Merge branch 'releases/Release_2_10_2b1_Branch'

[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)
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+++ 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
+{
+  final Color GAP_COLOUR; // default colour to use at gaps
+
+  final Color RESIDUE_COLOUR; // default colour to use at residues
+
+  final Color HIDDEN_COLOUR; // colour for hidden regions
+
+  boolean useLegacy = false;
+
+  public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
+
+  public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
+
+  public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
+          .darker();
+
+  /**
+   * Constructor without colour settings (used by applet)
+   */
+  public OverviewResColourFinder()
+  {
+    this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
+  }
+
+  /**
+   * Constructor with colour settings
+   * 
+   * @param useLegacyColouring
+   *          whether to use legacy gap colouring (white gaps, grey residues)
+   * @param gapCol
+   *          gap colour if not legacy
+   * @param hiddenCol
+   *          hidden region colour (transparency applied by rendering code)
+   */
+  public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,
+          Color hiddenCol)
+  {
+    if (useLegacyColouring)
+    {
+      GAP_COLOUR = Color.white;
+      RESIDUE_COLOUR = Color.lightGray;
+      HIDDEN_COLOUR = hiddenCol;
+    }
+    else
+    {
+      GAP_COLOUR = gapCol;
+      RESIDUE_COLOUR = Color.white;
+      HIDDEN_COLOUR = hiddenCol;
+    }
+  }
+
+  @Override
+  public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
+  {
+    Color resBoxColour = RESIDUE_COLOUR;
+    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 = GAP_COLOUR;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(currentChar, i, seq);
+      }
+    }
+    else if (Comparison.isGap(currentChar))
+    {
+      resBoxColour = GAP_COLOUR;
+    }
+
+    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);
+  }
+
+  /**
+   * Supply hidden colour
+   * 
+   * @return colour of hidden regions
+   */
+  protected Color getHiddenColour()
+  {
+    return HIDDEN_COLOUR;
+  }
+}