JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...

[jalview.git] / src / jalview / io / VamsasAppDatastore.java

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index c3776d3..998166e 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -151,7 +151,7 @@ public class VamsasAppDatastore
   private void buildSkipList()
   {
     skipList = new Hashtable();
-    AlignFrame[] al = Desktop.getAlignFrames();
+    AlignFrame[] al = Desktop.getDesktopAlignFrames();
     for (int f = 0; al != null && f < al.length; f++)
     {
       skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
@@ -492,7 +492,8 @@ public class VamsasAppDatastore
           }
           else
           {
-            jalview.bin.Console.outPrintln("alignment in document left unchanged.");
+            jalview.bin.Console
+                    .outPrintln("alignment in document left unchanged.");
           }
         }
         else
@@ -1115,7 +1116,8 @@ public class VamsasAppDatastore
       // METHODS)
       {
         // verify existing alignment sequence annotation is up to date
-        jalview.bin.Console.outPrintln("update dataset sequence annotation.");
+        jalview.bin.Console
+                .outPrintln("update dataset sequence annotation.");
       }
       else
       {
@@ -1184,7 +1186,8 @@ public class VamsasAppDatastore
       // METHODS)
       {
         // verify existing alignment sequence annotation is up to date
-        jalview.bin.Console.outPrintln("update alignment sequence annotation.");
+        jalview.bin.Console
+                .outPrintln("update alignment sequence annotation.");
       }
       else
       {