Merge branch 'master' of https://github.com/xieguigang/mzkit

xieguigang · Nov 26, 2024 · a4667ca · a4667ca
2 parents 56d2d5e + 969afc8
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diff --git a/Rscript/Library/mzkit_app/@export/Linears.d.ts b/Rscript/Library/mzkit_app/@export/Linears.d.ts
@@ -28,6 +28,13 @@ declare namespace Linears {
       */
       function table(lines: object): object;
    }
+   /**
+    * load the experiment project
+    * 
+    * 
+     * @param file -
+   */
+   function load_experiment(file: string): object;
    /**
     * Get reference input points
     * 

diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/Linears/Linears.md b/Rscript/Library/mzkit_app/man/mz_quantify/Linears/Linears.md
@@ -3,6 +3,7 @@
 targeted linears
 
 + [lines.table](Linears/lines.table.1) export the table data of the reference linears
++ [load_experiment](Linears/load_experiment.1) load the experiment project
 + [write.points](Linears/write.points.1) save reference point data into a given table file
 + [points](Linears/points.1) Get reference input points
 + [write.ionPeaks](Linears/write.ionPeaks.1) Write peak data which is extract from the raw file with 

diff --git a/Rscript/Library/mzkit_app/man/mz_quantify/Linears/Linears/load_experiment.1 b/Rscript/Library/mzkit_app/man/mz_quantify/Linears/Linears/load_experiment.1
@@ -0,0 +1,20 @@
+.\" man page create by R# package system.
+.TH LINEARS 1 2000-Jan "load_experiment" "load_experiment"
+.SH NAME
+load_experiment \- load the experiment project
+.SH SYNOPSIS
+\fIload_experiment(\fBfile\fR as string);\fR
+.SH DESCRIPTION
+.PP
+load the experiment project
+.PP
+.SH OPTIONS
+.PP
+\fBfile\fB \fR\- -. 
+.PP
+.SH SEE ALSO
+Linears
+.SH FILES
+.PP
+mz_quantify.dll
+.PP
diff --git a/Rscript/Library/mzkit_app/src/mzquant/Linears.vb b/Rscript/Library/mzkit_app/src/mzquant/Linears.vb
@@ -78,9 +78,9 @@ Imports SMRUCC.Rsharp.Runtime.Components
 Imports SMRUCC.Rsharp.Runtime.Internal.Object
 Imports SMRUCC.Rsharp.Runtime.Interop
 Imports REnv = SMRUCC.Rsharp.Runtime
+Imports RInternal = SMRUCC.Rsharp.Runtime.Internal
 Imports Rlist = SMRUCC.Rsharp.Runtime.Internal.Object.list
 Imports std = System.Math
-Imports RInternal = SMRUCC.Rsharp.Runtime.Internal
 
 ''' <summary>
 ''' targeted linears
@@ -148,6 +148,17 @@ Module Linears
             .ToArray
     End Function
 
+    ''' <summary>
+    ''' load the experiment project
+    ''' </summary>
+    ''' <param name="file"></param>
+    ''' <returns></returns>
+    <ExportAPI("load_experiment")>
+    <RApiReturn(GetType(Experiment))>
+    Public Function loadExperiment(file As String) As Experiment
+        Return file.LoadXml(Of Experiment)
+    End Function
+
     ''' <summary>
     ''' save reference point data into a given table file
     ''' </summary>

diff --git a/...gnettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/DataFile.html b/...gnettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/DataFile.html
@@ -0,0 +1,59 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.DataFile</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>DataFile {BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>DataFile</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative
+export class DataFile {
+   compounds: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/IonPeakTableRow.html">IonPeakTableRow[]</a>;
+   filename: string;
+   FileType: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a>;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<li>use by <i>property</i> member <code>compounds</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/IonPeakTableRow.html">IonPeakTableRow</a></li>
+<li>use by <i>property</i> member <code>FileType</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a></li>
+</ol>
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.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("clr_ts");</script>
+
+</html>
diff --git a/...ettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/Experiment.html b/...ettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/Experiment.html
@@ -0,0 +1,62 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative.Experiment</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>Experiment {BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>Experiment</h2>
+
+        <h3>Description</h3>
+
+        <p>a experiment project</p>
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.Math.LinearQuantitative
+export class Experiment extends <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlDataModel.html">XmlDataModel</a> {
+   DataFiles: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/DataFile.html">DataFile[]</a>;
+   ProjectId: string;
+   Stylesheet: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlStyleProcessor.html">XmlStyleProcessor</a>;
+   TypeComment: <a href="/vignettes/clr/System/Xml/XmlComment.html">XmlComment</a>;
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<li>this class extends from <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlDataModel.html">XmlDataModel</a> class: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlDataModel.html">XmlDataModel</a></li>
+<li>use by <i>property</i> member <code>DataFiles</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/DataFile.html">DataFile</a></li>
+<li>use by <i>property</i> member <code>Stylesheet</code>: <a href="/vignettes/clr/Microsoft/VisualBasic/ComponentModel/XmlStyleProcessor.html">XmlStyleProcessor</a></li>
+<li>use by <i>property</i> member <code>TypeComment</code>: <a href="/vignettes/clr/System/Xml/XmlComment.html">XmlComment</a></li>
+</ol>
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.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("clr_ts");</script>
+
+</html>
diff --git a/.../clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/IonPeakTableRow.html b/.../clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/IonPeakTableRow.html
@@ -22,7 +22,7 @@ <h2>IonPeakTableRow</h2>
 
