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LittleCoinCoin committed Nov 8, 2023
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3 changes: 3 additions & 0 deletions FusionApiDev/toc.html
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<li>
<a href="../articles/Dev/about_code.html" name="" title="About the Code">About the Code</a>
</li>
<li>
<a href="../articles/Dev/about_graphs.html" name="" title="About Graphs Structures">About Graphs Structures</a>
</li>
<li>
<a href="../articles/Dev/about_modules.html" name="" title="About Modules">About Modules</a>
</li>
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2 changes: 1 addition & 1 deletion FusionApiDev/toc.json
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25 changes: 13 additions & 12 deletions api/ECellDive.GraphComponents.ContiguousGraph.html
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<meta name="docfx:docurl" content="https://github.com/ecell/ECell_Dive/new/main/apiSpec/new?filename=ECellDive_GraphComponents_ContiguousGraph.md&amp;value=---%0Auid%3A%20ECellDive.GraphComponents.ContiguousGraph%0Asummary%3A%20&#39;*You%20can%20override%20summary%20for%20the%20API%20here%20using%20*MARKDOWN*%20syntax&#39;%0A---%0A%0A*Please%20type%20below%20more%20information%20about%20this%20API%3A*%0A%0A">
<meta name="docfx:docurl" content="https://github.com/ecell/ECell_Dive/new/documentation/apiSpec/new?filename=ECellDive_GraphComponents_ContiguousGraph.md&amp;value=---%0Auid%3A%20ECellDive.GraphComponents.ContiguousGraph%0Asummary%3A%20&#39;*You%20can%20override%20summary%20for%20the%20API%20here%20using%20*MARKDOWN*%20syntax&#39;%0A---%0A%0A*Please%20type%20below%20more%20information%20about%20this%20API%3A*%0A%0A">
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<h1 id="ECellDive_GraphComponents_ContiguousGraph" data-uid="ECellDive.GraphComponents.ContiguousGraph" class="text-break">
Class ContiguousGraph
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L23"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L23"><i class="bi bi-code-slash"></i></a>
</h1>

<div class="facts text-secondary">
Expand Down Expand Up @@ -172,7 +173,7 @@ <h2 class="section" id="constructors">Constructors

<h3 id="ECellDive_GraphComponents_ContiguousGraph__ctor_System_String_" data-uid="ECellDive.GraphComponents.ContiguousGraph.#ctor(System.String)">
ContiguousGraph(string)
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L63"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L63"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"></div>
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<h3 id="ECellDive_GraphComponents_ContiguousGraph_m_edges" data-uid="ECellDive.GraphComponents.ContiguousGraph.m_edges">
m_edges
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L53"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L53"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The field of the property <a class="xref" href="ECellDive.GraphComponents.ContiguousGraph.html#ECellDive_GraphComponents_ContiguousGraph_edges">edges</a>.</p>
Expand Down Expand Up @@ -237,7 +238,7 @@ <h4 class="section">Field Value</h4>

<h3 id="ECellDive_GraphComponents_ContiguousGraph_m_name" data-uid="ECellDive.GraphComponents.ContiguousGraph.m_name">
m_name
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L29"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L29"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The field of the property <a class="xref" href="ECellDive.GraphComponents.ContiguousGraph.html#ECellDive_GraphComponents_ContiguousGraph_name">name</a>.</p>
Expand Down Expand Up @@ -268,7 +269,7 @@ <h4 class="section">Field Value</h4>

<h3 id="ECellDive_GraphComponents_ContiguousGraph_m_nodes" data-uid="ECellDive.GraphComponents.ContiguousGraph.m_nodes">
m_nodes
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L41"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L41"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The field of the property <a class="xref" href="ECellDive.GraphComponents.ContiguousGraph.html#ECellDive_GraphComponents_ContiguousGraph_nodes">nodes</a>.</p>
Expand Down Expand Up @@ -304,7 +305,7 @@ <h2 class="section" id="properties">Properties

