v5.7.0

Updated docs

Author: cariann09

docs/Details.html

@@ -13,9 +13,11 @@
 		<img src="./img/agcol_logo.gif" alt="AGCoL" style="width: 160px; border:1px solid black; background: white;"></a>
 <p class=sidetit>&nbsp;&nbsp;Queries</p>
 <p>
-<a href="#query">Query Setup</a>
+<a href="#instruct">&gt;Instructions</a>
+<a href="#query">&gt;Query Setup</a>
 <a href="#result">Result Panel</a>
-<a href="#rtab">Results</a>
+<a href="#but">&nbsp;&nbsp;&nbsp;Top buttons</a>
+<a href="#rtab">&gt;Results</a>
 
 <p>&nbsp;
 <a href="#top">Go to top</a>
@@ -82,7 +84,7 @@
 	<tr><td>&nbsp;
 	<tr><td>&nbsp;
 	<tr><td><ttl>Extra topic:</ttl>
-	<tr><td>&nbsp;&nbsp;&nbsp;<a href="#msp">3-chromosomes</a>
+	<tr><td>&nbsp;&nbsp;&nbsp;<a href="Details.html#q3" class="ext" target="_blank">3-chr queries</a>
 	</table>
 </table>
 
@@ -182,9 +184,8 @@ <h3>Rules</h3>
 <p>
 <table><tr><td>
 Not numbered: The <ttx>Gene#</ttx> column will show the chromosome followed by ".~".
-<p>Numbered: These are numbered sequentially, where the counts start after the annotated gene numbers.
-For example, if the last Gene# for Chr03 is 5550 (e.g. 3.5550.), the first pseudo gene number will be 6000 and
-the column will show 3.6000.~.
+<p>Numbered: These are numbered sequentially, where the counts start after the annotated gene numbers and
+any already number pseudo's for the chromosome, hence, providing a unique <ttx>Gene#</ttx>.
 
 <td><a href="img/query_pseudo.png"><img src="img/query_pseudo.png" alt="Pseudo genes" style="border: 1px solid black; width:  350px"></a>
 </table>
@@ -770,14 +771,14 @@ <h4>4.2 MSA...</h4>
 <br>&rarr; All executables were removed that did not seem necessary. However, I may have removed
 one(s) that are used in certain unusual situations when <tt>--auto</tt> is used. Try again with <tt>--auto</tt> unchecked.
 <br>&rarr; On Mac, if you are using MAFFT <tt>--auto</tt>, you may get a "Cannot be verified" for <tt>dndpre</tt>.
-See <a href="TroubleShoot.html#macos">MacOS and external programs</a> to fix this.
+See <a href="TroubleShoot.html#macos" class="ext" target="_blank">MacOS and external programs</a> to fix this.
 
 <a id="view2D"></a>
 <h4>4.3 View 2D</h4>
 
 
 <a href="img/query_2D.png"><img src="img/query_2D.png" alt="query 2D" style="border: 1px solid black; width: 400px"></a>
-<p>This displays the <ttl>2D</ttl> view for the selected entry (see <a href="#msp">3-chromosomes</a>).
+<p>This displays the <ttl>2D</ttl> view for the selected entry.
 The region displayed can be specified by the drop-down beside the <ttl>View 2D</ttl> button, as follows:
 
 <a id="group"></a>
@@ -833,6 +834,8 @@ <h4>4.3 View 2D</h4>
 	can be used with these rows.
 	<p><a href="img/query_columns_mult.png"><img src="img/query_columns_mult.png" alt="query multi columns" style="border: 1px solid black; width: 280px"></a>
 
+	<p>&nbsp;<p>It is possible to select two rows for a 3-chromosome <ttb>2D</ttb>,
+	see <a href="Details.html#q3" class="ext" target="_blank">3-chr queries</a>.
 	<td><a href="img/query_synteny.png"><img src="img/query_synteny.png" alt="query synteny" style="border: 1px solid black; width: 450px"></a>
 </table>
 
@@ -1060,7 +1063,6 @@ <h4>4.6 Search...</h4>
 <a id="rtab"></a>
 <h2><small>&gt;</small> Results</h2>
 
-
 <a href="img/query_result_tab.png"><img src="img/query_result_tab.png" alt="query results tab" style="border: 1px solid black; width: 600px"></a>
 <p>All query results are listed under the <ttb>&gt; Results</ttb> tab on the left.
 Clicking this tab shows the table of queries illustrated above.
@@ -1069,33 +1071,6 @@ <h2><small>&gt;</small> Results</h2>
 <p>The only way to remove query results from the left tab is by selecting them in this table followed
 by <ttl>Remove Selected</ttl>, remove all with <ttl>Remove All</ttl>.
 
