Update docs

JeffersonLab · Sep 25, 2024 · c98f966 · c98f966
1 parent 1905afe
commit c98f966
Show file tree

Hide file tree

Showing 23 changed files with 872 additions and 519 deletions.
diff --git a/doc-6.0/javadoc/index-all.html b/doc-6.0/javadoc/index-all.html
diff --git a/doc-6.0/javadoc/org/jlab/coda/hipo/Compressor.ByteBufferBackedInputStream.html b/doc-6.0/javadoc/org/jlab/coda/hipo/Compressor.ByteBufferBackedInputStream.html
@@ -146,7 +146,9 @@ <h3>Constructor Summary</h3>
 <th class="colOne" scope="col">Constructor and Description</th>
 </tr>
 <tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Compressor.ByteBufferBackedInputStream.html#ByteBufferBackedInputStream-java.nio.ByteBuffer-">ByteBufferBackedInputStream</a></span>(java.nio.ByteBuffer&nbsp;backendBuffer)</code>&nbsp;</td>
+<td class="colOne"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Compressor.ByteBufferBackedInputStream.html#ByteBufferBackedInputStream-java.nio.ByteBuffer-">ByteBufferBackedInputStream</a></span>(java.nio.ByteBuffer&nbsp;backendBuffer)</code>
+<div class="block">Get ByteBuffer backing the input stream (containing uncompressed gzip input).</div>
+</td>
 </tr>
 </table>
 </li>
@@ -230,6 +232,11 @@ <h3>Constructor Detail</h3>
 <li class="blockList">
 <h4>ByteBufferBackedInputStream</h4>
 <pre>public&nbsp;ByteBufferBackedInputStream(java.nio.ByteBuffer&nbsp;backendBuffer)</pre>
+<div class="block">Get ByteBuffer backing the input stream (containing uncompressed gzip input).</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>backendBuffer</code> - buffer to contain uncompressed gzip data during decompression process.</dd>
+</dl>
 </li>
 </ul>
 </li>

diff --git a/doc-6.0/javadoc/org/jlab/coda/hipo/DataUtils.html b/doc-6.0/javadoc/org/jlab/coda/hipo/DataUtils.html
@@ -79,13 +79,13 @@
 <li>Summary:&nbsp;</li>
 <li>Nested&nbsp;|&nbsp;</li>
 <li>Field&nbsp;|&nbsp;</li>
-<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
+<li>Constr&nbsp;|&nbsp;</li>
 <li><a href="#method.summary">Method</a></li>
 </ul>
 <ul class="subNavList">
 <li>Detail:&nbsp;</li>
 <li>Field&nbsp;|&nbsp;</li>
-<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
+<li>Constr&nbsp;|&nbsp;</li>
 <li><a href="#method.detail">Method</a></li>
 </ul>
 </div>
@@ -124,23 +124,6 @@ <h2 title="Class DataUtils" class="title">Class DataUtils</h2>
 <div class="summary">
 <ul class="blockList">
 <li class="blockList">
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->
-<ul class="blockList">
-<li class="blockList"><a name="constructor.summary">
-<!--   -->
-</a>
-<h3>Constructor Summary</h3>
-<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/DataUtils.html#DataUtils--">DataUtils</a></span>()</code>&nbsp;</td>
-</tr>
-</table>
-</li>
-</ul>
 <!-- ========== METHOD SUMMARY =========== -->
 <ul class="blockList">
 <li class="blockList"><a name="method.summary">
@@ -183,23 +166,6 @@ <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 <div class="details">
 <ul class="blockList">
 <li class="blockList">
-<!-- ========= CONSTRUCTOR DETAIL ======== -->
-<ul class="blockList">
-<li class="blockList"><a name="constructor.detail">
-<!--   -->
-</a>
-<h3>Constructor Detail</h3>
-<a name="DataUtils--">
-<!--   -->
-</a>
-<ul class="blockListLast">
-<li class="blockList">
-<h4>DataUtils</h4>
-<pre>public&nbsp;DataUtils()</pre>
-</li>
-</ul>
-</li>
-</ul>
 <!-- ============ METHOD DETAIL ========== -->
 <ul class="blockList">
 <li class="blockList"><a name="method.detail">
@@ -297,13 +263,13 @@ <h4>getStringArray</h4>
 <li>Summary:&nbsp;</li>
 <li>Nested&nbsp;|&nbsp;</li>
 <li>Field&nbsp;|&nbsp;</li>
-<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
+<li>Constr&nbsp;|&nbsp;</li>
 <li><a href="#method.summary">Method</a></li>
 </ul>
 <ul class="subNavList">
 <li>Detail:&nbsp;</li>
 <li>Field&nbsp;|&nbsp;</li>
-<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
+<li>Constr&nbsp;|&nbsp;</li>
 <li><a href="#method.detail">Method</a></li>
 </ul>
 </div>

