JAL-4019 Help pages for Nucleotide Ambiguity colour scheme

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 1710bbc..cd415ea 100755 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
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 (executable)
--- 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 (executable)
--- 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.