Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index dd4b72c..c3776d3 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -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.");
       }
     }