run package msbuild

@export/Builder.d.ts

@@ -5,6 +5,8 @@
 // ref=CellRender.Builder@CellRender, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null
 
 /**
+ * Helper functions for build virtualcell model
+ * 
 */
 declare namespace Builder {
    /**

@export/index.d.ts

@@ -17,6 +17,9 @@ declare namespace CellRender {
    /**
    */
    function assemble_transcript_graph(app: any, context: any): object;
+   /**
+   */
+   function compile_genbank(cad_registry: any, gbff: any): object;
    /**
      * @param workdir default value Is ``./``.
      * @param upstream_size default value Is ``150``.
@@ -38,6 +41,11 @@ declare namespace CellRender {
      * @param outputdir default value Is ``null``.
    */
    function modelling_kinetics(src: any, outputdir?: any): object;
+   /**
+     * @param host default value Is ``localhost``.
+     * @param port default value Is ``3306``.
+   */
+   function open_registry(user: any, passwd: any, host?: any, port?: any): object;
    /**
    */
    function tfbs_motif_scanning(app: any, context: any): object;

man/.onLoad.1

@@ -5,7 +5,7 @@
 \fI.onLoad()\fR
 .SH FILES
 .PP
-SMRUCC/R#.declare_function..onLoad at zzz.R:line 4
+SMRUCC/R#.declare_function..onLoad at zzz.R:line 6
 .PP
 .SH COPYRIGHT
 Copyright © xieguigang <[email protected]>, MIT License Licensed 2024

man/CellRender/Builder/Builder.md

@@ -1,5 +1,5 @@
 # Builder
 
-
+Helper functions for build virtualcell model
 
 + [create_modelfile](Builder/create_modelfile.1) 

man/compile_genbank.1

@@ -0,0 +1,18 @@
+.TH COMPILE_GENBANK 1 2024-Nov "" "Compile the virtual cell model from ncbi genbank file"
+.SH NAME
+compile_genbank \- compile_genbank(cad.registry, gbff)
+.SH SYNOPSIS
+\fIcompile_genbank(cad.registry, gbff)\fR
+.SH OPTIONS
+.PP
+\fBcad.registry\fB \fR\- . 
+.PP
+.PP
+\fBgbff\fB \fR\- . the file path to the template ncbi genbank file
+.PP
+.SH FILES
+.PP
+SMRUCC/R#.declare_function.compile_genbank at compiler.R:line 6
+.PP
+.SH COPYRIGHT
+Copyright © xieguigang <[email protected]>, MIT License Licensed 2024

