v5.8.0

Improve Linux interface

Author: cariann09

docs/Release.html

@@ -68,7 +68,25 @@ <h3>Summary of recent major releases</h3>
 <tr><td><a href="#v540">v5.4.0</a><td>(06-Apr-23)<td>Improved <ttx>Cluster Hit</ttx> algorithm <ttx>Algo1</ttx> for the detection of gene homology.
 </table>
 
+<h3>Release: v5.8.0 (14-Feb-2026)</h3>
+Improved the Linux interface and a few other small improvements.
+<p>
+<ul>
+<li>Improve a few links to the web documentation.
+<li>If CPU was changed, some actions set it back to previous value.
+<li><ttp>2D</ttp>:
+<ul>
+<li>The <ttb>Sequence Filter</ttb> <ttx>Gene#</ttx> search was not clearing properly when the associated checkbox was unselected.
+<li>Place the <ttx>Gene#</ttx> on top of the exons.
+<li>Self-synteny self-chr: the hit popup now lists the correct genes on the end.
+</ul>
+<li><small>Really tiny stuff:
+Queries 2D Group-chr leaves extra space at top and bottom.
+2D Gene# has better spacing if overlap another. Manager's lower buttons stay fixed grouping.</small>
+</ul>
+
 <h3>Documentation update (6-Feb-2026)</h3>
+
 <a id="v579"></a>
 <h3>Release: v5.7.8-v5.7.9c (4-Jan-2026)</h3>
 <p>

docs/SystemGuide.html

@@ -64,6 +64,7 @@
 <li><a href="MUMmer.html" class="ext" target="_blank">MUMmer with SyMAP</a>
 <li><a href="Demo.html" class="ext" target="_blank">Demo Results</a>
 <li><a href="TroubleShoot.html" class="ext" target="_blank">Trouble-shoot</a>
+<li><a href="UserGuide.html#term" class="ext" target="_blank">Terminology</a>
 </ul>
 1. <u>Introduction</u>
 <ul>

docs/SystemHelp.html

@@ -119,6 +119,7 @@ <h3>1.a Start SyMAP</h3>
 <li><a href="SystemGuide.html#machine" class="ext" target="_blank">System Guide</a> for setup and system requirements.
 <li><a href="SystemGuide.html#demo" class="ext" target="_blank">Demo</a> to run the demo (do not skip this step!).
 <li><a href="input/index.html" class="ext" target="_blank">Input</a> for file formats.
+<li><a href="UserGuide.html#term" class="ext" target="_blank">Terminology</a>.
 </ul>
 </table>
 
@@ -420,7 +421,7 @@ <h3>2.c Load project</h3>
 		enter it later and it will be removed from all sequence names. However, <i><u>this is not reversible</u></i>,
 		a prefix cannot be added to the sequence names.
 	<tr><td style="vertical-align: text-top;">5.
-	<td>This is case-sensitive.
+	<td>This is case-insensitive.
 	</table>
 <td><a href="img/demoPrefix.png"><img src="img/demoPrefix.png" alt="Demo prefix" style="border: 1px solid black; width: 80px"></a>
 </table>
@@ -569,12 +570,17 @@ <h3>3.a Parameter panel</h3>
 		click the lower-left drop-down and select <ttx>Synteny Only</ttx>
 		(see <a href="#drop">drop-down</a>).
 	</table>
-	<p>&nbsp;<p>The parameters are described in the following 3 sections: <a href="#align2">Alignment</a>,
-	<a href="#clust">Cluster hits</a> and <a href="#syn">Synteny</a>.
+	<p>If the <ttl>Align&amp;Synteny</ttl> has already been run, the last row will have an extra
+	drop-down, as shown below (see <a href="#drop">drop-down</a>):
+	<br><a href="img/parameters2last.png">
+	<img src="img/parameters2last.png" alt="pair parameters" style="border: 1px solid black; width: 340px"></a>
 
 	<td>&nbsp;&nbsp;&nbsp;
 	<a href="img/parameters2.png"><img src="img/parameters2.png" alt="pair parameters" style="border: 1px solid black; width: 340px"></a>
 </table>
+<p>The parameters are described in the following 3 sections: <a href="#align2">Alignment</a>,
+	<a href="#clust">Cluster hits</a> and <a href="#syn">Synteny</a>.
+
 
