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micro-manager · Feb 9, 2024 · 99e35af · 99e35af
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diff --git a/deprecated-list.html b/deprecated-list.html
@@ -404,35 +404,35 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/PropertyMap.html#copy--">org.micromanager.PropertyMap.copy()</a></td>
-</tr>
-<tr class="altColor">
-<td class="colOne"><a href="org/micromanager/acquisition/SequenceSettings.html#copy--">org.micromanager.acquisition.SequenceSettings.copy()</a>
-<div class="block"><span class="deprecationComment">When used correctly, SequenceSettings are immutable.
-     If you really need a copy, use copyBuilder().build();</span></div>
-</td>
-</tr>
-<tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/data/SummaryMetadata.html#copy--">org.micromanager.data.SummaryMetadata.copy()</a>
 <div class="block"><span class="deprecationComment">- Use SummaryMetadata.Builder.copyBuilder instead</span></div>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/data/Coords.html#copy--">org.micromanager.data.Coords.copy()</a>
-<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/data/Coords.html#copyBuilder--"><code>copyBuilder</code></a> instead</span></div>
-</td>
-</tr>
-<tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/data/Metadata.html#copy--">org.micromanager.data.Metadata.copy()</a>
 <div class="block"><span class="deprecationComment">Use the appropriate of the following:
      <a href="org/micromanager/data/Metadata.html#copyBuilderPreservingUUID--"><code>Metadata.copyBuilderPreservingUUID()</code></a>, <a href="org/micromanager/data/Metadata.html#copyBuilderWithNewUUID--"><code>Metadata.copyBuilderWithNewUUID()</code></a>,
      <a href="org/micromanager/data/Metadata.html#copyBuilderRemovingUUID--"><code>Metadata.copyBuilderRemovingUUID()</code></a>. This method is equivalent to
      <code>copyBuilderPreservingUUID</code>.</span></div>
 </td>
 </tr>
+<tr class="rowColor">
+<td class="colOne"><a href="org/micromanager/data/Coords.html#copy--">org.micromanager.data.Coords.copy()</a>
+<div class="block"><span class="deprecationComment">Use <a href="org/micromanager/data/Coords.html#copyBuilder--"><code>copyBuilder</code></a> instead</span></div>
+</td>
+</tr>
 <tr class="altColor">
+<td class="colOne"><a href="org/micromanager/PropertyMap.html#copy--">org.micromanager.PropertyMap.copy()</a></td>
+</tr>
+<tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/display/DisplaySettings.html#copy--">org.micromanager.display.DisplaySettings.copy()</a></td>
 </tr>
+<tr class="altColor">
+<td class="colOne"><a href="org/micromanager/acquisition/SequenceSettings.html#copy--">org.micromanager.acquisition.SequenceSettings.copy()</a>
+<div class="block"><span class="deprecationComment">When used correctly, SequenceSettings are immutable.
+     If you really need a copy, use copyBuilder().build();</span></div>
+</td>
+</tr>
 <tr class="rowColor">
 <td class="colOne"><a href="org/micromanager/data/DataManager.html#createCoords-java.lang.String-">org.micromanager.data.DataManager.createCoords(String)</a>
 <div class="block"><span class="deprecationComment">use of Strings for Coords is discouraged</span></div>
@@ -538,13 +538,13 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/display/DataViewer.html#getDatastore--">org.micromanager.display.DataViewer.getDatastore()</a>
-<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#getDataProvider--"><code>DataViewer.getDataProvider()</code></a> instead</span></div>
+<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#getDatastore--">org.micromanager.display.AbstractDataViewer.getDatastore()</a>
+<div class="block"><span class="deprecationComment">user code should call <code>getDataProvider</code></span></div>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#getDatastore--">org.micromanager.display.AbstractDataViewer.getDatastore()</a>
-<div class="block"><span class="deprecationComment">user code should call <code>getDataProvider</code></span></div>
+<td class="colOne"><a href="org/micromanager/display/DataViewer.html#getDatastore--">org.micromanager.display.DataViewer.getDatastore()</a>
+<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#getDataProvider--"><code>DataViewer.getDataProvider()</code></a> instead</span></div>
 </td>
 </tr>
 <tr class="rowColor">
@@ -916,13 +916,13 @@ <h2 title="Contents">Contents</h2>
 </td>
 </tr>
 <tr class="altColor">
-<td class="colOne"><a href="org/micromanager/display/DataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.DataViewer.setDisplayedImageTo(Coords)</a>
-<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#setDisplayPosition-org.micromanager.data.Coords-"><code>DataViewer.setDisplayPosition(Coords)</code></a> instead</span></div>
+<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.AbstractDataViewer.setDisplayedImageTo(Coords)</a>
+<div class="block"><span class="deprecationComment">user code should call <code>setDisplayPosition</code></span></div>
 </td>
 </tr>
 <tr class="rowColor">
-<td class="colOne"><a href="org/micromanager/display/AbstractDataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.AbstractDataViewer.setDisplayedImageTo(Coords)</a>
-<div class="block"><span class="deprecationComment">user code should call <code>setDisplayPosition</code></span></div>
