From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 30 Aug 2017 12:28:40 +0000 (+0100)
Subject: JAL-2527 Code comments, tidy
X-Git-Tag: Release_2_10_3b1~142^2~2^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=69dbb53dd5e77aed29eeea737414ebe2d74cebd4;p=jalview.git

JAL-2527 Code comments, tidy
---

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 301387b..5f6a1f6 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -59,6 +59,8 @@ public class OverviewCanvas extends JComponent
 
   private AlignViewportI av;
 
+  private OverviewResColourFinder cf;
+
   public OverviewCanvas(OverviewDimensions overviewDims,
           AlignViewportI alignvp)
   {
@@ -68,6 +70,12 @@ public class OverviewCanvas extends JComponent
     sr = new SequenceRenderer(av);
     sr.renderGaps = false;
     fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+
+    boolean useLegacy = Cache.getDefault("USE_LEGACY_GAP", false);
+    Color gapCol = Cache.getDefaultColour("GAP_COLOUR", Color.lightGray);
+    Color hiddenCol = Cache.getDefaultColour("HIDDEN_COLOUR",
+            Color.DARK_GRAY.darker());
+    cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
   }
 
   /**
@@ -127,12 +135,6 @@ public class OverviewCanvas extends JComponent
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    boolean useLegacy = Cache.getDefault("USE_LEGACY_GAP", false);
-    Color gapCol = Cache.getDefaultColour("GAP_COLOUR", Color.lightGray);
-    Color hiddenCol = Cache.getDefaultColour("HIDDEN_COLOUR", Color.DARK_GRAY.darker());
-    OverviewResColourFinder cf = new OverviewResColourFinder(useLegacy,
-            gapCol, hiddenCol);
-
     or = new OverviewRenderer(fr, od, av.getAlignment(),
             av.getResidueShading(), cf);
     miniMe = or.draw(od.getRows(av.getAlignment()),
diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 8fa0e23..07fc6e3 100644
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -28,21 +28,34 @@ import java.awt.Color;
 
 public class OverviewResColourFinder extends ResidueColourFinder
 {
-  final Color GAP_COLOUR;
+  final Color GAP_COLOUR; // default colour to use at gaps
 
-  final Color RESIDUE_COLOUR;
+  final Color RESIDUE_COLOUR; // default colour to use at residues
 
-  final Color HIDDEN_COLOUR;
+  final Color HIDDEN_COLOUR; // colour for hidden regions
 
   boolean useLegacy = false;
 
+  /**
+   * Constructor without colour settings (used by applet)
+   */
   public OverviewResColourFinder()
   {
-    GAP_COLOUR = Color.lightGray; // new Color(240, 240, 240);
+    GAP_COLOUR = Color.lightGray;
     RESIDUE_COLOUR = Color.white;
     HIDDEN_COLOUR = Color.DARK_GRAY.darker();
   }
 
+  /**
+   * 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)
   {
@@ -113,6 +126,11 @@ public class OverviewResColourFinder extends ResidueColourFinder
     return getBoxColour(currentShader, seq, i);
   }
 
+  /**
+   * Supply hidden colour
+   * 
+   * @return colour of hidden regions
+   */
   protected Color getHiddenColour()
   {
     return HIDDEN_COLOUR;