JAL-4019 Clarification of position on 'X' in help text

[jalview.git] / help / help / html / colourSchemes / index.html

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index 672910e..9ba0578 100755 (executable)
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -198,7 +198,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:flower</td>
+                                                       <td>gecos Flower</td>
 
                                                        <td bgcolor="#b18a51"></td>
                                                        <td bgcolor="#83bff1"></td>
@@ -225,7 +225,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:blossom</td>
+                                                       <td>gecos Blossom</td>
                                                        <td bgcolor="#8bc4b4"></td>
                                                        <td bgcolor="#fc9502"></td>
                                                        <td bgcolor="#b5c206"></td>
@@ -251,7 +251,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:sunset</td>
+                                                       <td>gecos Sunset</td>
                                                        <td bgcolor="#fea0fd"></td>
                                                        <td bgcolor="#85746a"></td>
                                                        <td bgcolor="#abc8f5"></td>
@@ -277,7 +277,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:ocean</td>
+                                                       <td>gecos Ocean</td>
                                                        <td bgcolor="#c6ca9b"></td>
                                                        <td bgcolor="#0ca0a8"></td>
                                                        <td bgcolor="#0adfc3"></td>
@@ -459,13 +459,11 @@ td {
                                                        <td>I</td>
                                                        <!--Inosine-->
                                                        <td>X</td>
-                                                       <!--Xanthine-->
+                                                       <!--Unknown (sometimes Xanthine)-->
                                                        <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="#4f6f6f"></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>