+<td class="colOne"><a href="org/micromanager/display/DataViewer.html#setDisplayedImageTo-org.micromanager.data.Coords-">org.micromanager.display.DataViewer.setDisplayedImageTo(Coords)</a>
+<div class="block"><span class="deprecationComment">use <a href="org/micromanager/display/DataViewer.html#setDisplayPosition-org.micromanager.data.Coords-"><code>DataViewer.setDisplayPosition(Coords)</code></a> instead</span></div>
 </td>
 </tr>
 <tr class="altColor">

diff --git a/org/micromanager/class-use/PropertyMap.html b/org/micromanager/class-use/PropertyMap.html
@@ -194,8 +194,8 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#toPropertyMap--">toPropertyMap</a></span>()</code>
-<div class="block">Returns a propertymap describing this MultiStagePosition.</div>
+<td class="colLast"><span class="typeNameLabel">PositionList.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PositionList.html#toPropertyMap--">toPropertyMap</a></span>()</code>
+<div class="block">Creates a PropertyMap from this PositionList.</div>
 </td>
 </tr>
 <tr class="altColor">
@@ -206,8 +206,8 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">PositionList.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PositionList.html#toPropertyMap--">toPropertyMap</a></span>()</code>
-<div class="block">Creates a PropertyMap from this PositionList.</div>
+<td class="colLast"><span class="typeNameLabel">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#toPropertyMap--">toPropertyMap</a></span>()</code>
+<div class="block">Returns a propertymap describing this MultiStagePosition.</div>
 </td>
 </tr>
 </tbody>
@@ -239,17 +239,17 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 </tr>
 <tbody>
 <tr class="altColor">
-<td class="colFirst"><code>static <a href="../../../org/micromanager/MultiStagePosition.html" title="class in org.micromanager">MultiStagePosition</a></code></td>
-<td class="colLast"><span class="typeNameLabel">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#fromPropertyMap-org.micromanager.PropertyMap-">fromPropertyMap</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;pmap)</code>
-<div class="block">Generates a multistagePosition from the given PropertyMap.</div>
-</td>
-</tr>
-<tr class="rowColor">
 <td class="colFirst"><code>static <a href="../../../org/micromanager/StagePosition.html" title="class in org.micromanager">StagePosition</a></code></td>
 <td class="colLast"><span class="typeNameLabel">StagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/StagePosition.html#fromPropertyMap-org.micromanager.PropertyMap-">fromPropertyMap</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;pmap)</code>
 <div class="block">Returns the given PrropertyMap as a StagePosition.</div>
 </td>
 </tr>
+<tr class="rowColor">
+<td class="colFirst"><code>static <a href="../../../org/micromanager/MultiStagePosition.html" title="class in org.micromanager">MultiStagePosition</a></code></td>
+<td class="colLast"><span class="typeNameLabel">MultiStagePosition.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/MultiStagePosition.html#fromPropertyMap-org.micromanager.PropertyMap-">fromPropertyMap</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;pmap)</code>
+<div class="block">Generates a multistagePosition from the given PropertyMap.</div>
+</td>
+</tr>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
 <td class="colLast"><span class="typeNameLabel">PropertyMap.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/PropertyMap.html#getPropertyMap-java.lang.String-org.micromanager.PropertyMap-">getPropertyMap</a></span>(java.lang.String&nbsp;key,
@@ -468,13 +468,13 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 <tbody>
 <tr class="altColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#getConfiguration--">getConfiguration</a></span>()</code>
+<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#getConfiguration--">getConfiguration</a></span>()</code>
 <div class="block">Return the user-customizable settings for this overlay.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code><a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a></code></td>
-<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#getConfiguration--">getConfiguration</a></span>()</code>
+<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#getConfiguration--">getConfiguration</a></span>()</code>
 <div class="block">Return the user-customizable settings for this overlay.</div>
 </td>
 </tr>
@@ -489,13 +489,13 @@ <h3>Uses of <a href="../../../org/micromanager/PropertyMap.html" title="interfac
 <tbody>
 <tr class="altColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
+<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
 <div class="block">Configure the overlay with the given parameters.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code>void</code></td>
-<td class="colLast"><span class="typeNameLabel">Overlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/Overlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
+<td class="colLast"><span class="typeNameLabel">AbstractOverlay.</span><code><span class="memberNameLink"><a href="../../../org/micromanager/display/overlay/AbstractOverlay.html#setConfiguration-org.micromanager.PropertyMap-">setConfiguration</a></span>(<a href="../../../org/micromanager/PropertyMap.html" title="interface in org.micromanager">PropertyMap</a>&nbsp;config)</code>
 <div class="block">Configure the overlay with the given parameters.</div>
 </td>
 </tr>