Merge branch 'testing/JAL-3577_jalviewversion_autoset_fixed' into develop

diff --git a/build.gradle b/build.gradle
index 4bb52b0..7d0a1f9 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -1300,8 +1300,10 @@ task getdownWebsite() {
 
 // a helper task to allow getdown digest of any dir: `gradle getdownDigestDir -PDIGESTDIR=/path/to/my/random/getdown/dir
 task getdownDigestDir(type: JavaExec) {
+  group "Help"
+  description "A task to run a getdown Digest on a dir with getdown.txt. Provide a DIGESTDIR property via -PDIGESTDIR=..."
+
   def digestDirPropertyName = "DIGESTDIR"
-  description = "Digest a local dir (-P${digestDirPropertyName}=...) for getdown"
   doFirst {
     classpath = files(getdownLauncher)
     def digestDir = findProperty(digestDirPropertyName)
@@ -1421,7 +1423,8 @@ task copyInstall4jTemplate {
     // NB we're deleting the /other/ one!
     // Also remove the examples subdir from non-release versions
     def customizedIdToDelete = "PROGRAM_GROUP_RELEASE"
-    if (CHANNEL=="RELEASE") {
+    // 2.11.1.0 NOT releasing with the Examples folder in the Program Group
+    if (false && CHANNEL=="RELEASE") { // remove 'false && ' to include Examples folder in RELEASE channel
       customizedIdToDelete = "PROGRAM_GROUP_NON_RELEASE"
     } else {
       // remove the examples subdir from Full File Set

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index a1980c7..2186d4a 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -20,6 +20,13 @@
  */
 package jalview.renderer.seqfeatures;
 
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.ContiguousI;
@@ -32,13 +39,6 @@ import jalview.util.Comparison;
 import jalview.util.ReverseListIterator;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.AlphaComposite;
-import java.awt.Color;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.util.List;
-
 public class FeatureRenderer extends FeatureRendererModel
 {
   private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
@@ -112,6 +112,10 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
+      /*
+       * JAL-3045 text is always drawn over features, even if
+       * 'Show Text' is unchecked in the format menu
+       */
       g.setColor(Color.white);
       int charOffset = (charWidth - fm.charWidth(s)) / 2;
       g.drawString(String.valueOf(s),