make package document updates

xieguigang · May 7, 2024 · 151bcc3 · 151bcc3
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diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html
@@ -22,11 +22,9 @@ <h2>Ions</h2>
 
         <h3>Description</h3>
 
-        <p>Data model of a mgf ion</p>
-
-<blockquote>
-  <p><a href="http://www.matrixscience.com/help/data_file_help.html">http://www.matrixscience.com/help/data_file_help.html</a></p>
-</blockquote>
+        <p>Data model of a mgf ion
+
+ > http://www.matrixscience.com/help/data<em>file</em>help.html</p>
 
         <h3>Declare</h3>        
 

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html
@@ -35,7 +35,7 @@ <h3>Declare</h3>
    Collision_energy: string;
    # 如果这个文件是来自于MoNA数据库的话, 则在这里是物质的注释信息
    Comments: <a href="/vignettes/clr/System/Collections/Specialized/NameValueCollection.html">NameValueCollection</a>;
-   # <code>DB&#35;</code>
+   # <code>DB#</code>
    DB_id: string;
    Formula: string;
    InChIKey: string;

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html
@@ -24,7 +24,7 @@ <h3>Description</h3>
 
         <p>index work with <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/XmlSeek.html">XmlSeek</a></p>
 
-<p>这个模块主要是为了桌面软件可以尽可能快的加载原始数据文件的索引信息<br />
+<p>这个模块主要是为了桌面软件可以尽可能快的加载原始数据文件的索引信息
  而额外的基于最基础的字符串操作编写的</p>
 
         <h3>Declare</h3>        
@@ -39,6 +39,7 @@ <h3>Declare</h3>
    length: integer;
    maxInto: double;
    Ms2Index: list;
+   name: string;
    scan_time: double;
    TIC: double;
 }

diff --git a/...r/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html b/...r/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html
@@ -30,16 +30,16 @@ <h3>Declare</h3>
             <code id="clr_ts">
 # namespace BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML
 export class IntensitySummary extends <a href="/vignettes/clr/System/Enum.html">Enum</a> {
-   # get the average intensity signal value in a pixel
-   Average: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 2;
+   # sum all intensity signal value in a pixel
+   Total: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 0;
 
    # get a max intensity signal value in a pixel
    BasePeak: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 1;
 
-   Median: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 3;
+   # get the average intensity signal value in a pixel
+   Average: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 2;
 
-   # sum all intensity signal value in a pixel
-   Total: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 0;
+   Median: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a> = 3;
 
 }
 </code>
@@ -49,10 +49,10 @@ <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>Average</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
+<li>use by <i>field</i> member <code>Total</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
 <li>use by <i>field</i> member <code>BasePeak</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
+<li>use by <i>field</i> member <code>Average</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
 <li>use by <i>field</i> member <code>Median</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
-<li>use by <i>field</i> member <code>Total</code>: <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html">IntensitySummary</a></li>
 </ol>
 
 

diff --git a/...tes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html b/...tes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html
@@ -24,7 +24,7 @@ <h3>Description</h3>
 
         <p>total ions/base peak/average intensity</p>
 
-<p>spatial heatmap object consist with a collection of the <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/iPixelIntensity.html">iPixelIntensity</a> <br />
+<p>spatial heatmap object consist with a collection of the <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/iPixelIntensity.html">iPixelIntensity</a> 
  spot data in rows.</p>
 
         <h3>Declare</h3>        

diff --git a/...ioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cv.html b/...ioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cv.html
@@ -22,17 +22,17 @@ <h2>cv</h2>
 
