X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FEMBLLikeFlatFile.java;h=9e8cff6c7b32cc08117d2a890ae4e8774d06bc27;hp=64943b2011be211787fa5eadfc474c5af601fafb;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hpb=c4e814d2930b175c789c2a004801b7b8a1dacd32

diff --git a/src/jalview/io/EMBLLikeFlatFile.java b/src/jalview/io/EMBLLikeFlatFile.java
index 64943b2..9e8cff6 100644
--- a/src/jalview/io/EMBLLikeFlatFile.java
+++ b/src/jalview/io/EMBLLikeFlatFile.java
@@ -291,7 +291,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       int slashPos = line.indexOf('/');
       if (slashPos == -1)
       {
-        Cache.log.error("Unexpected EMBL line ignored: " + line);
+        Cache.error("Unexpected EMBL line ignored: " + line);
         line = nextLine();
         continue;
       }
@@ -321,7 +321,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
           data.codonStart = Integer.parseInt(featureValue.trim());
         } catch (NumberFormatException e)
         {
-          Cache.log.error("Invalid codon_start in XML for " + this.accession
+          Cache.error("Invalid codon_start in XML for " + this.accession
                   + ": " + e.getMessage());
         }
       }
@@ -357,7 +357,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
     }
     else
     {
-      Cache.log.error("Ignoring CDS feature with no protein_id for "
+      Cache.error("Ignoring CDS feature with no protein_id for "
               + sourceDb + ":" + accession);
     }
 
@@ -382,7 +382,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
   {
     if (this.accession == null || this.sequenceString == null)
     {
-      Cache.log.error("Failed to parse data from EMBL");
+      Cache.error("Failed to parse data from EMBL");
       return;
     }
 
@@ -584,7 +584,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
        * workaround until we handle all 'location' formats fully
        * e.g. X53828.1:60..1058 or <123..>289
        */
-      Cache.log.error(String.format(
+      Cache.error(String.format(
               "Implementation Notice: EMBLCDS location '%s'not properly supported yet"
                       + " - Making up the CDNA region of (%s:%s)... may be incorrect",
               data.cdsLocation, sourceDb, this.accession));
@@ -594,12 +594,12 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       if (peptideLength * 3 == completeCodonsLength)
       {
         // this might occur for CDS sequences where no features are marked
-        Cache.log.warn("Assuming no stop codon at end of cDNA fragment");
+        Cache.warn("Assuming no stop codon at end of cDNA fragment");
         mappedDnaEnd = dna.getEnd();
       }
       else if ((peptideLength + 1) * 3 == completeCodonsLength)
       {
-        Cache.log.warn("Assuming stop codon at end of cDNA fragment");
+        Cache.warn("Assuming stop codon at end of cDNA fragment");
         mappedDnaEnd = dna.getEnd() - 3;
       }
 
@@ -673,7 +673,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       return MappingUtils.rangeListToArray(ranges);
     } catch (ParseException e)
     {
-      Cache.log.warn(
+      Cache.warn(
               String.format("Not parsing inexact CDS location %s in ENA %s",
                       location, accession));
       return new int[] {};
@@ -718,7 +718,7 @@ public abstract class EMBLLikeFlatFile extends AlignFile
       String[] tokens = line.split(WHITESPACE);
       if (tokens.length < 2)
       {
-        Cache.log.error("Ignoring bad EMBL line for " + this.accession
+        Cache.error("Ignoring bad EMBL line for " + this.accession
                 + ": " + line);
         break;
       }