 <a id="align"></a>
 <a id="align2"></a>
@@ -946,34 +952,33 @@ <h3>3.e Save</h3>
 
 <a id="drop"></a>
 <h4>Lower-left drop-down</h4>
-On the lower left side of the parameters window is a drop-down with the following options:
+<table class="tx"><tr>
+<td>If the <ttl>Align&amp;Synteny</ttl> has already been run,
+the lower left side of the parameters window will have a drop-down with the following options:
+<td><a href="img/parameters2last.png">
+	<img src="img/parameters2last.png" alt="pair parameters" style="border: 1px solid black; width: 340px"></a>
+</table>
+
 <table class="tx">
-<tr><td><ttx>Align&Synteny</ttx>
-	<td>If the pair has a blank in the <ttl>Available Syntenies</ttl> table,
-	this will be the only option.
 <tr><td><ttx>Clust&Synteny</ttx>
-	<td>If the pair has an <b>A</b> in the <ttl>Available Syntenies</ttl> table,
-	this option will replace the <ttx>Align&Synteny</ttx> in the drop-down.
-	Use this option if you have changed the clustering parameters.
-<tr><td><ttx>Synteny Only</ttx><td>
-If the pair has a &#10004; in the <ttl>Available Syntenies</ttl> table, this option will
-be available.
-<br>If you have only changed synteny parameters, select this option.
-<tr><td><ttx>Number Pseudo</ttx><td>
-If the pair has a &#10004; in the <ttl>Available Syntenies</ttl> table, this option will
-be available.
-<br>If you only want the pseudos number, select this option (see <a href="#pseudo"> Pseudos</a>).
+	<td>If you have changed the
+	<a href="#clParam">clustering</a> parameters, select this option.
+<tr><td><ttx>Synteny Only</ttx>
+	<td>If you have only changed
+	<a href="#syn">synteny</a> parameters, select this option.
+<tr><td><ttx>Number Pseudo</ttx>
+	<td>If you want to add <a href="#pseudo">pseudo numbers</a>, select this option.
 </table>
-<ul>
-<li>Select <ttb>Save</ttb> after changing this.
-<p>
-<li><ttp>Manager</ttp>: The <ttb>Selected pair</ttb> button
+
+<p><ttp>Manager</ttp>: The <ttb>Selected Pair</ttb> button
 will have its label replace to reflect the drop-down setting, as follows:
-<ttx>Align&amp;Synteny &rarr; Selected Pair
-<br>Clust&amp;Synteny &rarr; Selected Redo
-<br>Synteny Only &nbsp;&rarr; Synteny Only
-<br>Number Pseudo &rarr; Pseudo Only</ttx>
-</ul>
+<br>
+
+<br>&nbsp;&nbsp;<ttx>Clust&amp;Synteny</ttx> &rarr; <ttb>Selected Redo</ttb>
+<br>&nbsp;&nbsp;<ttx>Synteny Only</ttx> &nbsp;&rarr; <ttb>Synteny Only</ttb>
+<br>&nbsp;&nbsp;<ttx>Number Pseudo</ttx> &rarr; <ttb>Pseudo Only</ttb>
+<p>If you have changed the <a href="#align2">alignment</a> parameters, you must remove them using the <ttb>Clear Pair</ttb>
+option on the <ttp>Manager</ttp> panel.
 <!--------------------->
 <h4>Saving pairs parameters</h4>
 

docs/UserGuide.html

@@ -1585,7 +1585,6 @@ <h3>Self-synteny</h3>
 <li><ttp>2D</ttp>: From the <ttp>Chromosome Explorer</ttp>, it does not directly work for a self-chromosome.
 However, by going through the <ttp>Dot Plot</ttp> or <ttp>Blocks view</ttp>, you can click on a self-chromosome block and view it in
 the <ttp>2D</ttp> view. Also, the <ttp>Queries</ttp> <ttp>2D</ttp> option can show self-chromosomes.
-<br>Problem: the Hit popup will show the same <ttx>Gene#</ttx> for both sides of a 2G hit.
 <p>
 <li><ttp>Queries</ttp> works for self-synteny (as of v5.7.5), but it has multiple problems:
 <ul>

docs/img/parameters2.png

@@ -59,11 +59,12 @@
 detecting, displaying, and querying syntenic relationships between sequenced genomes.
 <ul>
 	<li>It is designed for divergent eukaryotic genomes (not bacteria).
-	<li>It can mask the non-genic sequence for gene synteny, or leave it un-masked for new gene discovery and whole genome synteny.
-	<li>It can align a draft genome to a fully sequenced genome (see <a href="./peach.html">Peach</a>) and order the draft.
+	<li>For gene synteny and fast computation, have SyMAP mask the non-genic sequence.
+	    <br>For new gene discovery but slower computation, leave the sequence un-masked.
+	<li>It can align a draft genome to a fully sequenced genome and order the draft (see <a href="./peach.html">Peach</a>).
 	<li>The query and display is designed for the comparison of a few genomes at a time (i.e. 2-4).
 </ul>
-<p>Latest SyMAP release: v5.7.9c (4-Jan-2026), see <a href="./Release.html">Release Notes</a>.
+<p>Latest SyMAP release: v5.8.0 (14-Feb-2026), see <a href="./Release.html">Release Notes</a>.
 </div>
 