<h3 id="ECellDive_GraphComponents_ContiguousGraph_edges" data-uid="ECellDive.GraphComponents.ContiguousGraph.edges">
edges
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L56"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L56"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The edges of this graph.</p>
Expand Down Expand Up @@ -336,7 +337,7 @@ <h4 class="section">Property Value</h4>

<h3 id="ECellDive_GraphComponents_ContiguousGraph_name" data-uid="ECellDive.GraphComponents.ContiguousGraph.name">
name
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L32"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L32"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The name of the graph.</p>
Expand Down Expand Up @@ -368,7 +369,7 @@ <h4 class="section">Property Value</h4>

<h3 id="ECellDive_GraphComponents_ContiguousGraph_nodes" data-uid="ECellDive.GraphComponents.ContiguousGraph.nodes">
nodes
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L44"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L44"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The nodes of this graph.</p>
Expand Down Expand Up @@ -404,7 +405,7 @@ <h2 class="section" id="methods">Methods

<h3 id="ECellDive_GraphComponents_ContiguousGraph_Populate_System_Collections_Generic_List_System_Int32__" data-uid="ECellDive.GraphComponents.ContiguousGraph.Populate(System.Collections.Generic.List{System.Int32})">
Populate(List&lt;int&gt;)
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L72"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L72"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Populate the nodes and edges of the graph.
Expand Down Expand Up @@ -437,7 +438,7 @@ <h4 class="section">Parameters</h4>
</article>

<div class="contribution d-print-none">
<a href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\ContiguousGraph.cs/#L23" class="edit-link">Edit this page</a>
<a href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\ContiguousGraph.cs/#L23" class="edit-link">Edit this page</a>
</div>


Expand All @@ -449,7 +450,7 @@ <h4 class="section">Parameters</h4>
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27 changes: 14 additions & 13 deletions api/ECellDive.GraphComponents.CyJsonPathway.html
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<meta name="docfx:docurl" content="https://github.com/ecell/ECell_Dive/new/main/apiSpec/new?filename=ECellDive_GraphComponents_CyJsonPathway.md&amp;value=---%0Auid%3A%20ECellDive.GraphComponents.CyJsonPathway%0Asummary%3A%20&#39;*You%20can%20override%20summary%20for%20the%20API%20here%20using%20*MARKDOWN*%20syntax&#39;%0A---%0A%0A*Please%20type%20below%20more%20information%20about%20this%20API%3A*%0A%0A">
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<meta name="loc:inThisArticle" content="In this article">
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Expand All @@ -29,6 +29,7 @@
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Expand Down Expand Up @@ -86,7 +87,7 @@ <h5 class="offcanvas-title" id="tocOffcanvasLabel">Table of Contents</h5>

<h1 id="ECellDive_GraphComponents_CyJsonPathway" data-uid="ECellDive.GraphComponents.CyJsonPathway" class="text-break">
Class CyJsonPathway
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L14"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L14"><i class="bi bi-code-slash"></i></a>
</h1>

<div class="facts text-secondary">
Expand Down Expand Up @@ -160,7 +161,7 @@ <h2 class="section" id="constructors">Constructors

<h3 id="ECellDive_GraphComponents_CyJsonPathway__ctor_JObject_System_String_" data-uid="ECellDive.GraphComponents.CyJsonPathway.#ctor(JObject,System.String)">
CyJsonPathway(JObject, string)
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L61"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L61"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Instantiate from a JObject (from Newtonsoft.Json.Linq)
Expand Down Expand Up @@ -197,7 +198,7 @@ <h4 class="section">Parameters</h4>

<h3 id="ECellDive_GraphComponents_CyJsonPathway__ctor_System_String_System_String_" data-uid="ECellDive.GraphComponents.CyJsonPathway.#ctor(System.String,System.String)">
CyJsonPathway(string, string)
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L38"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L38"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Instantiate from a Cytoscape Json file.</p>
Expand Down Expand Up @@ -236,7 +237,7 @@ <h2 class="section" id="fields">Fields

