From 3f5088fe082c479c0de91f897ed26a5adf540f98 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 12 May 2022 15:35:12 +0100 Subject: [PATCH] JAL-4014 4 gecos colour schemes added to help documentation --- help/help/help.jhm | 4 + help/help/helpTOC.xml | 4 + help/help/html/colourSchemes/gecos-blossom.html | 83 ++++++++++++++++++ help/help/html/colourSchemes/gecos-flower.html | 83 ++++++++++++++++++ help/help/html/colourSchemes/gecos-ocean.html | 83 ++++++++++++++++++ help/help/html/colourSchemes/gecos-sunset.html | 83 ++++++++++++++++++ help/help/html/colourSchemes/index.html | 105 +++++++++++++++++++++++ help/help/html/menus/alignmentMenu.html | 1 + help/help/html/menus/alwcolour.html | 1 + 9 files changed, 447 insertions(+) create mode 100755 help/help/html/colourSchemes/gecos-blossom.html create mode 100755 help/help/html/colourSchemes/gecos-flower.html create mode 100755 help/help/html/colourSchemes/gecos-ocean.html create mode 100755 help/help/html/colourSchemes/gecos-sunset.html diff --git a/help/help/help.jhm b/help/help/help.jhm index 6b06d36..1710bbc 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -95,6 +95,10 @@ + + + + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index a9b9788..1b4156e 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -90,6 +90,10 @@ + + + + diff --git a/help/help/html/colourSchemes/gecos-blossom.html b/help/help/html/colourSchemes/gecos-blossom.html new file mode 100755 index 0000000..08ca8a6 --- /dev/null +++ b/help/help/html/colourSchemes/gecos-blossom.html @@ -0,0 +1,83 @@ + + + +Blossom Colour Scheme + + + + +

+ Blossom +

+

+ This colour scheme was generated by the gecos software. See
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. BMC Bioinformatics 21, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6
+ and https://gecos.biotite-python.org/ .
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix. +

+

+ blossom is a light color scheme with high contrast, based on BLOSUM62. +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACDE
FGHI
KLMN
PQRS
TVWY
+
+ + diff --git a/help/help/html/colourSchemes/gecos-flower.html b/help/help/html/colourSchemes/gecos-flower.html new file mode 100755 index 0000000..94452e8 --- /dev/null +++ b/help/help/html/colourSchemes/gecos-flower.html @@ -0,0 +1,83 @@ + + + +Flower Colour Scheme + + + + +

+ Flower +

+

+ This colour scheme was generated by the gecos software. See
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. BMC Bioinformatics 21, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6
+ and https://gecos.biotite-python.org/ .
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix. +

+

+ flower is a light color scheme, based on BLOSUM62. +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACDE
FGHI
KLMN
PQRS
TVWY
+
+ + diff --git a/help/help/html/colourSchemes/gecos-ocean.html b/help/help/html/colourSchemes/gecos-ocean.html new file mode 100755 index 0000000..5407bdc --- /dev/null +++ b/help/help/html/colourSchemes/gecos-ocean.html @@ -0,0 +1,83 @@ + + + +Ocean Colour Scheme + + + + +

+ Ocean +

+

+ This colour scheme was generated by the gecos software. See
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. BMC Bioinformatics 21, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6
+ and https://gecos.biotite-python.org/ .
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix. +

+

+ ocean is a blue shifted, light color scheme, based on BLOSUM62. +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACDE
FGHI
KLMN
PQRS
TVWY
+
+ + diff --git a/help/help/html/colourSchemes/gecos-sunset.html b/help/help/html/colourSchemes/gecos-sunset.html new file mode 100755 index 0000000..82eedb4 --- /dev/null +++ b/help/help/html/colourSchemes/gecos-sunset.html @@ -0,0 +1,83 @@ + + + +Sunset Colour Scheme + + + + +

+ Sunset +

+

+ This colour scheme was generated by the gecos software. See
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. BMC Bioinformatics 21, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6
+ and https://gecos.biotite-python.org/ .
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix. +

+

+ sunset is a red-green color vision deficiency adapated color scheme, based on BLOSUM62. +

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ACDE
FGHI
KLMN
PQRS
TVWY
+
+ + diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html index f0ae161..672910e 100755 --- a/help/help/html/colourSchemes/index.html +++ b/help/help/html/colourSchemes/index.html @@ -198,6 +198,111 @@ td { + gecos:flower + + + + + + + + + + + + + + + + + + + + + + + + + + + gecos:blossom + + + + + + + + + + + + + + + + + + + + + + + + + + gecos:sunset + + + + + + + + + + + + + + + + + + + + + + + + + + gecos:ocean + + + + + + + + + + + + + + + + + + + + + + + + + Hydrophobicity diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html index e26707f..6532933 100755 --- a/help/help/html/menus/alignmentMenu.html +++ b/help/help/html/menus/alignmentMenu.html @@ -477,6 +477,7 @@ and the intensity threshold for transition between them.
  • Colour Scheme options: None, ClustalX, 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 Defined
    diff --git a/help/help/html/menus/alwcolour.html b/help/help/html/menus/alwcolour.html index 9a96595..0e10f44 100755 --- a/help/help/html/menus/alwcolour.html +++ b/help/help/html/menus/alwcolour.html @@ -38,6 +38,7 @@ the intensity threshold for transition between them.
  • Colour Scheme options: None, ClustalX, 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 Defined
    -- 1.7.10.2