From: Ben Soares Date: Sun, 13 Nov 2022 10:51:22 +0000 (+0000) Subject: JAL-4019 Help pages for Nucleotide Ambiguity colour scheme X-Git-Tag: Release_2_11_3_0~23^2~8^2~4^2~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=184fb2cb4f0420156e2601a7187b77b41406b52d;p=jalview.git 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 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -105,6 +105,7 @@ + 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 @@ + 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 { I X - + R Y - N - W S @@ -481,7 +479,9 @@ td { D V - + + N + Nucleotide @@ -505,6 +505,27 @@ td { + Nucleotide Ambiguity + + + + + + + + + + + + + + + + + + + + Purine/Pyrimidine 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 @@ + + + +Nucleotide Colour Scheme + + + + +

+ Nucleotide Ambiguity Colours +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
AAdenine
CCytosine
GGuanine
TThymine
UUracil
IInosine
XXanthine (sometimes Unknown)
RUnknown Purine
YUnknown Pyrimidine
WWeak nucleotide (A or T)
SStrong nucleotide (G or C)
MAmino (A or C)
KKeto (G or T)
BNot A (G or C or T)
HNot G (A or C or T)
DNot C (A or G or T)
VNot T (A or G or C)
NUnknown
+
+ + 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
See colours 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
See colours for a description of all colour schemes.