JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 2a27cce..374147a 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -21,7 +21,7 @@
 package jalview.ws.seqfetcher;
 
 import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
@@ -112,7 +112,7 @@ public class ASequenceFetcher
         return true;
       }
     }
-    Cache.log.warn("isFetchable doesn't know about '" + source + "'");
+    Console.warn("isFetchable doesn't know about '" + source + "'");
     return false;
   }
 
@@ -191,9 +191,9 @@ public class ASequenceFetcher
               seqset = fetcher.getSequenceRecords(qsb.toString());
             } catch (Exception ex)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Failed to retrieve the following from " + db);
-              System.err.println(qsb);
+              jalview.bin.Console.errPrintln(qsb);
               ex.printStackTrace(System.err);
             }
             // TODO: Merge alignment together - perhaps
@@ -208,7 +208,8 @@ public class ASequenceFetcher
                   // BH 2015.01.25 check about version/accessid being null here
                   List<DBRefEntry> frefs = DBRefUtils.searchRefs(
                           seqs[is].getDBRefs(),
-                          new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
+                          new DBRefEntry(db, null, null),
+                          DBRefUtils.SEARCH_MODE_FULL);
                   for (DBRefEntry dbr : frefs)
                   {
                     queriesFound.add(dbr.getAccessionId());
@@ -221,7 +222,7 @@ public class ASequenceFetcher
               {
                 if (fetcher.getRawRecords() != null)
                 {
-                  System.out.println(
+                  jalview.bin.Console.outPrintln(
                           "# Retrieved from " + db + ":" + qsb.toString());
                   StringBuffer rrb = fetcher.getRawRecords();
                   /*
@@ -234,12 +235,12 @@ public class ASequenceFetcher
                   /*
                    * } else { hdr = "# part "+rr; }
                    */
-                  System.out.println(hdr);
+                  jalview.bin.Console.outPrintln(hdr);
                   if (rrb != null)
                   {
-                    System.out.println(rrb);
+                    jalview.bin.Console.outPrintln(rrb);
                   }
-                  System.out.println("# end of " + hdr);
+                  jalview.bin.Console.outPrintln("# end of " + hdr);
                 }
 
               }
@@ -252,7 +253,7 @@ public class ASequenceFetcher
         }
         if (queriesMade.size() > 0)
         {
-          System.out.println("# Adding " + queriesMade.size()
+          jalview.bin.Console.outPrintln("# Adding " + queriesMade.size()
                   + " ids back to queries list for searching again (" + db
                   + ")");
           queriesLeft.addAll(queriesMade);
@@ -278,7 +279,7 @@ public class ASequenceFetcher
           Exception ex)
   {
 
-    System.err.println(
+    jalview.bin.Console.errPrintln(
             "Failed to retrieve the following references from " + db);
     int n = 0;
     for (String qv : queriesMade)
@@ -286,11 +287,11 @@ public class ASequenceFetcher
       System.err.print(" " + qv + ";");
       if (n++ > 10)
       {
-        System.err.println();
+        jalview.bin.Console.errPrintln();
         n = 0;
       }
     }
-    System.err.println();
+    jalview.bin.Console.errPrintln();
     ex.printStackTrace();
   }
 
@@ -365,8 +366,7 @@ public class ASequenceFetcher
               .get(proxy.getDbSource());
       if (slist == null)
       {
-        fetchableDbs.put(proxy.getDbSource(),
-                slist = new Hashtable<>());
+        fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
       }
       slist.put(proxy.getDbName(), proxy);
     }