Merge branch 'develop' into merge/JAL-3310_and_JAL-3300

diff --git a/build.gradle b/build.gradle
index 9aedd2f..71eb491 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -484,13 +484,20 @@ task convertBuildingMD(type: Exec) {
   def buildingMD = "$jalviewDir/$docDir/building.md"
   def css = "$jalviewDir/$docDir/github.css"
 
-  def pandoc = pandoc_exec
+  def pandoc = null
+  pandoc_exec.split(",").each {
+    if (file(it.trim()).exists()) {
+      pandoc = it.trim()
+      return true
+    }
+  }
+
   def hostname = "hostname".execute().text.trim()
-  if (! file(pandoc).exists() && hostname.equals("jv-bamboo")) {
+  if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
     pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
   }
 
-  if (file(pandoc).exists()) {
+  if (pandoc != null && file(pandoc).exists()) {
     commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
   } else {
     commandLine "true"

diff --git a/gradle.properties b/gradle.properties
index f5c6f49..08bcbd7 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -109,6 +109,6 @@ JSIGN_SH = echo
 
 eclipse_extra_jdt_prefs_file = .settings/org.eclipse.jdt.core.jalview.prefs
 
-pandoc_exec = /usr/local/bin/pandoc
+pandoc_exec = /usr/local/bin/pandoc,/usr/bin/pandoc
 dev = false
 

diff --git a/src/jalview/util/ShortcutKeyMaskExWrapper.java b/src/jalview/util/ShortcutKeyMaskExWrapper.java
index c9ed231..f73b8d4 100644 (file)
--- a/src/jalview/util/ShortcutKeyMaskExWrapper.java
+++ b/src/jalview/util/ShortcutKeyMaskExWrapper.java
@@ -23,14 +23,16 @@ public class ShortcutKeyMaskExWrapper
 
     if (specversion >= modern)
     {
-      wrapper = new ShortcutKeyMaskExWrapper11();
+      wrapper = new jalview.util.ShortcutKeyMaskExWrapper11();
+      SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.SHIFT_DOWN_MASK;
+      ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper11.ALT_DOWN_MASK;
     }
     else
     {
-      wrapper = new ShortcutKeyMaskExWrapper8();
+      wrapper = new jalview.util.ShortcutKeyMaskExWrapper8();
+      SHIFT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.SHIFT_DOWN_MASK;
+      ALT_DOWN_MASK = jalview.util.ShortcutKeyMaskExWrapper8.ALT_DOWN_MASK;
     }
-    SHIFT_DOWN_MASK = wrapper.SHIFT_DOWN_MASK;
-    ALT_DOWN_MASK = wrapper.ALT_DOWN_MASK;
   }
 
   public static int getMenuShortcutKeyMaskEx()

diff --git a/src/jalview/util/ShortcutKeyMaskExWrapper11.java b/src/jalview/util/ShortcutKeyMaskExWrapper11.java
index 41a6aa0..7a3c8ca 100644 (file)
--- a/src/jalview/util/ShortcutKeyMaskExWrapper11.java
+++ b/src/jalview/util/ShortcutKeyMaskExWrapper11.java
@@ -7,8 +7,15 @@ import java.awt.event.MouseEvent;
 
 public class ShortcutKeyMaskExWrapper11 implements ShortcutKeyMaskExWrapperI
 {
-  public final static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
-  public final static int ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+  public final static int SHIFT_DOWN_MASK;
+
+  public final static int ALT_DOWN_MASK;
+
+  static
+  {
+    SHIFT_DOWN_MASK = KeyEvent.SHIFT_DOWN_MASK;
+    ALT_DOWN_MASK = KeyEvent.ALT_DOWN_MASK;
+  }
 
   @Override
   public int getMenuShortcutKeyMaskEx()
@@ -31,4 +38,5 @@ public class ShortcutKeyMaskExWrapper11 implements ShortcutKeyMaskExWrapperI
     return e.getModifiersEx();
   }
 
+
 }

diff --git a/src/jalview/util/ShortcutKeyMaskExWrapper8.java b/src/jalview/util/ShortcutKeyMaskExWrapper8.java
index 78254b5..a7817bd 100644 (file)
--- a/src/jalview/util/ShortcutKeyMaskExWrapper8.java
+++ b/src/jalview/util/ShortcutKeyMaskExWrapper8.java
@@ -7,8 +7,15 @@ import java.awt.event.MouseEvent;
 
 public class ShortcutKeyMaskExWrapper8 implements ShortcutKeyMaskExWrapperI
 {
-  public final static int SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
-  public final static int ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+  public final static int SHIFT_DOWN_MASK;
+
+  public final static int ALT_DOWN_MASK;
+
+  static
+  {
+    SHIFT_DOWN_MASK = KeyEvent.SHIFT_MASK;
+    ALT_DOWN_MASK = KeyEvent.ALT_MASK;
+  }
 
   @Override
   public int getMenuShortcutKeyMaskEx()