 <p><table><tr>
@@ -73,7 +74,7 @@
 			<tr><td>&nbsp;<img src="./img/bullet.gif" alt="" style="height: 8px; width: 8px;">
 				<td><a href="https://github.com/csoderlund/SyMAP/releases" class="ext" target="_blank">symap_5.tar.gz</a>
 			<tr><td>&nbsp;
-				<td><ttt> - executable and demo files</ttt>
+				<td><ttt> - Executable and demo files</ttt>
 			<tr><td colspan="3">&nbsp;
 			<tr><td colspan="2"><b>Documentation</b>
 			<tr><td>&nbsp;<img src="./img/bullet.gif"  alt="" style="height: 8px; width: 8px;">
@@ -108,8 +109,8 @@
 			<tr>
 				<td><a href="./img/dotplot-3g.png">
 				<img src="./img/dotplot-3g.png"  alt="dotplot-3g" style="height: 112px; width: 140px;border: 1px solid black;"></a>
-				<td><a href="./img/circle-2g.png">
-				<img src="./img/circle-2g.png"  alt="circle-two-genome" style="height: 112px; width: 140px;border: 1px solid black;"></a>
+				<td style="text-align: center;"><a href="./img/circle-2g.png">
+				<img src="./img/circle-2g.png"  alt="circle-two-genome" style="height: 112px; border: 1px solid black;"></a>
 				<td><a href="./img/block.png">
 				<img src="./img/block.png"  alt="" style="height: 112px; width: 140px;border: 1px solid black;"></a>
 		</table>

docs/img/parameters2c.png

@@ -31,12 +31,13 @@
 
 import colordialog.ColorDialogHandler;
 import props.PersistentProps;
+import symap.Ext;
 import symap.frame.HelpBar;
 import symap.frame.HelpListener;
 import util.ImageViewer;
 import util.Jcomp;
+import util.Jhtml;
 import util.Popup;
-import util.Utilities;
 
 /*******************************************************************
  * Control Panel for Circle View
@@ -99,7 +100,7 @@ public void mousePressed(MouseEvent e) {
             }
         });
 
-		viewPopupButton = Jcomp.createButtonGray(this,helpPanel, null /*has own listener*/,"View",
+		viewPopupButton = Jcomp.createButton(this,helpPanel, null /*has own listener*/,"View",
 				"Click button for menu of options");
 		createViewPopup();
 
@@ -116,7 +117,9 @@ public void mousePressed(MouseEvent e) {
 							"Save image" );
 		infoButton = Jcomp.createIconButton(this,helpPanel,buttonListener,"/images/info.png",
 							"Quick Circle Help" );
-		helpButton = util.Jhtml.createHelpIconUserLg(util.Jhtml.circle);
+		
+		helpButton = (Ext.isLinux()) ? Jhtml.createHelpIconUserSm(Jhtml.circle)
+				   					 : Jhtml.createHelpIconUserLg(Jhtml.circle);
 
 		//// build row ///////////
 		JPanel row = Jcomp.createRowPanelGray(); 
@@ -129,6 +132,7 @@ public void mousePressed(MouseEvent e) {
 		gbc.ipady = 0;
 
 		String sp1=" ", sp2="  ";
+		if (Ext.isLinux()) {sp1="  "; sp2="   ";}
 		addToGrid(row, gbl,gbc,homeButton,	 sp2); 
 		addToGrid(row, gbl,gbc,plusButton,	 sp1);					
 		addToGrid(row, gbl,gbc,minusButton,	 sp2);

docs/img/parameters2last.png

@@ -15,10 +15,12 @@
 import javax.swing.JComboBox;
 
 import colordialog.ColorDialogHandler;
+import symap.Ext;
 import symap.frame.HelpBar;
 import symap.frame.HelpListener;
 import util.ImageViewer;
 import util.Jcomp;
+import util.Jhtml;
 import util.Utilities;
 import util.Popup;
 
@@ -62,14 +64,17 @@ protected ControlPanel(Data d, Plot p, HelpBar hb, ColorDialogHandler cdh) {
 		hb.addHelpListener(referenceSelector, this);
 
 		filter = new Filter(d, this);
-		filterButton     = Jcomp.createButtonGray(this,hb, buttonListener, 
+		filterButton     = Jcomp.createButton(this,hb, buttonListener, 
 				"Filters", "Filters and display options");
 
 		showImageButton  =  Jcomp.createIconButton(this, hb, buttonListener,
 				"/images/print.gif", "Save as image");
 		editColorsButton = Jcomp.createIconButton(this, hb, buttonListener,
 				"/images/colorchooser.gif", "Edit the color settings");
-		helpButtonLg     = util.Jhtml.createHelpIconUserLg(util.Jhtml.dotplot);
+		
+		helpButtonLg = (Ext.isLinux()) ? Jhtml.createHelpIconUserSm(Jhtml.dotplot)
+				   					   : Jhtml.createHelpIconUserLg(Jhtml.dotplot);
+		
 		helpButtonSm     = Jcomp.createIconButton(this, hb, buttonListener,
 				"/images/info.png", "Quick Help Popup");
 		statsButton = (JButton) Jcomp.createIconButton(this, hb, buttonListener,
@@ -84,6 +89,7 @@ protected ControlPanel(Data d, Plot p, HelpBar hb, ColorDialogHandler cdh) {
 		gbc.ipadx = gbc.ipady = 0;
 
 		String sp1=" ", sp2="  ";
+		if (Ext.isLinux()) {sp1="  "; sp2="    ";}
 		addToGrid(row, gbl,gbc,homeButton,sp1);	
 		addToGrid(row, gbl,gbc,plusButton, sp1);
 		addToGrid(row, gbl,gbc,minusButton,sp1);