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

[jalview.git] / src / jalview / analysis / CrossRef.java

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 9b90ca5..41582b4 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -293,7 +293,7 @@ public class CrossRef
             if (matchInDataset != null && xref.getMap().getTo() != null
                     && matchInDataset != xref.getMap().getTo())
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
                               + "Found:" + matchInDataset + "\nExpected:"
                               + xref.getMap().getTo() + "\nFor xref:"
@@ -424,7 +424,7 @@ public class CrossRef
       retrieved = sftch.getSequences(sourceRefs, !fromDna);
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Problem whilst retrieving cross references for Sequence : "
                       + seq.getName());
       e.printStackTrace();
@@ -607,7 +607,7 @@ public class CrossRef
                 String msg = "Mapping updated from " + ms.getName()
                         + " to retrieved crossreference "
                         + matched.getName();
-                System.out.println(msg);
+                jalview.bin.Console.outPrintln(msg);
 
                 List<DBRefEntry> toRefs = map.getTo().getDBRefs();
                 if (toRefs != null)
@@ -662,7 +662,7 @@ public class CrossRef
               cf.addMap(retrievedSequence, map.getTo(), map.getMap());
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Exception when consolidating Mapped sequence set...");
               e.printStackTrace(System.err);
             }
@@ -1029,7 +1029,7 @@ public class CrossRef
     }
     if (dataset.getSequences() == null)
     {
-      System.err.println("Empty dataset sequence set - NO VECTOR");
+      jalview.bin.Console.errPrintln("Empty dataset sequence set - NO VECTOR");
       return false;
     }
     List<SequenceI> ds = dataset.getSequences();
@@ -1041,7 +1041,7 @@ public class CrossRef
         {
           if (nxt.getDatasetSequence() != null)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
                             + nxt.getDisplayId(true) + " has ds reference "
                             + nxt.getDatasetSequence().getDisplayId(true)