<mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
<mapID target="colours.zappo" url="html/colourSchemes/zappo.html" />
<mapID target="colours.taylor" url="html/colourSchemes/taylor.html" />
+ <mapID target="colours.gecos-flower" url="html/colourSchemes/gecos-flower.html" />
+ <mapID target="colours.gecos-blossom" url="html/colourSchemes/gecos-blossom.html" />
+ <mapID target="colours.gecos-sunset" url="html/colourSchemes/gecos-sunset.html" />
+ <mapID target="colours.gecos-ocean" url="html/colourSchemes/gecos-ocean.html" />
<mapID target="colours.hydro" url="html/colourSchemes/hydrophobic.html" />
<mapID target="colours.helix" url="html/colourSchemes/helix.html" />
<mapID target="colours.strand" url="html/colourSchemes/strand.html" />
<tocitem text="ClustalX" target="colours.clustal" />
<tocitem text="Zappo" target="colours.zappo" />
<tocitem text="Taylor" target="colours.taylor" />
+ <tocitem text="gecos:flower" target="colours.gecos-flower" />
+ <tocitem text="gecos:blossom" target="colours.gecos-blossom" />
+ <tocitem text="gecos:sunset" target="colours.gecos-sunset" />
+ <tocitem text="gecos:ocean" target="colours.gecos-ocean" />
<tocitem text="Hydrophobicity" target="colours.hydro" />
<tocitem text="Helix propensity" target="colours.helix" />
<tocitem text="Strand propensity" target="colours.strand" />
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Blossom Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-blossom">Blossom</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ blossom is a light color scheme with high contrast, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#8bc4b4">A</td>
+ <td bgcolor="#0893fe">C</td>
+ <td bgcolor="#5fa505">D</td>
+ <td bgcolor="#dbb501">E</td>
+</tr>
+<tr>
+ <td bgcolor="#f74fa8">F</td>
+ <td bgcolor="#00d382">G</td>
+ <td bgcolor="#ff5701">H</td>
+ <td bgcolor="#9abaf3">I</td>
+</tr>
+<tr>
+ <td bgcolor="#fea527">K</td>
+ <td bgcolor="#cda5dc">L</td>
+ <td bgcolor="#f5a1b8">M</td>
+ <td bgcolor="#b5c206">N</td>
+</tr>
+<tr>
+ <td bgcolor="#10d631">P</td>
+ <td bgcolor="#bf8527">Q</td>
+ <td bgcolor="#fc9502">R</td>
+ <td bgcolor="#7e9d59">S</td>
+</tr>
+<tr>
+ <td bgcolor="#00a29c">T</td>
+ <td bgcolor="#87c0e4">V</td>
+ <td bgcolor="#fe08fb">W</td>
+ <td bgcolor="#ff4e7a">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Flower Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-flower">Flower</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ flower is a light color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#b18a51">A</td>
+ <td bgcolor="#ff5701">C</td>
+ <td bgcolor="#01a578">D</td>
+ <td bgcolor="#2da0a1">E</td>
+</tr>
+<tr>
+ <td bgcolor="#fa559d">F</td>
+ <td bgcolor="#b1c23c">G</td>
+ <td bgcolor="#0194f9">H</td>
+ <td bgcolor="#f27663">I</td>
+</tr>
+<tr>
+ <td bgcolor="#7fc3d7">K</td>
+ <td bgcolor="#df6e75">L</td>
+ <td bgcolor="#fe9daf">M</td>
+ <td bgcolor="#0bcec6">N</td>
+</tr>
+<tr>
+ <td bgcolor="#4fa32a">P</td>
+ <td bgcolor="#7295ae">Q</td>
+ <td bgcolor="#83bff1">R</td>
+ <td bgcolor="#b4bd9b">S</td>
+</tr>
+<tr>
+ <td bgcolor="#d2b576">T</td>
+ <td bgcolor="#fd997b">V</td>
+ <td bgcolor="#ff2ded">W</td>
+ <td bgcolor="#c96ecf">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Ocean Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-ocean">Ocean</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ ocean is a blue shifted, light color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#c6ca9b">A</td>
+ <td bgcolor="#c68136">C</td>
+ <td bgcolor="#4cdfa1">D</td>
+ <td bgcolor="#60dac9">E</td>
+</tr>
+<tr>
+ <td bgcolor="#ab88ae">F</td>
+ <td bgcolor="#33a551">G</td>
+ <td bgcolor="#00cffe">H</td>
+ <td bgcolor="#f2baaa">I</td>
+</tr>
+<tr>
+ <td bgcolor="#40a090">K</td>
+ <td bgcolor="#bb8a83">L</td>
+ <td bgcolor="#a48b88">M</td>
+ <td bgcolor="#0adfc3">N</td>
+</tr>
+<tr>
+ <td bgcolor="#afd365">P</td>
+ <td bgcolor="#8bd3d1">Q</td>
+ <td bgcolor="#0ca0a8">R</td>
+ <td bgcolor="#6d9b74">S</td>
+</tr>
+<tr>
+ <td bgcolor="#8d9566">T</td>
+ <td bgcolor="#e9bea4">V</td>
+ <td bgcolor="#758aee">W</td>
+ <td bgcolor="#bac3fc">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Sunset Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong><a name="gecos-sunset">Sunset</a></strong>
+ </p>
+ <p>
+ This colour scheme was generated by the gecos software. See<br/>
+ Kunzmann, P., Mayer, B.E. & Hamacher, K. Substitution matrix based color schemes for sequence alignment visualization. <em>BMC Bioinformatics</em> <strong>21</strong>, 209 (2020). https://doi.org/10.1186/s12859-020-3526-6<br/>
+ and https://gecos.biotite-python.org/ .<br/>
+ Gecos sets perceptual differences in the colour scheme according to differences in the substitution matrix.
