Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0159bc7..4b858e1 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1577,7 +1577,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     /*
      * When we finally deprecate 1.1 compatibility, we can start to use
      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
-     * (UnsupportedEncodingException ex) { System.err.println("WARNING -
+     * (UnsupportedEncodingException ex) { jalview.bin.Console.errPrintln("WARNING -
      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
      * ex.printStackTrace(); }
      */
@@ -1586,7 +1586,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       url = viewport.applet.getCodeBase() + url;
     } catch (UnsupportedEncodingException ex)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
                       + url);
       ex.printStackTrace();
@@ -2975,7 +2975,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     if (viewport.applet.debug)
     {
-      System.err.println("Sorting " + alorder.getOrder().size()
+      jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size()
               + " in alignment '" + getTitle() + "'");
     }
     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
@@ -3061,7 +3061,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     if (viewport.applet == null)
     {
-      System.out.println("Not running as applet - no browser available.");
+      jalview.bin.Console.outPrintln("Not running as applet - no browser available.");
     }
     else
     {
@@ -3977,12 +3977,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewer = (Viewer) jmolviewer;
     } catch (ClassCastException ex)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Unsupported viewer object :" + jmolviewer.getClass());
     }
     if (viewer == null)
     {
-      System.err.println("Can't use this object as a structure viewer:"
+      jalview.bin.Console.errPrintln("Can't use this object as a structure viewer:"
               + jmolviewer.getClass());
       return null;
     }
@@ -4127,7 +4127,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     chains = (String[]) sqch[1];
     if (seqs == null || seqs.length == 0)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
     }
     if (protocol == null)
@@ -4142,7 +4142,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (protocol == null)
       {
-        System.err.println("Couldn't work out protocol to open structure: "
+        jalview.bin.Console.errPrintln("Couldn't work out protocol to open structure: "
                 + pdb.getId());
         return;
       }
@@ -4154,7 +4154,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               .setMapping(seqs, chains, pdb.getFile(), protocol,
                       null) == null)
       {
-        System.err.println("Failed to map " + pdb.getFile() + " ("
+        jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");
       }
       return;
@@ -4176,7 +4176,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       if (ajm != null)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
         // try and add the pdb structure
         // ajm.addS
@@ -4201,7 +4201,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           SequenceI[][] seqs, String[][] chains, String[] protocols)
   {
     // TODO Auto-generated method stub
-    System.err.println("Aligned Structure View: Not yet implemented.");
+    jalview.bin.Console.errPrintln("Aligned Structure View: Not yet implemented.");
   }
 
   /**
@@ -4258,9 +4258,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (!file.isValid())
     {
       // TODO: raise dialog for gui
-      System.err.println("Problems parsing T-Coffee scores: "
+      jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: "
               + file.getWarningMessage());
-      System.err.println("Origin was:\n" + source);
+      jalview.bin.Console.errPrintln("Origin was:\n" + source);
       return false;
     }
 
@@ -4273,7 +4273,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                     || aln.getWidth() != file.getWidth()))
     {
       // TODO: raise a dialog box here rather than bomb out.
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "The scores matrix does not match the alignment dimensions");
 
     }
@@ -4289,10 +4289,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      System.err.println("Problems resolving T-Coffee scores:");
+      jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:");
       if (file.getWarningMessage() != null)
       {
-        System.err.println(file.getWarningMessage());
+        jalview.bin.Console.errPrintln(file.getWarningMessage());
       }
     }
     return false;