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

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 56eda5e..949c52e 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -155,7 +155,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         String msg = "Aborting ID retrieval after " + v
                 + " chunks. Unexpected problem (" + r.getLocalizedMessage()
                 + ")";
-        System.err.println(msg);
+        jalview.bin.Console.errPrintln(msg);
         r.printStackTrace();
         break;
       }
@@ -240,7 +240,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       }
     } catch (IOException e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error transferring Ensembl features: " + e.getMessage());
     }
     // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
@@ -265,12 +265,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String accId = querySeq.getName();
     try
     {
-      System.out.println("Adding protein product for " + accId);
+      jalview.bin.Console.outPrintln("Adding protein product for " + accId);
       AlignmentI protein = new EnsemblProtein(getDomain())
               .getSequenceRecords(accId);
       if (protein == null || protein.getHeight() == 0)
       {
-        System.out.println("No protein product found for " + accId);
+        jalview.bin.Console.outPrintln("No protein product found for " + accId);
         return;
       }
       SequenceI proteinSeq = protein.getSequenceAt(0);
@@ -382,7 +382,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq.addDBRef(xrefs.get(i));
     }
 
-    // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
+    // jalview.bin.Console.outPrintln("primaries are " + seq.getPrimaryDBRefs().toString());
     /*
      * and add a reference to itself
      */
@@ -430,7 +430,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (seqs.size() != ids.size())
     {
-      System.out.println(String.format(
+      jalview.bin.Console.outPrintln(String.format(
               "Only retrieved %d sequences for %d query strings",
               seqs.size(), ids.size()));
     }
@@ -508,7 +508,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       result.add(sequence);
     } catch (ParseException | IOException e)
     {
-      System.err.println("Error processing JSON response: " + e.toString());
+      jalview.bin.Console.errPrintln("Error processing JSON response: " + e.toString());
       // ignore
     }
     // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
@@ -659,7 +659,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (regions.isEmpty())
     {
-      System.out.println("Failed to identify target sequence for " + accId
+      jalview.bin.Console.outPrintln("Failed to identify target sequence for " + accId
               + " from genomic features");
       return null;
     }
@@ -829,7 +829,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);
-    // System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+    // jalview.bin.Console.outPrintln("transferFeatures (" + (sfs.size()) + " --> "
     // + targetSequence.getFeatures().getFeatureCount(true) + ") to "
     // + targetSequence.getName() + " took "
     // + (System.currentTimeMillis() - start) + "ms");