diff --git a/doc-6.0/javadoc/org/jlab/coda/hipo/Evio6Converter.html b/doc-6.0/javadoc/org/jlab/coda/hipo/Evio6Converter.html
@@ -114,6 +114,7 @@ <h2 title="Class Evio6Converter" class="title">Class Evio6Converter</h2>
 <br>
 <pre>public class <span class="typeNameLabel">Evio6Converter</span>
 extends java.lang.Object</pre>
+<div class="block">Class used to convert evio files into hipo files.</div>
 <dl>
 <dt><span class="simpleTagLabel">Author:</span></dt>
 <dd>gavalian</dd>
@@ -157,18 +158,24 @@ <h3>Method Summary</h3>
 <td class="colFirst"><code>static void</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Evio6Converter.html#convert-java.lang.String-java.lang.String-int-">convert</a></span>(java.lang.String&nbsp;inFile,
        java.lang.String&nbsp;outFile,
-       int&nbsp;neventsToConvert)</code>&nbsp;</td>
+       int&nbsp;neventsToConvert)</code>
+<div class="block">Method to convert evio file into hipo file.</div>
+</td>
 </tr>
 <tr id="i1" class="rowColor">
 <td class="colFirst"><code>static void</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Evio6Converter.html#convert-java.lang.String-java.lang.String-int-org.jlab.coda.hipo.CompressionType-">convert</a></span>(java.lang.String&nbsp;inFile,
        java.lang.String&nbsp;outFile,
        int&nbsp;nthreads,
-       <a href="../../../../org/jlab/coda/hipo/CompressionType.html" title="enum in org.jlab.coda.hipo">CompressionType</a>&nbsp;compressionType)</code>&nbsp;</td>
+       <a href="../../../../org/jlab/coda/hipo/CompressionType.html" title="enum in org.jlab.coda.hipo">CompressionType</a>&nbsp;compressionType)</code>
+<div class="block">Method to convert evio file into hipo file.</div>
+</td>
 </tr>
 <tr id="i2" class="altColor">
 <td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Evio6Converter.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Evio6Converter.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>
+<div class="block">Example use of this class.</div>
+</td>
 </tr>
 </table>
 <ul class="blockList">
@@ -218,6 +225,16 @@ <h4>convert</h4>
 <pre>public static&nbsp;void&nbsp;convert(java.lang.String&nbsp;inFile,
                            java.lang.String&nbsp;outFile,
                            int&nbsp;neventsToConvert)</pre>
+<div class="block">Method to convert evio file into hipo file.
+ Uses EvioCompactReader internally and compresses data to lz4-best.
+ Note this only works with evio version 4 and earlier files, not version 6.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>inFile</code> - input evio format file.</dd>
+<dd><code>outFile</code> - output hipo format file.</dd>
+<dd><code>neventsToConvert</code> - number of events in input file to convert (starting from first),
+                         or &lt;= 0 for all events.</dd>
+</dl>
 </li>
 </ul>
 <a name="convert-java.lang.String-java.lang.String-int-org.jlab.coda.hipo.CompressionType-">
@@ -230,6 +247,15 @@ <h4>convert</h4>
                            java.lang.String&nbsp;outFile,
                            int&nbsp;nthreads,
                            <a href="../../../../org/jlab/coda/hipo/CompressionType.html" title="enum in org.jlab.coda.hipo">CompressionType</a>&nbsp;compressionType)</pre>
+<div class="block">Method to convert evio file into hipo file.
+ Internally uses EvioReader set to read events sequentially.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>inFile</code> - input evio format file.</dd>
+<dd><code>outFile</code> - output hipo format file.</dd>
+<dd><code>nthreads</code> - number of threads used to compress data.</dd>
+<dd><code>compressionType</code> - type of data compression to use.</dd>
+</dl>
 </li>
 </ul>
 <a name="main-java.lang.String:A-">
@@ -239,6 +265,13 @@ <h4>convert</h4>
 <li class="blockList">
 <h4>main</h4>
 <pre>public static&nbsp;void&nbsp;main(java.lang.String[]&nbsp;args)</pre>
+<div class="block">Example use of this class.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>args</code> - if any args, 1st = number of threads for compression,
+             2nd = compression type, 3rd = input file, 4th = output file.
+             If no args, use 2 threads for lz4-fast compression and default file names.</dd>
+</dl>
 </li>
 </ul>
 </li>