man/index.json

@@ -1 +1 @@
-{"annotation_workflow":{"author":null,"declares":{"name":"annotation_workflow","parameters":[],"sourceMap":{"File":"apps.R","Line":"5","Method":{"Method":"annotation_workflow","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":"this function has no return value","see_also":null,"title":"Register the virtual cell network modelling workflows"},"modelling_cellgraph":{"author":null,"declares":{"name":"modelling_cellgraph","parameters":[{"name":"src","text":null},{"name":"outputdir","text":"NULL"},{"name":"up.len","text":"150"},{"name":"biocyc","text":"'.\/biocyc'"},{"name":"regprecise","text":"'.\/RegPrecise.Xml'"}],"sourceMap":{"File":"main.R","Line":"16","Method":{"Method":"modelling_cellgraph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"src","text":"the ncbi genbank assembly source file its file path"},{"name":"outputdir","text":"the result outputdir and temp workspace location, default value is NULL means use the parent dir of the input src"},{"name":"biocyc","text":"the directory path to the biocyc reference pathway"},{"name":"regprecise","text":"the data repository xml file path to the regprecise motif database."}],"returns":"this function has no return value, and then generated virtual cell model file will be saved at the ``outputdir`` with a fixed file name: ``model.vcell``. and the output dir also contains a html\/pdf report about the virtual cell modelling result.","see_also":null,"title":"Run the cell graph structure modelling workflow"},"modelling_kinetics":{"author":null,"declares":{"name":"modelling_kinetics","parameters":[{"name":"src","text":null},{"name":"outputdir","text":"NULL"}],"sourceMap":{"File":"main.R","Line":"37","Method":{"Method":"modelling_kinetics","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"src","text":"the GCModeller virtual cell model assembly file its file path"}],"returns":null,"see_also":null,"title":"Run the kinetics parameter fitting based on the omics expression data"},".onLoad":{"author":null,"declares":{"name":".onLoad","parameters":[],"sourceMap":{"File":"zzz.R","Line":"4","Method":{"Method":".onLoad","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":null,"details":null,"examples":null,"keywords":null,"parameters":null,"returns":null,"see_also":null,"title":".onLoad"},"assemble_metabolic_graph":{"author":null,"declares":{"name":"assemble_metabolic_graph","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"assemble_metabolic_graph.R","Line":"3","Method":{"Method":"assemble_metabolic_graph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"the metabolic pathway network is modelling via the reference BioCyc database"},"assemble_transcript_graph":{"author":null,"declares":{"name":"assemble_transcript_graph","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"assemble_transcript_graph.R","Line":"5","Method":{"Method":"assemble_transcript_graph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"The network modelling workflow is based on the regprecise database","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Workflow model for create the transcription regulation network"},"extract_gene_table":{"author":null,"declares":{"name":"extract_gene_table","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"extract_gene_table.R","Line":"6","Method":{"Method":"extract_gene_table","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"app","text":"the current workflow app object"},{"name":"context","text":"the workflow context object"}],"returns":null,"see_also":null,"title":"Extract the genbank source"},"tfbs_motif_scanning":{"author":null,"declares":{"name":"tfbs_motif_scanning","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"tfbs_motif_scanning.R","Line":"6","Method":{"Method":"tfbs_motif_scanning","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Create the motif TFBS motif data from the gene upstream data"},"extract_gbff":{"author":null,"declares":{"name":"extract_gbff","parameters":[{"name":"src","text":null},{"name":"workdir","text":"'.\/'"},{"name":"upstream.size","text":"150"},{"name":"tag.genbank.accid","text":"FALSE"},{"name":"verbose","text":"TRUE"}],"sourceMap":{"File":"extract_gbff.R","Line":"7","Method":{"Method":"extract_gbff","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Helper function for extract the annotation features from genbank file"}}
