JAL-3730 retry ping before failing; sysout logging changed to Cache.log

[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 fd8800f..fe61a87 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -265,12 +265,12 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String accId = querySeq.getName();
     try
     {
-      System.out.println("Adding protein product for " + accId);
+      Cache.log.info("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);
+        Cache.log.info("No protein product found for " + accId);
         return;
       }
       SequenceI proteinSeq = protein.getSequenceAt(0);
@@ -429,7 +429,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (seqs.size() != ids.size())
     {
-      System.out.println(String.format(
+      Cache.log.warn(String.format(
               "Only retrieved %d sequences for %d query strings",
               seqs.size(), ids.size()));
     }
@@ -657,7 +657,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (regions.isEmpty())
     {
-      System.out.println("Failed to identify target sequence for " + accId
+      Cache.log.warn("Failed to identify target sequence for " + accId
               + " from genomic features");
       return null;
     }