JAL-4014 4 gecos colour schemes added

diff --git a/src/jalview/schemes/BlossomColourScheme.java b/src/jalview/schemes/BlossomColourScheme.java
new file mode 100755 (executable)
index 0000000..9b92405
--- /dev/null
+++ b/src/jalview/schemes/BlossomColourScheme.java
@@ -0,0 +1,64 @@
+/*
+ * 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();
+  }
+}

diff --git a/src/jalview/schemes/FlowerColourScheme.java b/src/jalview/schemes/FlowerColourScheme.java
new file mode 100755 (executable)
index 0000000..040e6e4
--- /dev/null
+++ b/src/jalview/schemes/FlowerColourScheme.java
@@ -0,0 +1,64 @@
+/*
+ * 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();
+  }
+}

diff --git a/src/jalview/schemes/JalviewColourScheme.java b/src/jalview/schemes/JalviewColourScheme.java
index 456397e..965a26b 100644 (file)
--- a/src/jalview/schemes/JalviewColourScheme.java
+++ b/src/jalview/schemes/JalviewColourScheme.java
@@ -34,6 +34,10 @@ public enum JalviewColourScheme
   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),

diff --git a/src/jalview/schemes/OceanColourScheme.java b/src/jalview/schemes/OceanColourScheme.java
new file mode 100755 (executable)
index 0000000..23834a6
--- /dev/null
+++ b/src/jalview/schemes/OceanColourScheme.java
@@ -0,0 +1,64 @@
+/*
+ * 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();
+  }
+}

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index ab86400..7ad35c3 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -407,6 +407,125 @@ public class ResidueProperties
       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

diff --git a/src/jalview/schemes/SunsetColourScheme.java b/src/jalview/schemes/SunsetColourScheme.java
new file mode 100755 (executable)
index 0000000..4af7566
--- /dev/null
+++ b/src/jalview/schemes/SunsetColourScheme.java
@@ -0,0 +1,64 @@
+/*
+ * 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();
+  }
+}