diff --git a/doc-6.0/javadoc/org/jlab/coda/hipo/FileEventIndex.html b/doc-6.0/javadoc/org/jlab/coda/hipo/FileEventIndex.html
@@ -218,7 +218,9 @@ <h3>Method Summary</h3>
 </tr>
 <tr id="i9" class="rowColor">
 <td class="colFirst"><code>static void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/FileEventIndex.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/FileEventIndex.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>
+<div class="block">Example use of this class.</div>
+</td>
 </tr>
 <tr id="i10" class="altColor">
 <td class="colFirst"><code>void</code></td>
@@ -495,6 +497,11 @@ <h4>toString</h4>
 <li class="blockList">
 <h4>main</h4>
 <pre>public static&nbsp;void&nbsp;main(java.lang.String[]&nbsp;args)</pre>
+<div class="block">Example use of this class.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>args</code> - unused.</dd>
+</dl>
 </li>
 </ul>
 </li>

diff --git a/doc-6.0/javadoc/org/jlab/coda/hipo/Reader.RecordPosition.html b/doc-6.0/javadoc/org/jlab/coda/hipo/Reader.RecordPosition.html
@@ -141,37 +141,54 @@ <h3>Method Summary</h3>
 </tr>
 <tr id="i0" class="altColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#clear--">clear</a></span>()</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#clear--">clear</a></span>()</code>
+<div class="block">Clear the field of this object to 0.</div>
+</td>
 </tr>
 <tr id="i1" class="rowColor">
 <td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getCount--">getCount</a></span>()</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getCount--">getCount</a></span>()</code>
+<div class="block">Get the count or number of entries in this record.</div>
+</td>
 </tr>
 <tr id="i2" class="altColor">
 <td class="colFirst"><code>int</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getLength--">getLength</a></span>()</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getLength--">getLength</a></span>()</code>
+<div class="block">Get the length of this record.</div>
+</td>
 </tr>
 <tr id="i3" class="rowColor">
 <td class="colFirst"><code>long</code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getPosition--">getPosition</a></span>()</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#getPosition--">getPosition</a></span>()</code>
+<div class="block">Get the position of this record in file/buffer.</div>
+</td>
 </tr>
 <tr id="i4" class="altColor">
 <td class="colFirst"><code>void</code></td>
 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setAll-long-int-int-">setAll</a></span>(long&nbsp;pos,
       int&nbsp;len,
-      int&nbsp;cnt)</code>&nbsp;</td>
+      int&nbsp;cnt)</code>
+<div class="block">Set the position of this record in file/buffer, its length,
+ and the number of entries in it.</div>
+</td>
 </tr>
 <tr id="i5" class="rowColor">
 <td class="colFirst"><code><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setCount-int-">setCount</a></span>(int&nbsp;_cnt)</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setCount-int-">setCount</a></span>(int&nbsp;_cnt)</code>
+<div class="block">Set the count or number of entries in this record.</div>
+</td>
 </tr>
 <tr id="i6" class="altColor">
 <td class="colFirst"><code><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setLength-int-">setLength</a></span>(int&nbsp;_len)</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setLength-int-">setLength</a></span>(int&nbsp;_len)</code>
+<div class="block">Set length of this record.</div>
+</td>
 </tr>
 <tr id="i7" class="rowColor">
 <td class="colFirst"><code><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a></code></td>
-<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setPosition-long-">setPosition</a></span>(long&nbsp;_pos)</code>&nbsp;</td>
