X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp%2Fhtml%2FcolourSchemes%2Findex.html;h=6b77d913404f0b4096e84a265d245cac867e70b1;hb=56ce5cb6fd0b54f831cf35859886cd69a7f522a3;hp=e0066186b295c115f90bd0af6ccec230d1d192c7;hpb=7283c5058e1ae501fe3ab99f6a6453afc6bf8240;p=jalview.git

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index e006618..6b77d91 100755
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -94,7 +94,8 @@ td {
 				<td>
 					<table border="1">
 						<tr>
-							<td nowrap></td>
+							<td nowrap>Name</td>
+							<td nowrap>CLI name</td>
 							<td>A</td>
 							<td>R</td>
 							<td>N</td>
@@ -121,6 +122,7 @@ td {
 						</tr>
 						<tr>
 							<td height="24">Clustal</td>
+							<td>clustal</td>
 							<td bgcolor="#80a0f0"></td>
 							<td bgcolor="#f01505"></td>
 							<td bgcolor="#00ff00"></td>
@@ -147,6 +149,7 @@ td {
 						</tr>
 						<tr>
 							<td height="24">Zappo</td>
+							<td>zappo</td>
 							<td bgcolor="#ffafaf"></td>
 							<td bgcolor="#6464ff"></td>
 							<td bgcolor="#00ff00"></td>
@@ -173,6 +176,7 @@ td {
 						</tr>
 						<tr>
 							<td>Taylor</td>
+							<td>taylor</td>
 							<td bgcolor="#ccff00"></td>
 							<td bgcolor="#0000ff"></td>
 							<td bgcolor="#cc00ff"></td>
@@ -199,7 +203,7 @@ td {
 						</tr>
 						<tr>
 							<td>gecos Flower</td>
-
+							<td>gecos-flower</td>
 							<td bgcolor="#b18a51"></td>
 							<td bgcolor="#83bff1"></td>
 							<td bgcolor="#0bcec6"></td>
@@ -226,6 +230,7 @@ td {
 						</tr>
 						<tr>
 							<td>gecos Blossom</td>
+							<td>gecos-blossom</td>
 							<td bgcolor="#8bc4b4"></td>
 							<td bgcolor="#fc9502"></td>
 							<td bgcolor="#b5c206"></td>
@@ -252,6 +257,7 @@ td {
 						</tr>
 						<tr>
 							<td>gecos Sunset</td>
+							<td>gecos-sunset</td>
 							<td bgcolor="#fea0fd"></td>
 							<td bgcolor="#85746a"></td>
 							<td bgcolor="#abc8f5"></td>
@@ -278,6 +284,7 @@ td {
 						</tr>
 						<tr>
 							<td>gecos Ocean</td>
+							<td>gecos-ocean</td>
 							<td bgcolor="#c6ca9b"></td>
 							<td bgcolor="#0ca0a8"></td>
 							<td bgcolor="#0adfc3"></td>
@@ -304,6 +311,7 @@ td {
 						</tr>
 						<tr>
 							<td>Hydrophobicity</td>
+							<td>hydrophobicity</td>
 							<td bgcolor="#ad0052"></td>
 							<td bgcolor="#0000ff"></td>
 							<td bgcolor="#0c00f3"></td>
@@ -330,6 +338,7 @@ td {
 						</tr>
 						<tr>
 							<td>Helix Propensity</td>
+							<td>helix-propensity</td>
 							<td bgcolor="#e718e7"></td>
 							<td bgcolor="#6f906f"></td>
 							<td bgcolor="#1be41b"></td>
@@ -356,6 +365,7 @@ td {
 						</tr>
 						<tr>
 							<td nowrap>Strand Propensity</td>
+							<td>strand-propensity</td>
 							<td bgcolor="#5858a7"></td>
 							<td bgcolor="#6b6b94"></td>
 							<td bgcolor="#64649b"></td>
@@ -382,6 +392,7 @@ td {
 						</tr>
 						<tr>
 							<td>Turn Propensity</td>
+							<td>turn-propensity</td>
 							<td bgcolor="#2cd3d3"></td>
 							<td bgcolor="#708f8f"></td>
 							<td bgcolor="#ff0000"></td>
@@ -408,6 +419,7 @@ td {
 						</tr>
 						<tr>
 							<td>Buried Index</td>
+							<td>buried-index</td>
 							<td bgcolor="#00a35c"></td>
 							<td bgcolor="#00fc03"></td>
 							<td bgcolor="#00eb14"></td>
@@ -445,7 +457,8 @@ td {
 				<td>
 					<table border="1">
 						<tr>
-							<td nowrap></td>
+							<td nowrap>Name</td>
+							<td nowrap>CLI name</td>
 							<td>A</td>
 							<!--Adenine-->
 							<td>C</td>
@@ -459,13 +472,11 @@ 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>
@@ -481,10 +492,13 @@ 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>
+							<td>nucleotide</td>
 							<td bgcolor="#64F73F"></td>
 							<td bgcolor="#FFB340"></td>
 							<td bgcolor="#EB413C"></td>
@@ -505,7 +519,30 @@ td {
 							<td></td>
 						</tr>
 						<tr>
+							<td height="24">Nucleotide Ambiguity</td>
+							<td>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>purine-pyrimidine</td>
 							<td bgcolor="#FF83FA"></td>
 							<td bgcolor="#40E0D0"></td>
 							<td bgcolor="#FF83FA"></td>