         <h3>Description</h3>
 
-        <p>The Controlled Vocabularies (CV's) of the Proteomic Standard Initiative<br />
- (PSI) provide a consensus annotation system to standardize the meaning, <br />
- syntax and formalism of terms used across proteomics, as required by the<br />
- PSI Working Groups. Each PSI working group develops the CV's required <br />
- by the technology or data type it aims to standardize, following common <br />
- recommendations for devoplement and maintenance. At the PSI meeting in <br />
- Washington (Science 296, 827), it was decided that all PSI working groups <br />
- should adopt the same CV's standardizing some overlapping concepts (units<br />
- and resources). Finally, we propose a common mapping schema to describe <br />
- for each data file schema the associations between its specific elements<br />
- and the PSI CV's or other external ontology resources. Such mappings <br />
+        <p>The Controlled Vocabularies (CV's) of the Proteomic Standard Initiative
+ (PSI) provide a consensus annotation system to standardize the meaning, 
+ syntax and formalism of terms used across proteomics, as required by the
+ PSI Working Groups. Each PSI working group develops the CV's required 
+ by the technology or data type it aims to standardize, following common 
+ recommendations for devoplement and maintenance. At the PSI meeting in 
+ Washington (Science 296, 827), it was decided that all PSI working groups 
+ should adopt the same CV's standardizing some overlapping concepts (units
+ and resources). Finally, we propose a common mapping schema to describe 
+ for each data file schema the associations between its specific elements
+ and the PSI CV's or other external ontology resources. Such mappings 
  support the validation of XML files.</p>
 
         <h3>Declare</h3>        

diff --git a/...oGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cvParam.html b/...oGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cvParam.html
@@ -22,7 +22,7 @@ <h2>cvParam</h2>
 
         <h3>Description</h3>
 
-        <p>a named parameter value,  <br />
+        <p>a named parameter value,  
  value indexed by name [<a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cvParam.html">cvParam</a>.<a href="#">name</a> => <a href="/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzML/ControlVocabulary/cvParam.html">cvParam</a>]</p>
 
         <h3>Declare</h3>        

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/peaks.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/peaks.html
@@ -32,14 +32,9 @@ <h3>Declare</h3>
 export class peaks {
    byteOrder: string;
    compressedLen: integer;
-   # <ol>
-   # <li>zlib
-   # 
-   # <ol start="2">
-   # <li>gzip</li>
-   # <li>none</li>
-   # </ol></li>
-   # </ol>
+   # 1. zlib
+   #  2. gzip
+   #  3. none
    compressionType: string;
    contentType: string;
    precision: double;

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/scan.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/mzXML/scan.html
@@ -33,20 +33,12 @@ <h3>Declare</h3>
    basePeakIntensity: double;
    basePeakMz: double;
    # <code>profile</code> and <code>centroid</code> in Mass Spectrometry?
-   # 
-   # <ol>
-   # <li>Profile means the continuous wave form in a mass spectrum.
-   # 
-   # <ul>
-   # <li>Number of data points Is large.</li>
-   # </ul></li>
-   # <li>Centroid means the peaks in a profile data Is changed to bars.
-   # 
-   # <ul>
-   # <li>location of the bar Is center of the profile peak.</li>
-   # <li>height of the bar Is area of the profile peak.</li>
-   # </ul></li>
-   # </ol>
+   #  
+   #  1. Profile means the continuous wave form in a mass spectrum.
+   #    + Number of data points Is large.
+   #  2. Centroid means the peaks in a profile data Is changed to bars.
+   #    + location of the bar Is center of the profile peak.
+   #    + height of the bar Is area of the profile peak.
    centroided: string;
    collisionEnergy: string;
    highMz: double;

diff --git a/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/nmrML/fidData.html b/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/nmrML/fidData.html
@@ -22,9 +22,9 @@ <h2>fidData</h2>
 
         <h3>Description</h3>
 
-        <p>The signal we detect is called a Free Induction Decay (FID). <br />
- The FID is produced by the macroscopic magnetization after <br />
- the pulse. The magnetization will undergo several processes <br />
+        <p>The signal we detect is called a Free Induction Decay (FID). 
+ The FID is produced by the macroscopic magnetization after 
+ the pulse. The magnetization will undergo several processes 
  as it returns to equilibrium.</p>
 
         <h3>Declare</h3>