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

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 64c1547..8968742 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -155,16 +155,16 @@ public class StructureSelectionManager
   {
     if (mappings.isEmpty())
     {
-      System.err.println("reportMapping: No PDB/Sequence mappings.");
+      jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "reportMapping: There are " + mappings.size() + " mappings.");
       int i = 0;
       for (StructureMapping sm : mappings)
       {
-        System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+        jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
       }
     }
   }
@@ -617,12 +617,12 @@ public class StructureSelectionManager
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
-              System.err.println(e.getMessage());
+              jalview.bin.Console.errPrintln(e.getMessage());
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
-              System.err.println(e.getMessage());
+              jalview.bin.Console.errPrintln(e.getMessage());
             }
           }
           if (!foundSiftsMappings.isEmpty())
@@ -1254,7 +1254,7 @@ public class StructureSelectionManager
      * 
      * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
      * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
-     * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+     * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
      * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
@@ -1351,7 +1351,7 @@ public class StructureSelectionManager
       boolean removed = seqmappings.remove(acf);
       if (removed && seqmappings.isEmpty())
       { // debug
-        System.out.println("All mappings removed");
+        jalview.bin.Console.outPrintln("All mappings removed");
       }
     }
   }