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

[jalview.git] / src / jalview / datamodel / AlignmentView.java

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e6604d1..6ab71c7 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -1128,11 +1128,11 @@ public class AlignmentView
   public static void testSelectionViews(AlignmentI alignment,
           HiddenColumns hidden, SequenceGroup selection)
   {
-    System.out.println("Testing standard view creation:\n");
+    jalview.bin.Console.outPrintln("Testing standard view creation:\n");
     AlignmentView view = null;
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               false);
@@ -1141,12 +1141,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, false,
               true);
@@ -1154,12 +1154,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               false);
@@ -1167,12 +1167,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View with no hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, false, true,
               true);
@@ -1180,12 +1180,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               false);
@@ -1193,12 +1193,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, no limit to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, false,
               true);
@@ -1206,12 +1206,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection marked but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection and no groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               false);
@@ -1219,12 +1219,12 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted but no groups marked.");
     }
     try
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "View *with* hidden columns, limited to selection, and all groups to be collected:");
       view = new AlignmentView(alignment, hidden, selection, true, true,
               true);
@@ -1232,7 +1232,7 @@ public class AlignmentView
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Failed to generate alignment with selection restricted and groups marked.");
     }