+{"annotation_workflow":{"author":null,"declares":{"name":"annotation_workflow","parameters":[],"sourceMap":{"File":"apps.R","Line":"5","Method":{"Method":"annotation_workflow","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":"this function has no return value","see_also":null,"title":"Register the virtual cell network modelling workflows"},"modelling_cellgraph":{"author":null,"declares":{"name":"modelling_cellgraph","parameters":[{"name":"src","text":null},{"name":"outputdir","text":"NULL"},{"name":"up.len","text":"150"},{"name":"biocyc","text":"'.\/biocyc'"},{"name":"regprecise","text":"'.\/RegPrecise.Xml'"}],"sourceMap":{"File":"main.R","Line":"16","Method":{"Method":"modelling_cellgraph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"src","text":"the ncbi genbank assembly source file its file path"},{"name":"outputdir","text":"the result outputdir and temp workspace location, default value is NULL means use the parent dir of the input src"},{"name":"biocyc","text":"the directory path to the biocyc reference pathway"},{"name":"regprecise","text":"the data repository xml file path to the regprecise motif database."}],"returns":"this function has no return value, and then generated virtual cell model file will be saved at the ``outputdir`` with a fixed file name: ``model.vcell``. and the output dir also contains a html\/pdf report about the virtual cell modelling result.","see_also":null,"title":"Run the cell graph structure modelling workflow"},"modelling_kinetics":{"author":null,"declares":{"name":"modelling_kinetics","parameters":[{"name":"src","text":null},{"name":"outputdir","text":"NULL"}],"sourceMap":{"File":"main.R","Line":"37","Method":{"Method":"modelling_kinetics","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"src","text":"the GCModeller virtual cell model assembly file its file path"}],"returns":null,"see_also":null,"title":"Run the kinetics parameter fitting based on the omics expression data"},".onLoad":{"author":null,"declares":{"name":".onLoad","parameters":[],"sourceMap":{"File":"zzz.R","Line":"6","Method":{"Method":".onLoad","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":null,"details":null,"examples":null,"keywords":null,"parameters":null,"returns":null,"see_also":null,"title":".onLoad"},"assemble_metabolic_graph":{"author":null,"declares":{"name":"assemble_metabolic_graph","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"assemble_metabolic_graph.R","Line":"3","Method":{"Method":"assemble_metabolic_graph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"the metabolic pathway network is modelling via the reference BioCyc database"},"assemble_transcript_graph":{"author":null,"declares":{"name":"assemble_transcript_graph","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"assemble_transcript_graph.R","Line":"5","Method":{"Method":"assemble_transcript_graph","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"The network modelling workflow is based on the regprecise database","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Workflow model for create the transcription regulation network"},"extract_gene_table":{"author":null,"declares":{"name":"extract_gene_table","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"extract_gene_table.R","Line":"6","Method":{"Method":"extract_gene_table","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"app","text":"the current workflow app object"},{"name":"context","text":"the workflow context object"}],"returns":null,"see_also":null,"title":"Extract the genbank source"},"tfbs_motif_scanning":{"author":null,"declares":{"name":"tfbs_motif_scanning","parameters":[{"name":"app","text":null},{"name":"context","text":null}],"sourceMap":{"File":"tfbs_motif_scanning.R","Line":"6","Method":{"Method":"tfbs_motif_scanning","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Create the motif TFBS motif data from the gene upstream data"},"compile_genbank":{"author":null,"declares":{"name":"compile_genbank","parameters":[{"name":"cad.registry","text":null},{"name":"gbff","text":null}],"sourceMap":{"File":"compiler.R","Line":"6","Method":{"Method":"compile_genbank","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[{"name":"cad_registry","text":"the mysql connection to the biocad registry"},{"name":"gbff","text":"the file path to the template ncbi genbank file"}],"returns":null,"see_also":null,"title":"Compile the virtual cell model from ncbi genbank file"},"open_registry":{"author":null,"declares":{"name":"open_registry","parameters":[{"name":"user","text":null},{"name":"passwd","text":null},{"name":"host","text":"'localhost'"},{"name":"port","text":"3306"}],"sourceMap":{"File":"open.R","Line":"3","Method":{"Method":"open_registry","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"open mysql connection to the cad registry"},"extract_gbff":{"author":null,"declares":{"name":"extract_gbff","parameters":[{"name":"src","text":null},{"name":"workdir","text":"'.\/'"},{"name":"upstream.size","text":"150"},{"name":"tag.genbank.accid","text":"FALSE"},{"name":"verbose","text":"TRUE"}],"sourceMap":{"File":"extract_gbff.R","Line":"7","Method":{"Method":"extract_gbff","Module":"declare_function","Namespace":"SMRUCC\/R#"}}},"description":"","details":"","examples":null,"keywords":[],"parameters":[],"returns":null,"see_also":null,"title":"Helper function for extract the annotation features from genbank file"}}

