JAL-2588 Added tests

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

diff --git a/src/jalview/renderer/ResidueColourFinder.java b/src/jalview/renderer/ResidueColourFinder.java
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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()
+  {
+  }
+
+  public Color getResidueColour(ResidueShaderI shader,
+          SequenceGroup[] allGroups,
+          final SequenceI seq, int position, FeatureColourFinder finder)
+  {
+    Color col = getResidueBoxColour(shader, allGroups, seq, position);
+
+    if (finder != null)
+    {
+      col = finder.findFeatureColour(col, seq, position);
+    }
+    return col;
+  }
+
+  private Color getResidueBoxColour(ResidueShaderI shader,
+          SequenceGroup[] allGroups,
+          SequenceI seq, int i)
+  {
+
+    ResidueShaderI currentShader;
+
+    SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+            i);
+    if (currentSequenceGroup != null)
+    {
+      currentShader = currentSequenceGroup.getGroupColourScheme();
+    }
+    else
+    {
+      currentShader = shader;
+    }
+
+    return getBoxColour(currentShader, seq, i);
+  }
+
+  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
+   *          DOCUMENT ME!
+   * @param seq
+   *          DOCUMENT ME!
+   * @param i
+   *          DOCUMENT ME!
+   */
+  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;
+  }
+
+}