commit nothing

xieguigang · Jan 9, 2024 · d445ea0 · d445ea0
1 parent da4b8e4
commit d445ea0
Show file tree

Hide file tree

Showing 9 changed files with 217 additions and 4 deletions.
diff --git a/Rscript/Library/mzkit_app/@export/Oligonucleotide_MS.d.ts b/Rscript/Library/mzkit_app/@export/Oligonucleotide_MS.d.ts
@@ -0,0 +1,20 @@
+// export R# package module type define for javascript/typescript language
+//
+//    imports "Oligonucleotide_MS" from "mzDIA";
+//
+// ref=mzkit.Oligonucleotide_MS@mzDIA, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null
+
+/**
+ * 
+*/
+declare namespace Oligonucleotide_MS {
+   /**
+    * evaluate the exact mass for the gene sequence
+    * 
+    * 
+     * @param fa should be a collection of the gene sequence.
+     * @param env 
+     * + default value Is ``null``.
+   */
+   function exact_mass(fa: any, env?: object): any;
+}
diff --git a/Rscript/Library/mzkit_app/man/mzDIA/Oligonucleotide_MS/Oligonucleotide_MS.md b/Rscript/Library/mzkit_app/man/mzDIA/Oligonucleotide_MS/Oligonucleotide_MS.md
@@ -0,0 +1,5 @@
+# Oligonucleotide_MS
+
+
+
++ [exact_mass](Oligonucleotide_MS/exact_mass.1) evaluate the exact mass for the gene sequence
diff --git a/Rscript/Library/mzkit_app/man/mzDIA/Oligonucleotide_MS/Oligonucleotide_MS/exact_mass.1 b/Rscript/Library/mzkit_app/man/mzDIA/Oligonucleotide_MS/Oligonucleotide_MS/exact_mass.1
@@ -0,0 +1,21 @@
+.\" man page create by R# package system.
+.TH OLIGONUCLEOTIDE_MS 1 2000-Jan "exact_mass" "exact_mass"
+.SH NAME
+exact_mass \- evaluate the exact mass for the gene sequence
+.SH SYNOPSIS
+\fIexact_mass(\fBfa\fR as any, 
+[\fB<Environment>\fR]);\fR
+.SH DESCRIPTION
+.PP
+evaluate the exact mass for the gene sequence
+.PP
+.SH OPTIONS
+.PP
+\fBfa\fB \fR\- should be a collection of the gene sequence.. 
+.PP
+.SH SEE ALSO
+Oligonucleotide_MS
+.SH FILES
+.PP
+mzDIA.dll
+.PP
diff --git a/Rscript/Library/mzkit_app/vignettes/_assets/R_syntax.js b/Rscript/Library/mzkit_app/vignettes/_assets/R_syntax.js
diff --git a/...es/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/precursorMz.html b/...es/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/precursorMz.html
@@ -30,13 +30,13 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.mzXML
 export class precursorMz extends <a href="/vignettes/clr/System/ValueType.html">ValueType</a> {
-   value: double;
    windowWideness: string;
    precursorCharge: double;
    # 母离子可以从这个属性指向的ms1 scan获取，这个属性对应着<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/scan.html">scan</a>.<a href="#">num</a>属性
    precursorScanNum: string;
    precursorIntensity: double;
    activationMethod: string;
+   value: double;
 }
 </code>
         </pre>

diff --git a/...mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html b/...mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html
@@ -55,6 +55,7 @@ <h3>Declare</h3>
    meta: list;
    # 获取得到二级碎片的响应强度值的和,这个响应强度值是和其对应的一级母离子的响应强度值是呈正相关的
    Ms2Intensity: double;
+   # the number of the fragments in current spectrum peaks
    fragments: integer;
 }
 </code>

diff --git a/Rscript/Library/mzkit_app/vignettes/index.html b/Rscript/Library/mzkit_app/vignettes/index.html
@@ -56,6 +56,7 @@ <h2>Library: mzDIA.dll</h2>
 <li><a href="./mzDIA/spectrumPool.html">spectrumPool</a></li>
 <li><a href="./mzDIA/MoleculeNetworking.html">MoleculeNetworking</a></li>
 <li><a href="./mzDIA/mzkit.simulator.html">mzkit.simulator</a></li>
+<li><a href="./mzDIA/Oligonucleotide_MS.html">Oligonucleotide_MS</a></li>
 </ul>
 <h2>Library: mzkit.dll</h2>
 <ul>

diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS.html
@@ -0,0 +1,95 @@
+<!DOCTYPE html><html lang="zh-CN">
+  <head>
+    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, minimum-scale=1.0, maximum-scale=1.0" />
+    <title>Oligonucleotide_MS</title>
+    <meta name="author" content="[email protected]" />
+    <meta name="copyright" content="SMRUCC genomics Copyright (c) 2022" />
+    <meta name="keywords" content="R#; Oligonucleotide_MS; mzDIA" />
+    <meta name="generator" content="https://github.com/rsharp-lang" />
+    <meta name="theme-color" content="#333" />
+    <meta name="description" content="..." />
+    <meta class="foundation-data-attribute-namespace" />
+    <meta class="foundation-mq-xxlarge" />
+    <meta class="foundation-mq-xlarge" />
+    <meta class="foundation-mq-large" />
+    <meta class="foundation-mq-medium" />
+    <meta class="foundation-mq-small" />
+    <meta class="foundation-mq-topbar" />
+    <style>
+
+.table-three-line {
+border-collapse:collapse; /* 关键属性：合并表格内外边框(其实表格边框有2px，外面1px，里面还有1px哦) */
+border:solid #000000; /* 设置边框属性；样式(solid=实线)、颜色(#999=灰) */
+border-width:2px 0 2px 0px; /* 设置边框状粗细：上 右 下 左 = 对应：1px 0 0 1px */
+}
+.left-1{
+    border:solid #000000;border-width:1px 1px 2px 0px;padding:2px;
+    font-weight:bolder;
+}
+.right-1{
+    border:solid #000000;border-width:1px 0px 2px 1px;padding:2px;
+    font-weight:bolder;
+}
+.mid-1{
+    border:solid #000000;border-width:1px 1px 2px 1px;padding:2px;
+    font-weight:bolder;
+}
+.left{
+    border:solid #000000;border-width:1px 1px 1px 0px;padding:2px;
+}
+.right{
+    border:solid #000000;border-width:1px 0px 1px 1px;padding:2px;
+}
+.mid{
+    border:solid #000000;border-width:1px 1px 1px 1px;padding:2px;
+}
+table caption {font-size:14px;font-weight:bolder;}
+</style>
+  </head>
+  <body>
+    <table width="100%" summary="page for {Oligonucleotide_MS}">
+      <tbody>
+        <tr>
+          <td>{Oligonucleotide_MS}</td>
+          <td style="text-align: right;">R# Documentation</td>
+        </tr>
+      </tbody>
+    </table>
+    <h1>Oligonucleotide_MS</h1>
+    <hr />
+    <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;">mzkit</span>);
+                               <br /><br /><span style="color: green;">{$desc_comments}</span><br /><span style="color: blue;">imports</span><span style="color: brown"> "Oligonucleotide_MS"</span><span style="color: blue;"> from</span><span style="color: brown"> "mzDIA"</span>;
+                           </code>
+    </p>
+    <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">
+        <caption>.NET clr type export</caption>
+        <tbody></tbody>
+      </table>
+      <br />
+      <br />
+      <table class="table-three-line">
+        <caption>.NET clr function exports</caption>
+        <tbody><tr>
+  <td id="exact_mass">
+    <a href="./Oligonucleotide_MS/exact_mass.html">exact_mass</a>
+  </td>
+  <td><p>evaluate the exact mass for the gene sequence</p></td>
+</tr></tbody>
+      </table>
+    </div>
+    <hr />
+    <div style="text-align: center;">[<a href="../index.html">Document Index</a>]</div>
+  </body>
+</html>
diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html
@@ -0,0 +1,70 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>evaluate the exact mass for the gene sequence</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="https://mzkit.org/assets/js/page.css">
+</head>
+
+<body>
+    <div class="container">
+
+        <table style="width: 100%;">
+            <tr>
+                <td>exact_mass {Oligonucleotide_MS}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>evaluate the exact mass for the gene sequence</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>exact_mass</strong>(<i>fa</i>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>fa</dt>
+<dd><p><p>should be a collection of the gene sequence.</p></p></dd>
+
+        </table>
+
+
+        <h3 style="display: none;">Details</h3>
+
+
+
+        <h3 style="display: block">Authors</h3>
+
+        BioNovoGene
+
+        <h3>Value</h3>
+
+        this function returns data object of type <i>any</i> kind.<h4>clr value class</h4><ul><li><i>any</i> kind</li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>Oligonucleotide_MS</em> version 1.0.0.0 <a
+                href="../Oligonucleotide_MS.html">Index</a>]
+        </div>
+    </div>
+</body>
+
+<script type="text/javascript" src="https://mzkit.org/assets/js/R_syntax.js"></script>
+<script type="text/javascript" src="https://mzkit.org/assets/js/highlights.js"></script>
+<script type="text/javascript">r_highlights("example_r");</script>
+
+</html>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,5 @@
		# Oligonucleotide_MS



		+ [exact_mass](Oligonucleotide_MS/exact_mass.1) evaluate the exact mass for the gene sequence