Add bioSyntax color schemes as sequence alignment renderers

gc4s-multiple-sequence-alignment-viewer-demo/src/main/java/org/sing_group/gc4s/msaviewer/demo/MultipleSequenceAlignmentViewerControlDemo.java

@@ -40,6 +40,8 @@
 
 import javax.swing.JFrame;
 
+import org.sing_group.gc4s.msaviewer.BaseColorSequenceAlignmentRenderer;
+import org.sing_group.gc4s.msaviewer.BioSyntaxBaseColorScheme;
 import org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentTracksModel;
 import org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerConfiguration;
 import org.sing_group.gc4s.msaviewer.MultipleSequenceAlignmentViewerControl;
@@ -153,12 +155,16 @@ public List<Track> getBottomTracks() {
 					return emptyList();
 				}
 			};
+
+		// For this second model, a BaseColorSequenceAlignmentRenderer will be created using
+		// a predefined color scheme provided by the BioSyntaxColorScheme.
+		SequenceAlignmentRenderer model2Renderer = new BaseColorSequenceAlignmentRenderer(new BioSyntaxBaseColorScheme());
 
-		// Now, a map is created to associate SequenceAlignmentRenderers to
-		// MultipleSequenceAlignmentTracksModel. In this case, a renderer is
-		// only associated to the first model.
+		// Now, a map is created to associate the SequenceAlignmentRenderer objects to
+		// their corresponding MultipleSequenceAlignmentTracksModel objects.
 		Map<MultipleSequenceAlignmentTracksModel, SequenceAlignmentRenderer> renderersMap = new HashMap<>();
 		renderersMap.put(model1, model1Renderer);
+		renderersMap.put(model2, model2Renderer);
 
 		// Then, a MultipleSequenceAlignmentViewerConfiguration is created to
 		// set the initial configuration of the viewer. This is optional since

gc4s-multiple-sequence-alignment-viewer/README.md

@@ -7,6 +7,10 @@ The `gc4s-multiple-sequence-alignment-viewer-demo` provides different examples o
 
 ![MultipleSequenceAlignmentViewerPanel](screenshots/MultipleSequenceAlignmentViewerPanel.png)
 
