
 import * as Operations from "./LongOperations";
 import * as Rx from "rx";
 

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/Inference.ts

@@ -1,4 +1,7 @@
-import * as Rx from 'rx';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as Rx from 'rx';
 import * as $ from 'jquery';
 import * as Operations from "./LongOperations";
 import * as crn from "../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces";
@@ -314,4 +317,4 @@ export class Operation implements Operations.IOperation {
             this.ongoingPromise = undefined;
         }
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/LongOperations.ts

@@ -1,4 +1,7 @@
-/** The interface for an operation that can be processed by the state machine. */
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+/** The interface for an operation that can be processed by the state machine. */
 export interface IOperation {
     Initiate(): JQueryPromise<any>;
     Abort(): void;
@@ -192,4 +195,4 @@ export class StateMachine {
     public SetChangeStateCallback(callback: (State: any) => void) {
         this.changeStateCallback = callback;
     }
-}
+}

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/LongOperationsKO.ts

@@ -1,4 +1,7 @@
-import * as $ from 'jquery';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as $ from 'jquery';
 import * as ko from 'knockout';
 import * as LongOperations from './LongOperations';
 

HTML5SharedGUI/HTML5CRN_Lib/Scripts/Operations/ModellingEngineExporter.ts

@@ -1,4 +1,7 @@
-import * as GenericCRNParser from '../Adapters/GenericCRNParser';
+// Copyright (c) Microsoft Corporation.
+// Licensed under the MIT License.
+
+import * as GenericCRNParser from '../Adapters/GenericCRNParser';
 import ME from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/CRNEngine';
 import * as Interfaces from '../../../../CRNEngine/CRNEngineTSWrapper/Scripts/Interfaces';
 import CRNSelector from '../../../CRNComponent/Scripts/CRNSelector';
@@ -58,4 +61,4 @@ export class Exporter implements Operations.IOperation {
     GetExitMessage(): string {
         return this.exitMessage;
     }
-}
+}