-<!---------------------------------------------------------------->
-<a id="msp"></a>
-<h3>3-chromosomes</h3>
-
-&rarr; <a href="#report">Report</a> is only way to view more than two species in a query row (described
-immediately above).
-<br>&rarr;As shown here, it is possible to bring up the 2D display with 3 chromosomes from the query table.
-<p>
-<table>
-	<tr>
-	<td style="vertical-align: text-top;">
-	Select two rows with the following requirements:
-	(1) Each row must have two genes.
-	(2) There must be a shared gene.
-
-	<p><small>Different species</small>
-	<br><a href="img/query_2D_2row.png"><img src="img/query_2D_2row.png" alt="Select 2 rows" style="border: 1px solid black; width: 280px"></a>
-
-	<p><small>Same species</small>
-	<br><a href="img/query_2D_2rowb.png"><img src="img/query_2D_2rowb.png" alt="Select 2 rows" style="border: 1px solid black; width: 240px"></a>
-	<p>Select <ttl>View 2D</ttl> with either the <ttx>Region</ttx> and <ttx>Collinear</ttx> options. The
-	image on the right used the <ttx>Collinear</ttx> options.
-	<p>&nbsp;<p>
-	<a href="Details.html#con" class="ext" target="_blank">2D Highlight Conserved Genes</a>
-shows how to highlight shared or unique genes in the 2D display of 3 chromosomes.
-	<td><a href="img/2d-3d-coset.png"><img src="img/2d-3chr-coset.png" alt="report A.thal ref" style="border: 1px solid black; width: 480px"></a>
-</table>
 
 <!---- END BODY -->
 <table style="width: 95%"><tr><td style="text-align: left">

docs/Query.html

@@ -67,6 +67,26 @@ <h3>Summary of recent major releases</h3>
 <tr><td><a href="#v540">v5.4.0</a><td>(6-Apr-23)<td>Improved <ttx>Cluster Hit</ttx> algorithm <ttx>Algo1</ttx> for the detection of gene homology.
 </table>
 
+<a id="v570"></a>
+<h3>Release: v5.7.0 (20-July-25)</h3>
+Small improvements.
+<ul>
+<li><ttb>Manager</ttb>: (1) For the <ttx>Selected</ttx> on the <ttb>Manager</ttb>, the <ttx>#Annotated</ttx> was
+wrong if pseudo genes were assigned; it has been changed to show <ttx>Exons</ttx> instead. (2) The <ttb>View</ttb> now has a <ttx>Gap</ttx> column (if any exists)
+and a <ttx>Totals</ttx> row.
+<li><ttb>2D</ttb>: The 3-track g2x2 (shared) and g2x1 (unique) was confusing because it only worked on visible hits;
+see <a href="Details.html#2dg2" class="ext" target="_blank">3-chr conserved</a> for the way it works now.
+<li>Tiny changes:
+<ul>
+<li><ttb>A&S</ttb> <ttl>Number Pseudo</ttl>: This option could duplicate pseudo <ttx>Gene#</ttx> for different synteny pairs;
+this worked but may be confusing when querying &gt;2 synteny pairs. This has been corrected. An existing SyMAP database can be updated running
+<tt>symap -pseudo</tt>.
+<li><ttb>2D</ttb>: Slight change in hit-wire information and popup (see <a href="UserGuide.html#info" class="ext" target="_blank">Hit popup</a>).
+<li><ttb>Queries</ttb>: Pseudo message in <ttx>Instructions</ttx> has been redone.
+<li>If a <ttl>Display Name</ttl> is re-used, it provides more information about the duplicate.
+</ul>
+</ul>
+
 <a id="v569"></a>
 <h3>Release: v5.6.9 (19-June-25)</h3>
 
@@ -142,7 +162,6 @@ <h3>Release: v5.6.7 (22-May-25)</h3>
 <p>
 <li><small>Developers: Rename synteny/SyGraph to Merge and move merge routines to it; add orient.
 Any java file I looked at, I took out old CASddd comments.</small>
-</small>
 </ul>
 