+ </p>
+ <p>
+ sunset is a red-green color vision deficiency adapated color scheme, based on BLOSUM62.
+ </p>
+ <div align="center">
+ <table width="400" border="1">
+
+<tr>
+ <td bgcolor="#fea0fd">A</td>
+ <td bgcolor="#fc0cfe">C</td>
+ <td bgcolor="#2e7bbe">D</td>
+ <td bgcolor="#677892">E</td>
+</tr>
+<tr>
+ <td bgcolor="#ff385d">F</td>
+ <td bgcolor="#2799ff">G</td>
+ <td bgcolor="#dbc58e">H</td>
+ <td bgcolor="#fa21a1">I</td>
+</tr>
+<tr>
+ <td bgcolor="#debecc">K</td>
+ <td bgcolor="#e01e82">L</td>
+ <td bgcolor="#d13e7b">M</td>
+ <td bgcolor="#abc8f5">N</td>
+</tr>
+<tr>
+ <td bgcolor="#5766f9">P</td>
+ <td bgcolor="#8c6e81">Q</td>
+ <td bgcolor="#85746a">R</td>
+ <td bgcolor="#e7b4fd">S</td>
+</tr>
+<tr>
+ <td bgcolor="#a658b7">T</td>
+ <td bgcolor="#fe51b8">V</td>
+ <td bgcolor="#ff3701">W</td>
+ <td bgcolor="#cb5339">Y</td>
+</tr>
+
+ </table>
+ </div>
+</body>
+</html>
<td></td>
</tr>
<tr>
+ <td>gecos:flower</td>
+
+ <td bgcolor="#b18a51"></td>
+ <td bgcolor="#83bff1"></td>
+ <td bgcolor="#0bcec6"></td>
+ <td bgcolor="#01a578"></td>
+ <td bgcolor="#ff5701"></td>
+ <td bgcolor="#7295ae"></td>
+ <td bgcolor="#2da0a1"></td>
+ <td bgcolor="#b1c23c"></td>
+ <td bgcolor="#0194f9"></td>
+ <td bgcolor="#f27663"></td>
+ <td bgcolor="#df6e75"></td>
+ <td bgcolor="#7fc3d7"></td>
+ <td bgcolor="#fe9daf"></td>
+ <td bgcolor="#fa559d"></td>
+ <td bgcolor="#4fa32a"></td>
+ <td bgcolor="#b4bd9b"></td>
+ <td bgcolor="#d2b576"></td>
+ <td bgcolor="#ff2ded"></td>
+ <td bgcolor="#c96ecf"></td>
+ <td bgcolor="#fd997b"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:blossom</td>
+ <td bgcolor="#8bc4b4"></td>
+ <td bgcolor="#fc9502"></td>
+ <td bgcolor="#b5c206"></td>
+ <td bgcolor="#5fa505"></td>
+ <td bgcolor="#0893fe"></td>
+ <td bgcolor="#bf8527"></td>
+ <td bgcolor="#dbb501"></td>
+ <td bgcolor="#00d382"></td>
+ <td bgcolor="#ff5701"></td>
+ <td bgcolor="#9abaf3"></td>
+ <td bgcolor="#cda5dc"></td>
+ <td bgcolor="#fea527"></td>
+ <td bgcolor="#f5a1b8"></td>
+ <td bgcolor="#f74fa8"></td>
+ <td bgcolor="#10d631"></td>
+ <td bgcolor="#7e9d59"></td>
+ <td bgcolor="#00a29c"></td>
+ <td bgcolor="#fe08fb"></td>
+ <td bgcolor="#ff4e7a"></td>
+ <td bgcolor="#87c0e4"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:sunset</td>
+ <td bgcolor="#fea0fd"></td>
+ <td bgcolor="#85746a"></td>
+ <td bgcolor="#abc8f5"></td>
+ <td bgcolor="#2e7bbe"></td>
+ <td bgcolor="#fc0cfe"></td>
+ <td bgcolor="#8c6e81"></td>
+ <td bgcolor="#677892"></td>
+ <td bgcolor="#2799ff"></td>
+ <td bgcolor="#dbc58e"></td>
+ <td bgcolor="#fa21a1"></td>
+ <td bgcolor="#e01e82"></td>
+ <td bgcolor="#debecc"></td>
+ <td bgcolor="#d13e7b"></td>
+ <td bgcolor="#ff385d"></td>
+ <td bgcolor="#5766f9"></td>
+ <td bgcolor="#e7b4fd"></td>
+ <td bgcolor="#a658b7"></td>
+ <td bgcolor="#ff3701"></td>
+ <td bgcolor="#cb5339"></td>
+ <td bgcolor="#fe51b8"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
+ <td>gecos:ocean</td>
+ <td bgcolor="#c6ca9b"></td>
+ <td bgcolor="#0ca0a8"></td>
+ <td bgcolor="#0adfc3"></td>
+ <td bgcolor="#4cdfa1"></td>
+ <td bgcolor="#c68136"></td>
+ <td bgcolor="#8bd3d1"></td>
+ <td bgcolor="#60dac9"></td>
+ <td bgcolor="#33a551"></td>
+ <td bgcolor="#00cffe"></td>
+ <td bgcolor="#f2baaa"></td>
