X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=a4d96330c34aeee5f8198264f47d47c08a060e18;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=06cbb1361c215711a5f5c22e7ec9520b592185c8;hpb=34524f89f84e7d9b85743300a6407aa1c0e2751a;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 06cbb13..a4d9633 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -43,7 +43,7 @@ import javax.xml.stream.XMLStreamReader;
 import com.stevesoft.pat.Regex;
 
 import jalview.analysis.SequenceIdMatcher;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -161,7 +161,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
       else
       {
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "No record found for '" + emprefx + ":" + query + "'");
       }
     }
@@ -283,11 +283,11 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       }
     } catch (Exception e)
     {
-      System.err.println("EMBL Record Features parsing error!");
+      jalview.bin.Console.errPrintln("EMBL Record Features parsing error!");
       System.err
               .println("Please report the following to help@jalview.org :");
-      System.err.println("EMBL Record " + accession);
-      System.err.println("Resulted in exception: " + e.getMessage());
+      jalview.bin.Console.errPrintln("EMBL Record " + accession);
+      jalview.bin.Console.errPrintln("Resulted in exception: " + e.getMessage());
       e.printStackTrace(System.err);
     }
 
@@ -354,7 +354,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
             codonStart = Integer.parseInt(value.trim());
           } catch (NumberFormatException e)
           {
-            System.err.println("Invalid codon_start in XML for "
+            jalview.bin.Console.errPrintln("Invalid codon_start in XML for "
                     + entry.getAccession() + ": " + e.getMessage());
           }
         }
@@ -406,13 +406,13 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
          * workaround until we handle dna location for CDS sequence
          * e.g. location="X53828.1:60..1058" correctly
          */
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
                         + sourceDb + ":" + entry.getAccession() + ")");
         int dnaLength = dna.getLength();
         if (translationLength * 3 == (1 - codonStart + dnaLength))
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Not allowing for additional stop codon at end of cDNA fragment... !");
           // this might occur for CDS sequences where no features are marked
           exons = new int[] { dna.getStart() + (codonStart - 1),
@@ -423,7 +423,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
         }
         if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
           exons = new int[] { dna.getStart() + (codonStart - 1),
               dna.getEnd() - 3 };
@@ -658,7 +658,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       return listToArray(ranges);
     } catch (ParseException e)
     {
-      Cache.log.warn(
+      Console.warn(
               String.format("Not parsing inexact CDS location %s in ENA %s",
                       location, accession));
       return new int[] {};