+<td class="colLast"><code><span class="memberNameLink"><a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html#setPosition-long-">setPosition</a></span>(long&nbsp;_pos)</code>
+<div class="block">Set position of this record in file/buffer.</div>
+</td>
 </tr>
 <tr id="i8" class="altColor">
 <td class="colFirst"><code>java.lang.String</code></td>
@@ -206,6 +223,13 @@ <h3>Method Detail</h3>
 <li class="blockList">
 <h4>setPosition</h4>
 <pre>public&nbsp;<a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a>&nbsp;setPosition(long&nbsp;_pos)</pre>
+<div class="block">Set position of this record in file/buffer.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>_pos</code> - new position of record.</dd>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>this object.</dd>
+</dl>
 </li>
 </ul>
 <a name="setLength-int-">
@@ -215,6 +239,13 @@ <h4>setPosition</h4>
 <li class="blockList">
 <h4>setLength</h4>
 <pre>public&nbsp;<a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a>&nbsp;setLength(int&nbsp;_len)</pre>
+<div class="block">Set length of this record.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>_len</code> - length of record in bytes.</dd>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>this object.</dd>
+</dl>
 </li>
 </ul>
 <a name="setCount-int-">
@@ -224,6 +255,13 @@ <h4>setLength</h4>
 <li class="blockList">
 <h4>setCount</h4>
 <pre>public&nbsp;<a href="../../../../org/jlab/coda/hipo/Reader.RecordPosition.html" title="class in org.jlab.coda.hipo">Reader.RecordPosition</a>&nbsp;setCount(int&nbsp;_cnt)</pre>
+<div class="block">Set the count or number of entries in this record.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>_cnt</code> - count or number of entries in this record.</dd>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>the object.</dd>
+</dl>
 </li>
 </ul>
 <a name="setAll-long-int-int-">
@@ -235,6 +273,14 @@ <h4>setAll</h4>
 <pre>public&nbsp;void&nbsp;setAll(long&nbsp;pos,
                    int&nbsp;len,
                    int&nbsp;cnt)</pre>
+<div class="block">Set the position of this record in file/buffer, its length,
+ and the number of entries in it.</div>
+<dl>
+<dt><span class="paramLabel">Parameters:</span></dt>
+<dd><code>pos</code> - new position of record.</dd>
+<dd><code>len</code> - length of record in bytes.</dd>
+<dd><code>cnt</code> - number of entries in this record.</dd>
+</dl>
 </li>
 </ul>
 <a name="getPosition--">
@@ -244,6 +290,11 @@ <h4>setAll</h4>
 <li class="blockList">
 <h4>getPosition</h4>
 <pre>public&nbsp;long&nbsp;getPosition()</pre>
+<div class="block">Get the position of this record in file/buffer.</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>position of this record.</dd>
+</dl>
 </li>
 </ul>
 <a name="getLength--">
@@ -253,6 +304,11 @@ <h4>getPosition</h4>
 <li class="blockList">
 <h4>getLength</h4>
 <pre>public&nbsp;int&nbsp;getLength()</pre>
+<div class="block">Get the length of this record.</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>length of this record in bytes.</dd>
+</dl>
 </li>
 </ul>
 <a name="getCount--">
@@ -262,6 +318,11 @@ <h4>getLength</h4>
 <li class="blockList">
 <h4>getCount</h4>
 <pre>public&nbsp;int&nbsp;getCount()</pre>
+<div class="block">Get the count or number of entries in this record.</div>
+<dl>
+<dt><span class="returnLabel">Returns:</span></dt>
+<dd>number of entries in this record.</dd>
+</dl>
 </li>
 </ul>
 <a name="clear--">
@@ -271,6 +332,7 @@ <h4>getCount</h4>
 <li class="blockList">
 <h4>clear</h4>
 <pre>public&nbsp;void&nbsp;clear()</pre>
+<div class="block">Clear the field of this object to 0.</div>
 </li>
 </ul>
 <a name="toString--">