+This module also provides the [bioSyntax](https://biosyntax.org/) nucleotide colouring scheme for the complete IUPAC ambiguous base set.
+
+![MultipleSequenceAlignmentViewerPanel with bioSyntax colouring scheme](screenshots/MultipleSequenceAlignmentViewerPanel_bioSyntax.png)
+
 Using this module
 -----------------------
 Add the following repository and dependency declarations to your `pom.xml`:
@@ -88,5 +92,4 @@ public class MinimalMultipleSequenceAlignmentViewerPanelDemo {
 		showComponent(viewerPanel, JFrame.MAXIMIZED_BOTH);
 	}
 }
-
 ```

gc4s-multiple-sequence-alignment-viewer/src/main/java/org/sing_group/gc4s/msaviewer/BaseColorScheme.java

@@ -0,0 +1,48 @@
+/*
+ * #%L
+ * GC4S multiple sequence alignment viewer
+ * %%
+ * Copyright (C) 2014 - 2018 Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato,
+ * 			Florentino Fdez-Riverola, Rosalía Laza-Fidalgo, Reyes Pavón-Rial
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program 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 Lesser Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Lesser Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/lgpl-3.0.html>.
+ * #L%
+ */
+package org.sing_group.gc4s.msaviewer;
+
+import java.awt.Color;
+import java.util.function.Function;
+
+/**
+ * The interface that defines a color scheme used by a {@code BaseColorSequenceAlignmentRenderer}.
+ *  
+ * @author hlfernandez
+ *
+ */
+public interface BaseColorScheme {
+  /**
+   * Returns a function that returns a background {@code Color} for each sequence base {@code Character}.
+   * 
+   * @return a function that returns a background {@code Color} for each sequence base {@code Character}
+   */
+  Function<Character, Color> getBaseBackgroundColorFunction();
+
+  /**
+   * Returns a function that returns a foreground {@code Color} for each sequence base {@code Character}.
+   * 
+   * @return a function that returns a foreground {@code Color} for each sequence base {@code Character}
+   */
+  Function<Character, Color> getBaseForegroundColorFunction();
+}

gc4s-multiple-sequence-alignment-viewer/src/main/java/org/sing_group/gc4s/msaviewer/BaseColorSequenceAlignmentRenderer.java

@@ -0,0 +1,63 @@
+/*
+ * #%L
+ * GC4S multiple sequence alignment viewer
+ * %%
+ * Copyright (C) 2014 - 2018 Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato,
+ * 			Florentino Fdez-Riverola, Rosalía Laza-Fidalgo, Reyes Pavón-Rial
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program 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 Lesser Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Lesser Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/lgpl-3.0.html>.
+ * #L%
+ */
+package org.sing_group.gc4s.msaviewer;
+
+import static java.util.Optional.of;
+
+import java.awt.Color;
+import java.util.Optional;
+import java.util.function.Function;
+
+/**
+ * A {@code DefaultSequenceAlignmentRenderer} implementation that renders each
+ * sequence base using the color specified by the {@code BaseColorScheme}.
+ * 
+ * @author hlfernandez
+ * @see BaseColorScheme
+ * @see DefaultSequenceAlignmentRenderer
+ *
+ */
+public class BaseColorSequenceAlignmentRenderer extends DefaultSequenceAlignmentRenderer {
+  private Function<Character, Color> backgroundColorProvider;
+  private Function<Character, Color> foregroundColorProvider;
+
+  /**
+   * Creates a new {@code BaseColorSequenceAlignmentRenderer} with the specified {@code colorScheme}.
+   * 
+   * @param colorScheme the {@code BaseColorScheme} to render sequence bases
+   */
+  public BaseColorSequenceAlignmentRenderer(
+    BaseColorScheme colorScheme
+  ) {
+    this.backgroundColorProvider = colorScheme.getBaseBackgroundColorFunction();
+    this.foregroundColorProvider = colorScheme.getBaseForegroundColorFunction();
+  }
+
+  @Override
+  public Optional<SequenceBaseRenderingInfo> render(Sequence sequence, int position) {
+    Character base = sequence.getSequence().charAt(position);
+    return of(
+      new SequenceBaseRenderingInfo(this.backgroundColorProvider.apply(base), this.foregroundColorProvider.apply(base), false, false)
+    );
+  }
+}

gc4s-multiple-sequence-alignment-viewer/src/main/java/org/sing_group/gc4s/msaviewer/BioSyntaxBaseColorScheme.java

@@ -0,0 +1,71 @@
+/*
+ * #%L
+ * GC4S multiple sequence alignment viewer
+ * %%
+ * Copyright (C) 2014 - 2018 Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato,
+ * 			Florentino Fdez-Riverola, Rosalía Laza-Fidalgo, Reyes Pavón-Rial
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program 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 Lesser Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Lesser Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/lgpl-3.0.html>.
+ * #L%
+ */
+package org.sing_group.gc4s.msaviewer;
+
+import static java.awt.Color.decode;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * An {@code DefaultBaseColorScheme} extension that returns the bioSyntax color scheme (https://biosyntax.org/,
+ * https://doi.org/10.1186/s12859-018-2315-y).
+ * 
+ * @author hlfernandez
+ *
+ */
+public class BioSyntaxBaseColorScheme extends DefaultBaseColorScheme {
+  public static final Map<Character, Color> BIO_SYNTAX_COLOR_SCHEME = new HashMap<>();
+
+  static {