 
@@ -255,7 +274,7 @@ <h3>Release: v5.6.3 (5-Apr-25)</h3>
 <li><ttl>Queries</ttl>
 <ul>
 <li>Bug fix on Linux: crashed on searching for a given collinear set.
-<li><ttl>MSA</ttl>: See <a href="Query.html#msaAlign" ext="class" target="_blank">MSA</a>.
+<li><ttl>MSA</ttl>: See <a href="Query.html#msaAlign" class="ext" target="_blank">MSA</a>.
 	<ul>
 	<li>MUSCLE is very slow, so MAFFT has been added which is many times faster.
 	<li>Bug fix: negative strand hits were not reversed complemented.
@@ -269,12 +288,12 @@ <h3>Release: v5.6.3 (5-Apr-25)</h3>
 	The results are sorted according to the lower table of information. The results are
 	in a split pane.
 	</ul>
-<li><ttl>Cluster genes</ttl>: See <a href="Query.html#clhit" ext="class" target="_blank">Cluster genes</a>.
+<li><ttl>Cluster genes</ttl>: See <a href="Query.html#clhit" class="ext" target="_blank">Cluster genes</a>.
 	<ul>
 	<li>A new filter called <ttl>Cluster hits</ttl> has replaced <ttl>PgeneF</ttl> (which can still
 	be run using <tt>viewSymap -g</tt>).
 	</ul>
-<li><ttl>Gene Pair Report...</ttl> See <a href="Query.html#report" ext="class" target="_blank">Report</a>.
+<li><ttl>Gene Pair Report...</ttl> See <a href="Query.html#report" class="ext" target="_blank">Report</a>.
 <ul>
 	<li><ttl>Multi-Hit Gene Report</ttl>:
 	(1) This was confusing because groups can be created from non-gene hits,
@@ -291,7 +310,8 @@ <h3>Release: v5.6.3 (5-Apr-25)</h3>
 </ul>
 <li>The <ttl>Grp#</ttl> and <ttl>Grp Size</ttl> have been merged into one column:
 <tt>Size-Grp#</tt>.
-<li>Other:<small>
+<li>Other:
+<small>
 <ul>
 <li>Rewrote the Instruction page since its HTML was obsolete in Java20.
 Formatted the table Statistics better. If a chromosome was selected, the statistics did not show the Groups counts; it does now.
@@ -341,7 +361,7 @@ <h3>Release: v5.6.2 (24-Feb-25)</h3>
 		<ul>
 		<li>It will display <ttl>View 2D</ttl> with 3-tracks (chromosomes) if two rows are selected which have a common reference gene,
 		and has 'both' genes in both rows. This works with the <ttx>Region</ttx> or <ttx>Collinear Set</ttx> options.
-		See <a href="Query.html#msp" class="ext" target="_blank">3-chromosome 2D</a>.
+		See <a href="Query.html#q3" class="ext" target="_blank">3-chromosome 2D</a>.
 		<li>A new <ttx>Gene#</ttx> checkbox for <ttl>View 2D</ttl> which shows the <ttx>Gene#</ttx> instead of the <ttx>Annotation</ttx>.
 		</ul>
 	<li><ttl>Report...</ttl>:

docs/Release.html

@@ -129,9 +129,11 @@ <h3>Overview</h3>
 SyMAP is a system for computing, displaying, and analyzing syntenic alignments between
 divergent eukaryotic genomes.  It is designed for the comparison of a few genomes at a time
 (i.e. 2-4) where synteny is computed between each pair.
-Its features include the following:
+
 <table class="tx">
 <tr><td>
+Its features include the following:
+<p>
 <ul>
 	<li><i>Compute</i>
 	<ul>
@@ -145,11 +147,13 @@ <h3>Overview</h3>
 		<li>Complete queries on annotation, collinear genes, multi-hit genes, etc.
 	</ul>
 </ul>
-<td><a href="img/symapPlants.png"><img src="img/symapPlants.png" alt="viewPlants"
-		style="width:220px;border: 1px solid black;"></a>
+<td>
+<center><small>Click an image to see the closeup.</small></center>
+<br><a href="img/symapPlants.png"><img src="img/symapPlants.png" alt="viewPlants"
+		style="width:390px;border: 1px solid black;"></a>
 </table>
 
-<center><small>Click an image to see the closeup.</small></center>
+
 <table class="tx">
 	<tr>
 		<td><a href="img/dotplot-3g.png"><img src="img/dotplot-3g.png" alt="dotplot-3-genome"