Merge branch 'feature/2588' into merge/develop_feature/2588_JAL-2588

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

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
new file mode 100644 (file)
index 0000000..5ed218b
--- /dev/null
+++ b/src/jalview/renderer/OverviewResColourFinder.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.util.Comparison;
+
+import java.awt.Color;
+
+public class OverviewResColourFinder extends ResidueColourFinder
+{
+  @Override
+  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  {
+    Color resBoxColour = Color.white;
+    char currentChar = seq.getCharAt(i);
+
+    // In the overview window, gaps are coloured grey, unless the colour scheme
+    // specifies a gap colour, in which case gaps honour the colour scheme
+    // settings
+    if (shader.getColourScheme() != null)
+    {
+      if (Comparison.isGap(currentChar)
+              && !shader.getColourScheme().hasGapColour())
+      {
+        resBoxColour = Color.lightGray;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(currentChar, i, seq);
+      }
+    }
+    else if (Comparison.isGap(currentChar))
+    {
+      resBoxColour = Color.lightGray;
+    }
+
+    return resBoxColour;
+  }
+
+  /**
+   * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
+   * overview displays the colours regardless.
+   */
+  @Override
+  protected Color getResidueBoxColour(boolean showBoxes,
+          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);
+  }
+}