JAL-1705 AlignmentUtils method renamed

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c957444..a10ec4e 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -630,7 +631,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         String file = (String) contents
                 .getTransferData(DataFlavor.stringFlavor);
 
-        String format = new IdentifyFile().Identify(file,
+        String format = new IdentifyFile().identify(file,
                 FormatAdapter.PASTE);
 
         new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
@@ -976,7 +977,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           }
           else
           {
-            format = new IdentifyFile().Identify(file, protocol);
+            format = new IdentifyFile().identify(file, protocol);
           }
 
           new FileLoader().LoadFile(file, protocol, format);
@@ -1027,7 +1028,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
       else
       {
-        format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+        format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
       }
 
       if (viewport != null)
@@ -1110,7 +1111,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     else
     {
-      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+      String format = new IdentifyFile().identify(url, FormatAdapter.URL);
 
       if (format.equals("URL NOT FOUND"))
       {
@@ -2381,6 +2382,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignFrame[] getAlignFrames()
   {
+    if (Jalview.isHeadlessMode())
+    {
+      // Desktop.desktop is null in headless mode
+      return new AlignFrame[] { currentAlignFrame };
+    }
+
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
     if (frames == null)