From 0615edf610baff76b1675e2f174f22d855fd3fe4 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 27 Apr 2018 15:24:21 +0100
Subject: [PATCH] JAL-2963 correctly dim PCA points with negative
 z-coordinates

---
 src/jalview/appletgui/RotatableCanvas.java |   30 ++++++++----------------
 src/jalview/gui/RotatableCanvas.java       |   34 +++++++++++++---------------
 2 files changed, 26 insertions(+), 38 deletions(-)

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 179a91d..3000363 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -344,29 +344,13 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
   public void drawScene(Graphics g)
   {
-    // boolean darker = false;
-
-    int halfwidth = getSize().width / 2;
-    int halfheight = getSize().height / 2;
-
     for (int i = 0; i < npoint; i++)
     {
       SequencePoint sp = points.elementAt(i);
-      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
-      int y = (int) ((sp.coord.y - centre.y) * scale)
-              + halfheight;
-      float z = sp.coord.y - centre.z;
-
       SequenceI sequence = sp.getSequence();
-      if (av.getSequenceColour(sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sequence));
-      }
-
+      Color sequenceColour = av.getSequenceColour(sequence);
+      g.setColor(
+              sequenceColour == Color.black ? Color.white : sequenceColour);
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
@@ -375,12 +359,18 @@ public class RotatableCanvas extends Panel implements MouseListener,
           g.setColor(Color.gray);
         }
       }
-      if (z < 0)
+
+      if (sp.coord.z < centre.z)
       {
         g.setColor(g.getColor().darker());
       }
 
+      int halfwidth = getSize().width / 2;
+      int halfheight = getSize().height / 2;
+      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+      int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
       g.fillRect(x - 3, y - 3, 6, 6);
+
       if (showLabels)
       {
         g.setColor(Color.red);
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 617180f..6fabd95 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -427,27 +427,17 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
             RenderingHints.VALUE_ANTIALIAS_ON);
 
-    int halfwidth = getWidth() / 2;
-    int halfheight = getHeight() / 2;
-
     for (int i = 0; i < npoint; i++)
     {
+      /*
+       * sequence point colour as sequence id, but
+       * gray if sequence is currently selected
+       */
       SequencePoint sp = points.elementAt(i);
-      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
-      int y = (int) ((sp.coord.y - centre.y) * scale)
-              + halfheight;
-      float z = sp.coord.y - centre.z; // todo sp.coord.z JAL-2963
-
       SequenceI sequence = sp.getSequence();
-      if (av.getSequenceColour(sequence) == Color.black)
-      {
-        g.setColor(Color.white);
-      }
-      else
-      {
-        g.setColor(av.getSequenceColour(sequence));
-      }
-
+      Color sequenceColour = av.getSequenceColour(sequence);
+      g.setColor(
+              sequenceColour == Color.black ? Color.white : sequenceColour);
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
@@ -457,12 +447,20 @@ public class RotatableCanvas extends JPanel implements MouseListener,
         }
       }
 
-      if (z < 0)
+      /*
+       * dim sequence points 'at the back'
+       */
+      if (sp.coord.z < centre.z)
       {
         g.setColor(g.getColor().darker());
       }
 
+      int halfwidth = getWidth() / 2;
+      int halfheight = getHeight() / 2;
+      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+      int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
       g.fillRect(x - 3, y - 3, 6, 6);
+
       if (showLabels)
       {
         g.setColor(Color.red);
-- 
1.7.10.2