+    BIO_SYNTAX_COLOR_SCHEME.put('A', decode("#47ff19"));
+    BIO_SYNTAX_COLOR_SCHEME.put('G', decode("#f09000"));
+    BIO_SYNTAX_COLOR_SCHEME.put('C', decode("#ff4641"));
+    BIO_SYNTAX_COLOR_SCHEME.put('T', decode("#4192ff"));
+
+    BIO_SYNTAX_COLOR_SCHEME.put('U', decode("#8a89ff"));
+
+    BIO_SYNTAX_COLOR_SCHEME.put('R', decode("#fffe80"));
+    BIO_SYNTAX_COLOR_SCHEME.put('S', decode("#ff9b80"));
+    BIO_SYNTAX_COLOR_SCHEME.put('Y', decode("#e180ff"));
+    BIO_SYNTAX_COLOR_SCHEME.put('W', decode("#80fff2"));
+
+    BIO_SYNTAX_COLOR_SCHEME.put('D', decode("#c7ffb9"));
+    BIO_SYNTAX_COLOR_SCHEME.put('V', decode("#ffe3b9"));
+    BIO_SYNTAX_COLOR_SCHEME.put('B', decode("#f8c1c0"));
+    BIO_SYNTAX_COLOR_SCHEME.put('H', decode("#bfd8f9"));
+
+    BIO_SYNTAX_COLOR_SCHEME.put('X', decode("#e6e6e6"));
+    BIO_SYNTAX_COLOR_SCHEME.put('N', decode("#ffffff"));
+    BIO_SYNTAX_COLOR_SCHEME.put('M', decode("#83831f"));
+    BIO_SYNTAX_COLOR_SCHEME.put('K', decode("#8b4915"));
+  }
+
+  /**
+   * Creates a new {@code BioSyntaxBaseColorScheme} instance.
+   */
+  public BioSyntaxBaseColorScheme() {
+    super(asFunction(BIO_SYNTAX_COLOR_SCHEME), (Character c) -> Color.BLACK);
+  }
+}

gc4s-multiple-sequence-alignment-viewer/src/main/java/org/sing_group/gc4s/msaviewer/BioSyntaxHighContrastBaseColorScheme.java

@@ -0,0 +1,96 @@
+/*
+ * #%L
+ * GC4S multiple sequence alignment viewer
+ * %%
+ * Copyright (C) 2014 - 2018 Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato,
+ * 			Florentino Fdez-Riverola, Rosalía Laza-Fidalgo, Reyes Pavón-Rial
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program 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 Lesser Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Lesser Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/lgpl-3.0.html>.
+ * #L%
+ */
+package org.sing_group.gc4s.msaviewer;
+
+import static java.awt.Color.decode;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * An {@code DefaultBaseColorScheme} extension that returns the bioSyntax color scheme (https://biosyntax.org/,
+ * https://doi.org/10.1186/s12859-018-2315-y).
+ * 
+ * @author hlfernandez
+ *
+ */
+public class BioSyntaxHighContrastBaseColorScheme extends DefaultBaseColorScheme {
+  public static final Map<Character, Color> BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST = new HashMap<>();
+
+  static {
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('A', decode("#d1d1d1"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('G', decode("#fe3101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('C', decode("#010101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('T', decode("#4091fe"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('U', decode("#495bfe"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('R', decode("#f399cd"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('S', decode("#7c0101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('Y', decode("#00007d"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('W', decode("#7cc7fe"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('D', decode("#edb78d"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('V', decode("#fe6331"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('B', decode("#8a4814"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('H', decode("#bed7f8"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('X', decode("#ffffff"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('N', decode("#ffffff"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('M', decode("#fefd7f"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST.put('K', decode("#9208a0"));
+  }
+
+  public static final Map<Character, Color> BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND = new HashMap<>();
+
+  static {
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('A', decode("#010101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('G', decode("#010101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('C', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('T', decode("#fefefe"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('U', decode("#fefefe"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('R', decode("#010101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('S', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('Y', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('W', decode("#010101"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('D', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('V', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('B', decode("#fefefe"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('H', decode("#010101"));
+
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('X', decode("#828282"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('N', decode("#828282"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('M', decode("#010101"));
+    BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND.put('K', decode("#010101"));
+  }
+
+  public BioSyntaxHighContrastBaseColorScheme() {
+    super(
+      asFunction(BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST), asFunction(BIO_SYNTAX_COLOR_SCHEME_HIGH_CONTRAST_FOREGROUND)
+    );
+  }
+}