man/open_registry.1

@@ -0,0 +1,28 @@
+.TH OPEN_REGISTRY 1 2024-Nov "" "open mysql connection to the cad registry"
+.SH NAME
+open_registry \- open_registry(user, passwd,
+    <i>host</i> = <span style='color: brown;'><strong>'localhost'</strong></span>,
+    <i>port</i> = <span style='color: green;'>3306</span>)
+.SH SYNOPSIS
+\fIopen_registry(user, passwd,
+    <i>host</i> = <span style='color: brown;'><strong>'localhost'</strong></span>,
+    <i>port</i> = <span style='color: green;'>3306</span>)\fR
+.SH OPTIONS
+.PP
+\fBuser\fB \fR\- . 
+.PP
+.PP
+\fBpasswd\fB \fR\- . 
+.PP
+.PP
+\fBhost\fB \fR\- 'localhost'. 
+.PP
+.PP
+\fBport\fB \fR\- 3306. 
+.PP
+.SH FILES
+.PP
+SMRUCC/R#.declare_function.open_registry at open.R:line 3
+.PP
+.SH COPYRIGHT
+Copyright © xieguigang <[email protected]>, MIT License Licensed 2024

vignettes/CellRender/Builder.html

@@ -10,7 +10,7 @@
     <meta name="keywords" content="R#; Builder; CellRender" />
     <meta name="generator" content="https://github.com/rsharp-lang" />
     <meta name="theme-color" content="#333" />
-    <meta name="description" content="..." />
+    <meta name="description" content="Helper functions for build virtualcell model..." />
     <meta class="foundation-data-attribute-namespace" />
     <meta class="foundation-mq-xxlarge" />
     <meta class="foundation-mq-xlarge" />
@@ -63,19 +63,24 @@ <h1>Builder</h1>
     <p style="     font-size: 1.125em;     line-height: .8em;     margin-left: 0.5%;     background-color: #fbfbfb;     padding: 24px; ">
       <code>
         <span style="color: blue;">require</span>(<span style="color: black; font-weight: bold;">CellRender</span>);
-                               <br /><br /><span style="color: green;">{$desc_comments}</span><br /><span style="color: blue;">imports</span><span style="color: brown"> "Builder"</span><span style="color: blue;"> from</span><span style="color: brown"> "CellRender"</span>;
+                               <br /><br /><span style="color: green;">#' Helper functions for build virtualcell model</span><br /><span style="color: blue;">imports</span><span style="color: brown"> "Builder"</span><span style="color: blue;"> from</span><span style="color: brown"> "CellRender"</span>;
                            </code>
     </p>
-    <p></p>
+    <p><p>Helper functions for build virtualcell model</p></p>
     <blockquote>
       <p style="font-style: italic; font-size: 0.9em;">
 
                            </p>
     </blockquote>
     <div id="main-wrapper">
-      <table class="table-three-line" style="display: none">
+      <table class="table-three-line" style="display: block">
         <caption>.NET clr type export</caption>
-        <tbody></tbody>
+        <tbody><tr>
+  <td id="cad_registry">
+    <a href="/vignettes/clr/CellRender/biocad_registry.html">cad_registry: biocad_registry</a>
+  </td>
+  <td></td>
+</tr></tbody>
       </table>
       <br />
       <br />

vignettes/R/docs/compile_genbank.html

@@ -0,0 +1,74 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>Compile the virtual cell model from ncbi genbank file</title>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+    <link rel="stylesheet" type="text/css" href="../../_assets/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>compile_genbank {CellRender}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>Compile the virtual cell model from ncbi genbank file</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Usage</h3>
+
+        <div style="width: 100%; padding-left: 3%; color: black;">
+            <pre><code class='language-R' style="color: black; font-weight:normal;"><strong>compile_genbank</strong>(<i>cad.registry</i>, <i>gbff</i>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>cad.registry</dt>
+<dd><p><p>the mysql connection to the biocad registry</p></p></dd>
+
+
+<dt>gbff</dt>
+<dd><p><p>the file path to the template ncbi genbank file</p></p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        xieguigang &lt;[email protected]>
+
+        <h3>Value</h3>
+
+        This function has no value returns.
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>CellRender</em> version 1.0.148 <a
+                href="../CellRender.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="../../_assets/R_syntax.js"></script>
+<script type="text/javascript" src="../../_assets/highlights.js"></script>
+<script type="text/javascript">r_highlights("example_r");</script>
+
+</html>