+ <td bgcolor="#bb8a83"></td>
+ <td bgcolor="#40a090"></td>
+ <td bgcolor="#a48b88"></td>
+ <td bgcolor="#ab88ae"></td>
+ <td bgcolor="#afd365"></td>
+ <td bgcolor="#6d9b74"></td>
+ <td bgcolor="#8d9566"></td>
+ <td bgcolor="#758aee"></td>
+ <td bgcolor="#bac3fc"></td>
+ <td bgcolor="#e9bea4"></td>
+ <td></td>
+ <td></td>
+ <td></td>
+ </tr>
+ <tr>
<td>Hydrophobicity</td>
<td bgcolor="#ad0052"></td>
<td bgcolor="#0000ff"></td>
and the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>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<br>
the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>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<br>
## New Features
+- <!-- JAL-4014 --> New GECOS amino acid colourschemes flower, blossum, ocean and sunset
- <!-- JAL-4036 --> Migrated Uniprot Free Text Search to latest Uniprot search API
- <!-- JAL-4034 --> Improved Structure Chooser's 3D-Beacons search button design and visual delay indicators
- <!-- JAL-4034 --> 3D beacons Fetch Uniprot References confirmation dialog is only shown when number of sequences exceeds a threshold
-Jalview 2.11.2.4 is the fourth patch release in the 2.11.2 series. It includes a new client for the latest Uniprot Search API (released June 2022), updated build documentation and improved user experience when discovering models and experimental structures from 3D-Beacons.
+Jalview 2.11.2.4 is the fourth patch release in the 2.11.2 series. It includes four new [colourschemes for protein alignments](colourSchemes/index.html) (Kunzman et al. 2020 BMC Bioinformatics), a new client for the latest Uniprot Search API (released June 2022), updated build documentation and improved user experience when discovering models and experimental structures from 3D-Beacons.
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BlossomColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new BlossomColourScheme object.
+ */
+ public BlossomColourScheme()
+ {
+ super(ResidueProperties.aaIndex, ResidueProperties.blossom);
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Blossom.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new BlossomColourScheme();
+ }
+}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FlowerColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new FlowerColourScheme object.
+ */
+ public FlowerColourScheme()
+ {
+ super(ResidueProperties.aaIndex, ResidueProperties.flower);
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Flower.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new FlowerColourScheme();
+ }
+}
PID("% Identity", PIDColourScheme.class),
Zappo("Zappo", ZappoColourScheme.class),
Taylor("Taylor", TaylorColourScheme.class),
+ Flower("gecos:flower", FlowerColourScheme.class),
+ Blossom("gecos:blossom", BlossomColourScheme.class),
+ Sunset("gecos:sunset", SunsetColourScheme.class),
+ Ocean("gecos:ocean", OceanColourScheme.class),
Hydrophobic("Hydrophobic", HydrophobicColourScheme.class),
Helix("Helix Propensity", HelixColourScheme.class),
Strand("Strand Propensity", StrandColourScheme.class),
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class OceanColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new OceanColourScheme object.
