From 184fb2cb4f0420156e2601a7187b77b41406b52d Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sun, 13 Nov 2022 10:51:22 +0000
Subject: [PATCH] JAL-4019 Help pages for Nucleotide Ambiguity colour scheme

---
 help/help/help.jhm                                 |    1 +
 help/help/helpTOC.xml                              |    1 +
 help/help/html/colourSchemes/index.html            |   29 ++++-
 .../html/colourSchemes/nucleotideambiguity.html    |  114 ++++++++++++++++++++
 help/help/html/menus/alignmentMenu.html            |    2 +-
 help/help/html/menus/alwcolour.html                |    2 +-
 6 files changed, 143 insertions(+), 6 deletions(-)
 create mode 100755 help/help/html/colourSchemes/nucleotideambiguity.html

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 1710bbc..cd415ea 100755
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -105,6 +105,7 @@
    <mapID target="colours.turn" url="html/colourSchemes/turn.html" />
    <mapID target="colours.buried" url="html/colourSchemes/buried.html" />
    <mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
+   <mapID target="colours.nucleotideambiguity" url="html/colourSchemes/nucleotideambiguity.html" />
    <mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
    <mapID target="colours.pid" url="html/colourSchemes/pid.html" />
    <mapID target="colours.user" url="html/colourSchemes/user.html"/>
diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 3308456..877c758 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -100,6 +100,7 @@
 			<tocitem text="Turn propensity" target="colours.turn" />
 			<tocitem text="Buried index" target="colours.buried" />
 			<tocitem text="Nucleotide colours" target="colours.nucleotide" />
+			<tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
 			<tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
 			<tocitem text="Blosum62" target="colours.blosum" />
 			<tocitem text="by Percentage Identity" target="colours.pid" />
diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index e006618..a816cca 100755
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -459,13 +459,11 @@ td {
 							<td>I</td>
 							<!--Inosine-->
 							<td>X</td>
-							<!--Xanthine-->
+							<!--Xanthine (sometimes Unknown)-->
 							<td>R</td>
 							<!--Unknown Purine-->
 							<td>Y</td>
 							<!--Unknown Pyrimidine-->
-							<td>N</td>
-							<!--Unknown-->
 							<td>W</td>
 							<!--Weak nucleotide (A or T)-->
 							<td>S</td>
@@ -481,7 +479,9 @@ td {
 							<td>D</td>
 							<!--Not C (A or G or T)-->
 							<td>V</td>
-							<!--Not T (A or G or C-->
+							<!--Not T (A or G or C)-->
+							<td>N</td>
+							<!--Unknown-->
 						</tr>
 						<tr>
 							<td height="24">Nucleotide</td>
@@ -505,6 +505,27 @@ td {
 							<td></td>
 						</tr>
 						<tr>
+							<td height="24">Nucleotide Ambiguity</td>
+							<td bgcolor="#f0fff0"></td>
+							<td bgcolor="#f0fff0"></td>
+							<td bgcolor="#f0fff0"></td>
+							<td bgcolor="#f0fff0"></td>
+							<td bgcolor="#f0fff0"></td>
+							<td bgcolor="#ffffff"></td>
+							<td bgcolor="#2f4f4f"></td>
+							<td bgcolor="#CD5C5C"></td>
+							<td bgcolor="#008000"></td>
+							<td bgcolor="#4682B4"></td>
+							<td bgcolor="#FF8C00"></td>
+							<td bgcolor="#9ACD32"></td>
+							<td bgcolor="#9932CC"></td>
+							<td bgcolor="#8b4513"></td>
+							<td bgcolor="#808080"></td>
+							<td bgcolor="#483D8B"></td>
+							<td bgcolor="#b8860b"></td>
+							<td bgcolor="#2f4f4f"></td>
+						</tr>
+						<tr>
 							<td height="24">Purine/Pyrimidine</td>
 							<td bgcolor="#FF83FA"></td>
 							<td bgcolor="#40E0D0"></td>
diff --git a/help/help/html/colourSchemes/nucleotideambiguity.html b/help/help/html/colourSchemes/nucleotideambiguity.html
new file mode 100755
index 0000000..b6660fb
--- /dev/null
+++ b/help/help/html/colourSchemes/nucleotideambiguity.html
@@ -0,0 +1,114 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Nucleotide Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+	text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+  <p>
+    <strong>Nucleotide Ambiguity Colours</strong>
+  </p>
+  <div align="center">
+    <table width="200" border="1">
+      <tr>
+        <td bgcolor="#f0fff0">A</td>
+        <td>Adenine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#f0fff0">C</td>
+        <td>Cytosine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#f0fff0">G</td>
+        <td>Guanine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#f0fff0">T</td>
+        <td>Thymine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#f0fff0">U</td>
+        <td>Uracil</td>
+      </tr>
+      <tr>
+        <td bgcolor="#ffffff">I</td>
+        <td>Inosine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#4f6f6f">X</td>
+        <td>Xanthine (sometimes Unknown)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#CD5C5C">R</td>
+        <td>Unknown Purine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#008000">Y</td>
+        <td>Unknown Pyrimidine</td>
+      </tr>
+      <tr>
+        <td bgcolor="#4682B4">W</td>
+        <td>Weak nucleotide (A or T)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#FF8C00">S</td>
+        <td>Strong nucleotide (G or C)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#9ACD32">M</td>
+        <td>Amino (A or C)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#9932CC">K</td>
+        <td>Keto (G or T)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#8b4513">B</td>
+        <td>Not A (G or C or T)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#808080">H</td>
+        <td>Not G (A or C or T)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#483D8B">D</td>
+        <td>Not C (A or G or T)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#b8860b">V</td>
+        <td>Not T (A or G or C)</td>
+      </tr>
+      <tr>
+        <td bgcolor="#2f4f4f">N</td>
+        <td>Unknown</td>
+      </tr>
+    </table>
+  </div>
+</body>
+</html>
diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html
index 6532933..549a1f3 100755
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -479,7 +479,7 @@
           Blosum62 Score, Percentage Identity, Zappo, Taylor,
 	  gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
           Hydrophobicity, Helix Propensity, Strand Propensity, Turn
-          Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+          Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
           Defined<br>
       </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
           for a description of all colour schemes.
diff --git a/help/help/html/menus/alwcolour.html b/help/help/html/menus/alwcolour.html
index 0e10f44..5b8d00b 100755
--- a/help/help/html/menus/alwcolour.html
+++ b/help/help/html/menus/alwcolour.html
@@ -40,7 +40,7 @@
         Blosum62 Score, Percentage Identity, Zappo, Taylor,
 	gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
         Hydrophobicity, Helix Propensity, Strand Propensity, Turn
-        Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+        Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
         Defined<br>
     </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
         a description of all colour schemes.
-- 
1.7.10.2