X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=46b75c8860cc67c18c1ad62af9df31abc550bcf4;hb=893f21fe8df6a9d47ced8140e3ba75f03407be00;hp=5365dfaa4800e93149e1c3b979cda81dee9d2515;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 5365dfa..46b75c8 100644
--- 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]);
@@ -460,7 +460,7 @@ public class VamsasAppDatastore
           {
             // removeValignmentSequences(alignment, docseqs);
             docseqs.removeAllElements();
-            System.out.println(
+            jalview.bin.Console.outPrintln(
                     "Sequence deletion from alignment is not implemented.");
 
           }
@@ -488,11 +488,11 @@ public class VamsasAppDatastore
           }
           if (alismod)
           {
-            System.out.println("update alignment in document.");
+            jalview.bin.Console.outPrintln("update alignment in document.");
           }
           else
           {
-            System.out.println("alignment in document left unchanged.");
+            jalview.bin.Console.outPrintln("alignment in document left unchanged.");
           }
         }
         else
@@ -500,7 +500,7 @@ public class VamsasAppDatastore
           // unbind alignment from view.
           // create new binding and new alignment.
           // mark trail on new alignment as being derived from old ?
-          System.out.println(
+          jalview.bin.Console.outPrintln(
                   "update edited alignment to new alignment in document.");
         }
       }
@@ -1115,12 +1115,12 @@ public class VamsasAppDatastore
       // METHODS)
       {
         // verify existing alignment sequence annotation is up to date
-        System.out.println("update dataset sequence annotation.");
+        jalview.bin.Console.outPrintln("update dataset sequence annotation.");
       }
       else
       {
         // verify existing alignment sequence annotation is up to date
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "make new alignment dataset sequence annotation if modification has happened.");
       }
     }
@@ -1184,12 +1184,12 @@ public class VamsasAppDatastore
       // METHODS)
       {
         // verify existing alignment sequence annotation is up to date
-        System.out.println("update alignment sequence annotation.");
+        jalview.bin.Console.outPrintln("update alignment sequence annotation.");
       }
       else
       {
         // verify existing alignment sequence annotation is up to date
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "make new alignment sequence annotation if modification has happened.");
       }
     }
@@ -1427,7 +1427,7 @@ public class VamsasAppDatastore
       String seqsetidobj = av.getSequenceSetId();
       views = Desktop.getViewports(seqsetidobj);
       Console.debug("Found " + (views == null ? " no " : "" + views.length)
-                      + " views for '" + av.getSequenceSetId() + "'");
+              + " views for '" + av.getSequenceSetId() + "'");
       if (views.length > 1)
       {
         // we need to close the original document view.