JAL-3130 JAL-3007 Added gradle build for Java 11 and additional taskbar icon change...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cd7d1af..cda02fc 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -41,6 +41,8 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
+import java.awt.Image;
+import java.awt.Taskbar;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -335,6 +337,29 @@ public class Jalview
     {
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
+
+      if (Taskbar.isTaskbarSupported())
+      {
+        Taskbar tb = Taskbar.getTaskbar();
+        if (tb.isSupported(Taskbar.Feature.ICON_IMAGE))
+        {
+          try
+          {
+            java.net.URL url = getClass()
+                    .getResource("/images/JalviewLogo_Huge.png");
+            if (url != null)
+            {
+              Image image = java.awt.Toolkit.getDefaultToolkit()
+                      .createImage(url);
+              tb.setIconImage(image);
+            }
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+          }
+        }
+      }
+
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -538,7 +563,8 @@ public class Jalview
           data.replaceAll("%20", " ");
 
           ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport().getAlignment(), data);
+                  .getColourScheme(af.getViewport(),
+                          af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
@@ -828,9 +854,6 @@ public class Jalview
                     // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
-                    + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
-                    + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
-                    + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     // +
                     // "-vdoc vamsas-document\tImport vamsas document into new