         <h3>Description</h3>
 
-
+        <p>the peaktable data for a single ion</p>
 
         <h3>Declare</h3>        
 

diff --git a/...es/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/TargettedData.html b/...es/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/TargettedData.html
@@ -22,7 +22,7 @@ <h2>TargettedData</h2>
 
         <h3>Description</h3>
 
-
+        <p>type of the targetted data</p>
 
         <h3>Declare</h3>        
 

diff --git a/.../vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html b/.../vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html
@@ -22,7 +22,7 @@ <h2>IonChromatogram</h2>
 
         <h3>Description</h3>
 
-
+        <p>the raw data</p>
 
         <h3>Declare</h3>        
 

diff --git a/...ary/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html b/...ary/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html
@@ -0,0 +1,64 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>BioNovoGene.Analytical.MassSpectrometry.Math.SampleFiles</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>SampleFiles {BioNovoGene.Analytical.MassSpectrometry.Math}</td>
+                <td style="text-align: right;">.NET clr documentation</td>
+            </tr>
+        </table>
+
+        <h2>SampleFiles</h2>
+
+        <h3>Description</h3>
+
+
+
+        <h3>Declare</h3>        
+
+        <pre>
+            <code id="clr_ts">
+# namespace BioNovoGene.Analytical.MassSpectrometry.Math
+export class SampleFiles extends <a href="/vignettes/clr/System/Enum.html">Enum</a> {
+   Sample: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a> = 0;
+
+   QC: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a> = 1;
+
+   KB: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a> = 2;
+
+}
+</code>
+        </pre>
+
+        <h3>.NET clr type reference tree</h3>
+
+        <ol>
+<li>this class extends from <a href="/vignettes/clr/System/Enum.html">Enum</a> class: <a href="/vignettes/clr/System/Enum.html">Enum</a></li>
+<li>use by <i>field</i> member <code>Sample</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a></li>
+<li>use by <i>field</i> member <code>QC</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a></li>
+<li>use by <i>field</i> member <code>KB</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/SampleFiles.html">SampleFiles</a></li>
+</ol>
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>{$package}</em> version {$version} <a
+                href="../{$package}.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("clr_ts");</script>
+
+</html>
diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears.html
@@ -87,6 +87,12 @@ <h1>Linears</h1>
   </td>
   <td><p>export the table data of the reference linears</p></td>
 </tr>
+<tr>
+  <td id="load_experiment">
+    <a href="./Linears/load_experiment.html">load_experiment</a>
+  </td>
+  <td><p>load the experiment project</p></td>
+</tr>
 <tr>
   <td id="write.points">
     <a href="./Linears/write.points.html">write.points</a>

diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/load_experiment.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/load_experiment.html
@@ -0,0 +1,70 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>load the experiment project</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>load_experiment {Linears}</td>
+                <td style="text-align: right;">R Documentation</td>
+            </tr>
+        </table>
+
+        <h2>load the experiment project</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>load_experiment</strong>(<i>file</i>);</code></pre>
+        </div>
+
+        <h3>Arguments</h3>
+
+        <table>
+
+<dt>file</dt>
+<dd><p>[as string]</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 <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/Experiment.html">Experiment</a>.<h4>clr value class</h4><ul><li><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/LinearQuantitative/Experiment.html">Experiment</a></li></ul>
+
+        <h3 style="display: none;">Examples</h3>
+
+
+
+        <hr />
+        <div style="text-align: center;">[Package <em>Linears</em> version 1.0.0.0 <a
+                href="../Linears.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>
diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear.html
@@ -85,7 +85,7 @@ <h1>MRMLinear</h1>
   <td id="as.data.frame.ionchromatogram">
     <a href="./MRMLinear/as.data.frame.ionchromatogram.html">as.data.frame.ionchromatogram</a>
   </td>
-  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html">IonChromatogram</a>: </td>
+  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html">IonChromatogram</a>: <p>the raw data</p></td>
 </tr>
 <tr>
   <td id="as.data.frame.ionpair">

diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual.html
@@ -85,7 +85,7 @@ <h1>visual</h1>
   <td id="plot.ionchromatogram">
     <a href="./visual/plot.ionchromatogram.html">plot.ionchromatogram</a>
   </td>
-  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html">IonChromatogram</a>: </td>
+  <td><a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/MRM/Data/IonChromatogram.html">IonChromatogram</a>: <p>the raw data</p></td>
 </tr>
 <tr>
   <td id="plot.rtshift">
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,7 +22,7 @@ <h2>IonPeakTableRow</h2>

		<h3>Description</h3>


		<p>the peaktable data for a single ion</p>

		<h3>Declare</h3>

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,7 +22,7 @@ <h2>TargettedData</h2>

		<h3>Description</h3>


		<p>type of the targetted data</p>

		<h3>Declare</h3>

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,7 +22,7 @@ <h2>IonChromatogram</h2>

		<h3>Description</h3>


		<p>the raw data</p>

		<h3>Declare</h3>

Expand Down