JAL-4281 reinstate access to legacy id width calculation so we can import old files...

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 9defed4..28f6c59 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -202,8 +202,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
     } catch (Exception e)
     {
-      Console.error("Couldn't instantiate vamsas client !",
-              e);
+      Console.error("Couldn't instantiate vamsas client !", e);
       return false;
     }
     return true;
@@ -272,8 +271,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     addStoreDocumentHandler();
     startSession();
     inInitialUpdate = true;
-    Console.debug(
-            "Jalview loading the Vamsas Session for the first time.");
+    Console.debug("Jalview loading the Vamsas Session for the first time.");
     dealWithDocumentUpdate(false); // we don't push an update out to the
     inInitialUpdate = false;
     // document yet.
@@ -482,8 +480,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
             } catch (Exception e)
             {
               errorsDuringUpdate = true;
-              Console.error("Exception synchronizing " + af.getTitle()
-                      + " "
+              Console.error("Exception synchronizing " + af.getTitle() + " "
                       + (af.getViewport().getViewName() == null ? ""
                               : " view " + af.getViewport().getViewName())
                       + " to document.", e);
@@ -617,7 +614,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       cdoc = null;
     } catch (Exception ee)
     {
-      System.err.println("Exception whilst updating :");
+      jalview.bin.Console.errPrintln("Exception whilst updating :");
       ee.printStackTrace(System.err);
       // recover object map backup, since its probably corrupted with references
       // to Vobjects that don't exist anymore.
@@ -806,7 +803,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               // we only care about AlignmentSequence selections
               SelectionMessage sm = (SelectionMessage) message;
               sm.validate();
-              System.err.println("Received\n" + sm.getRawMessage());
+              jalview.bin.Console.errPrintln("Received\n" + sm.getRawMessage());
               Object[] jvobjs = sm.getVorbaIDs() == null ? null
                       : new Object[sm.getVorbaIDs().length];
               if (jvobjs == null)