Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[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..6b77d91 100755 (executable)
--- 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>
@@ -198,8 +202,8 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:flower</td>
-
+                                                       <td>gecos Flower</td>
+                                                       <td>gecos-flower</td>
                                                        <td bgcolor="#b18a51"></td>
                                                        <td bgcolor="#83bff1"></td>
                                                        <td bgcolor="#0bcec6"></td>
@@ -225,7 +229,8 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:blossom</td>
+                                                       <td>gecos Blossom</td>
+                                                       <td>gecos-blossom</td>
                                                        <td bgcolor="#8bc4b4"></td>
                                                        <td bgcolor="#fc9502"></td>
                                                        <td bgcolor="#b5c206"></td>
@@ -251,7 +256,8 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:sunset</td>
+                                                       <td>gecos Sunset</td>
+                                                       <td>gecos-sunset</td>
                                                        <td bgcolor="#fea0fd"></td>
                                                        <td bgcolor="#85746a"></td>
                                                        <td bgcolor="#abc8f5"></td>
@@ -277,7 +283,8 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:ocean</td>
+                                                       <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>