Merge branch 'develop' into features/JAL-4219_extended_fasta_rna_ss

[jalview.git] / src / jalview / io / StructureFile.java

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 6ec0298..3fb62c5 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -242,7 +242,7 @@ public abstract class StructureFile extends AlignFile
   protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
           throws Exception
   {
-    // System.out.println("this is a PDB format and RNA sequence");
+    // jalview.bin.Console.outPrintln("this is a PDB format and RNA sequence");
     // note: we use reflection here so that the applet can compile and run
     // without the HTTPClient bits and pieces needed for accessing Annotate3D
     // web service
@@ -336,7 +336,8 @@ public abstract class StructureFile extends AlignFile
         processPdbFileWithAnnotate3d(rnaSequences);
       } catch (Exception x)
       {
-        System.err.println("Exceptions when dealing with RNA in pdb file");
+        jalview.bin.Console
+                .errPrintln("Exceptions when dealing with RNA in pdb file");
         x.printStackTrace();
 
       }
@@ -352,7 +353,7 @@ public abstract class StructureFile extends AlignFile
         processWithJmolParser(proteinSequences, true);
       } catch (Exception x)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Exceptions from Jmol when processing data in pdb file");
         x.printStackTrace();
       }