+ */
+ public OceanColourScheme()
+ {
+ super(ResidueProperties.aaIndex, ResidueProperties.ocean);
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Ocean.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new OceanColourScheme();
+ }
+}
Color.white // ' '
};
+ /*
+ * flower, blossom, sunset, ocean colour schemes from geocos.
+ * See https://gecos.biotite-python.org/
+ * https://raw.githubusercontent.com/biotite-dev/biotite/master/src/biotite/sequence/graphics/color_schemes/flower.json
+ * and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3526-6
+ * (https://doi.org/10.1186/s12859-020-3526-6)
+ */
+ public static final Color[] flower = { new Color(177, 138, 81), // A
+ new Color(131, 191, 241), // R
+ new Color(11, 206, 198), // N
+ new Color(1, 165, 120), // D
+ new Color(255, 87, 1), // C
+ new Color(114, 149, 174), // Q
+ new Color(45, 160, 161), // E
+ new Color(177, 194, 60), // G
+ new Color(1, 148, 249), // H
+ new Color(242, 118, 99), // I
+ new Color(223, 110, 117), // L
+ new Color(127, 195, 215), // K
+ new Color(254, 157, 175), // M
+ new Color(250, 85, 157), // F
+ new Color(79, 163, 42), // P
+ new Color(180, 189, 155), // S
+ new Color(210, 181, 118), // T
+ new Color(255, 45, 237), // W
+ new Color(201, 110, 207), // Y
+ new Color(253, 153, 123), // V
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white // .
+ };
+
+ public static final Color[] blossom = { new Color(139, 196, 180), // A
+ new Color(252, 149, 2), // R
+ new Color(181, 194, 6), // N
+ new Color(95, 165, 5), // D
+ new Color(8, 147, 254), // C
+ new Color(191, 133, 39), // Q
+ new Color(219, 181, 1), // E
+ new Color(0, 211, 130), // G
+ new Color(255, 87, 1), // H
+ new Color(154, 186, 243), // I
+ new Color(205, 165, 220), // L
+ new Color(254, 165, 39), // K
+ new Color(245, 161, 184), // M
+ new Color(247, 79, 168), // F
+ new Color(16, 214, 49), // P
+ new Color(126, 157, 89), // S
+ new Color(0, 162, 156), // T
+ new Color(254, 8, 251), // W
+ new Color(255, 78, 122), // Y
+ new Color(135, 192, 228), // V
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white // .
+ };
+
+ public static final Color[] sunset = { new Color(254, 160, 253), // A
+ new Color(133, 116, 106), // R
+ new Color(171, 200, 245), // N
+ new Color(46, 123, 190), // D
+ new Color(252, 12, 254), // C
+ new Color(140, 110, 129), // Q
+ new Color(103, 120, 146), // E
+ new Color(39, 153, 255), // G
+ new Color(219, 197, 142), // H
+ new Color(250, 33, 161), // I
+ new Color(224, 30, 130), // L
+ new Color(222, 190, 204), // K
+ new Color(209, 62, 123), // M
+ new Color(255, 56, 93), // F
+ new Color(87, 102, 249), // P
+ new Color(231, 180, 253), // S
+ new Color(166, 88, 183), // T
+ new Color(255, 55, 1), // W
+ new Color(203, 83, 57), // Y
+ new Color(254, 81, 184), // V
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white // .
+ };
+
+ public static final Color[] ocean = { new Color(198, 202, 155), // A
+ new Color(12, 160, 168), // R
+ new Color(10, 223, 195), // N
+ new Color(76, 223, 161), // D
+ new Color(198, 129, 54), // C
+ new Color(139, 211, 209), // Q
+ new Color(96, 218, 201), // E
+ new Color(51, 165, 81), // G
+ new Color(0, 207, 254), // H
+ new Color(242, 186, 170), // I
+ new Color(187, 138, 131), // L
+ new Color(64, 160, 144), // K
+ new Color(164, 139, 136), // M
+ new Color(171, 136, 174), // F
+ new Color(175, 211, 101), // P
+ new Color(109, 155, 116), // S
+ new Color(141, 149, 102), // T
+ new Color(117, 138, 238), // W
+ new Color(186, 195, 252), // Y
+ new Color(233, 190, 164), // V
+ Color.white, // B
+ Color.white, // Z
+ Color.white, // X
+ Color.white, // -
+ Color.white, // *
+ Color.white // .
+ };
+
// Dunno where I got these numbers from
public static final double[] hyd2 = { 0.62, // A
0.29, // R
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SunsetColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new SunsetColourScheme object.
+ */
+ public SunsetColourScheme()
+ {
+ super(ResidueProperties.aaIndex, ResidueProperties.sunset);
+ }
+
+ @Override
+ public boolean isPeptideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.Sunset.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new SunsetColourScheme();
+ }
+}
git://source.jalview.org / jalview.git / commitdiff