Merge remote-tracking branch 'origin/feature/2588' into feature/JAL-2527

[jalview.git] / src / jalview / renderer / ResidueColourFinder.java

diff --git a/src/jalview/renderer/ResidueColourFinder.java b/src/jalview/renderer/ResidueColourFinder.java
new file mode 100644 (file)
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+++ b/src/jalview/renderer/ResidueColourFinder.java
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+/*
+ * 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.renderer;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+
+import java.awt.Color;
+
+public class ResidueColourFinder
+{
+  public ResidueColourFinder()
+  {
+  }
+
+  /**
+   * Get the colour of a residue in a sequence
+   * 
+   * @param showBoxes
+   *          true if the viewport's Show Boxes setting is true
+   * @param shader
+   *          the viewport's colour scheme
+   * @param allGroups
+   *          all the groups which seq participates in
+   * @param seq
+   *          the sequence containing the residue
+   * @param position
+   *          the position of the residue in the sequence
+   * @param finder
+   *          FeatureColourFinder for the viewport
+   * @return colour of the residue
+   */
+  public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
+          SequenceGroup[] allGroups,
+          final SequenceI seq, int position, FeatureColourFinder finder)
+  {
+    Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq,
+            position);
+
+    // if there's a FeatureColourFinder we might override the residue colour
+    // here with feature colouring
+    if (finder != null)
+    {
+      col = finder.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
+  /**
+   * Get the residue colour without accounting for any features
+   * 
+   * @param showBoxes
+   *          true if the viewport's Show Boxes setting is true
+   * @param shader
+   *          the viewport's colour scheme
+   * @param allGroups
+   *          all the groups which seq participates in
+   * @param seq
+   *          the sequence containing the residue
+   * @param i
+   *          the position of the residue in the sequence
+   * @return
+   */
+  protected Color getResidueBoxColour(boolean showBoxes,
+          ResidueShaderI shader,
+          SequenceGroup[] allGroups,
+          SequenceI seq, int i)
+  {
+    SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+            i);
+    if (currentSequenceGroup != null)
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        return getBoxColour(currentSequenceGroup.getGroupColourScheme(),
+                seq, i);
+      }
+    }
+    else if (showBoxes)
+    {
+      return getBoxColour(shader, seq, i);
+    }
+  
+    return Color.white;
+  }
+
+  /**
+   * Search all the groups for a sequence to find the one which a given res
+   * falls into
+   * 
+   * @param allGroups
+   *          all the groups a sequence participates in
+   * @param res
+   *          the residue to search for
+   * @return a sequence group for res, or null if no sequence group applies
+   */
+  public SequenceGroup getCurrentSequenceGroup(SequenceGroup[] allGroups,
+          int res)
+  {
+    if (allGroups == null)
+    {
+      return null;
+    }
+
+    for (int i = 0; i < allGroups.length; i++)
+    {
+      if ((allGroups[i].getStartRes() <= res)
+              && (allGroups[i].getEndRes() >= res))
+      {
+        return (allGroups[i]);
+      }
+    }
+
+    return null;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param shader
+   *          the viewport's colour scheme
+   * @param seq
+   *          the sequence containing the residue
+   * @param i
+   *          the position of the residue in the sequence
+   */
+  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  {
+    Color resBoxColour = Color.white;
+    if (shader.getColourScheme() != null)
+    {
+      resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
+    }
+    return resBoxColour;
+  }
+
+}