<h3 id="ECellDive_GraphComponents_CyJsonPathway_cyJsonGraphData" data-uid="ECellDive.GraphComponents.CyJsonPathway.cyJsonGraphData">
cyJsonGraphData
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L27"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L27"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"></div>
Expand Down Expand Up @@ -271,7 +272,7 @@ <h2 class="section" id="properties">Properties

<h3 id="ECellDive_GraphComponents_CyJsonPathway_edges" data-uid="ECellDive.GraphComponents.CyJsonPathway.edges">
edges
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L24"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L24"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The edges of this graph.</p>
Expand Down Expand Up @@ -303,7 +304,7 @@ <h4 class="section">Property Value</h4>

<h3 id="ECellDive_GraphComponents_CyJsonPathway_name" data-uid="ECellDive.GraphComponents.CyJsonPathway.name">
name
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L18"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L18"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The name of the graph.</p>
Expand Down Expand Up @@ -335,7 +336,7 @@ <h4 class="section">Property Value</h4>

<h3 id="ECellDive_GraphComponents_CyJsonPathway_nodes" data-uid="ECellDive.GraphComponents.CyJsonPathway.nodes">
nodes
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L21"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L21"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>The nodes of this graph.</p>
Expand Down Expand Up @@ -371,7 +372,7 @@ <h2 class="section" id="methods">Methods

<h3 id="ECellDive_GraphComponents_CyJsonPathway_MapInOutEdgesIntoNodes" data-uid="ECellDive.GraphComponents.CyJsonPathway.MapInOutEdgesIntoNodes">
MapInOutEdgesIntoNodes()
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L76"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L76"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Uses the information stored in the <a class="xref" href="ECellDive.GraphComponents.CyJsonPathway.html#ECellDive_GraphComponents_CyJsonPathway_edges">edges</a> to fill the
Expand Down Expand Up @@ -399,7 +400,7 @@ <h3 id="ECellDive_GraphComponents_CyJsonPathway_MapInOutEdgesIntoNodes" data-uid

<h3 id="ECellDive_GraphComponents_CyJsonPathway_PopulateEdges" data-uid="ECellDive.GraphComponents.CyJsonPathway.PopulateEdges">
PopulateEdges()
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L117"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L117"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Populates the <a class="xref" href="ECellDive.GraphComponents.CyJsonPathway.html#ECellDive_GraphComponents_CyJsonPathway_edges">edges</a> array.</p>
Expand All @@ -426,7 +427,7 @@ <h3 id="ECellDive_GraphComponents_CyJsonPathway_PopulateEdges" data-uid="ECellDi

<h3 id="ECellDive_GraphComponents_CyJsonPathway_PopulateNodes" data-uid="ECellDive.GraphComponents.CyJsonPathway.PopulateNodes">
PopulateNodes()
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L95"><i class="bi bi-code-slash"></i></a>
<a class="header-action link-secondary" title="View source" href="https://github.com/ecell/ECell_Dive/blob/documentation/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L95"><i class="bi bi-code-slash"></i></a>
</h3>

<div class="markdown level1 summary"><p>Populates the <a class="xref" href="ECellDive.GraphComponents.CyJsonPathway.html#ECellDive_GraphComponents_CyJsonPathway_nodes">nodes</a> array.</p>
Expand All @@ -453,7 +454,7 @@ <h3 id="ECellDive_GraphComponents_CyJsonPathway_PopulateNodes" data-uid="ECellDi
</article>

<div class="contribution d-print-none">
<a href="https://github.com/ecell/ECell_Dive/blob/main/Assets\Scripts\Modules\Graphs\CyJsonPathway.cs/#L14" class="edit-link">Edit this page</a>
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Expand All @@ -465,7 +466,7 @@ <h3 id="ECellDive_GraphComponents_CyJsonPathway_PopulateNodes" data-uid="ECellDi
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Expand Down Expand Up @@ -118,7 +119,7 @@ <h3 id="classes">
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