From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 2 Oct 2019 07:54:40 +0000 (+0100)
Subject: Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=edd94b99dba923b1d6da64e4cea1608dc640fae7;hp=3c2061bc480aa7b95051103203885be2008797f8;p=jalview.git

Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet
---

diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
index 703f220..712c9f4 100644
--- a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
+++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@ -23,10 +23,12 @@ package jalview.renderer.seqfeatures;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.Color;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
 
 /**
@@ -117,6 +119,53 @@ public class FeatureColourFinder
     return c;
   }
 
+  public int findFeatureColourInt(int defaultColour, SequenceI seq,
+          int column)
+  {
+    // if (noFeaturesDisplayed())
+    // {
+    // return defaultColour;
+    // }
+
+    Graphics2D g = null;
+
+    /*
+     * if transparency applies, provide a notional 1x1 graphics context 
+     * that has been primed with the default colour
+     */
+    if (featureRenderer.getTransparency() != 1f)
+    {
+      g = (Graphics2D) goff;
+      if (Platform.isJS())
+      {
+        // Clear the HTML5 canvas color.
+        // otherwise we get a smearing.
+        // For whatever reason, this is necessary BH 2019.10.01.
+        g.setColor(Color.white);
+        g.fillRect(0, 0, 1, 1);
+      }
+      if (defaultColour != 0)
+      {
+        offscreenImage.setRGB(0, 0, defaultColour);
+      }
+    }
+    Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
+    if (c == null)
+    {
+      return defaultColour;
+    }
+    if (g == null)
+    {
+      return c.getRGB();
+    }
+    if (Platform.isJS())
+    {
+      // BH 2019.10.01 because for JavaScript the pixel itself
+      // is a resource that needs to be recreated in getRGB(0,0)
+      offscreenImage.flush();
+    }
+    return offscreenImage.getRGB(0, 0);
+  }
   /**
    * Answers true if feature display is turned off, or there are no features
    * configured to be visible
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 72900a8..f0c74ee 100644
Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ
diff --git a/swingjs/timestamp b/swingjs/timestamp
index 9b20eae..cb055f8 100644
--- a/swingjs/timestamp
+++ b/swingjs/timestamp
@@ -1 +1 @@
-20191001111303 
+20191001230605 
diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip
index 72900a8..f0c74ee 100644
Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ
diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
index 9b20eae..cb055f8 100644
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20191001111303 
+20191001230605