Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 09859c9..7e2539f 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -317,7 +317,7 @@ public class AnnotationFile
               }
               else
               {
-                // System.err.println("Skipping NaN - not valid value.");
+                // jalview.bin.Console.errPrintln("Skipping NaN - not valid value.");
                 text.append(comma + 0f);// row.annotations[j].value);
               }
               comma = ",";
@@ -679,10 +679,10 @@ public class AnnotationFile
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Problem reading annotation file: " + ex);
+      jalview.bin.Console.outPrintln("Problem reading annotation file: " + ex);
       if (nlinesread > 0)
       {
-        System.out.println("Last read line " + nlinesread + ": '" + lastread
+        jalview.bin.Console.outPrintln("Last read line " + nlinesread + ": '" + lastread
                 + "' (first 80 chars) ...");
       }
       return false;
@@ -821,7 +821,7 @@ public class AnnotationFile
               if (refSeqIndex < 1)
               {
                 refSeqIndex = 1;
-                System.out.println(
+                jalview.bin.Console.outPrintln(
                         "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
               }
             } catch (Exception ex)
@@ -923,7 +923,7 @@ public class AnnotationFile
           {
             if (hidden == null)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
                               + line);
             }
@@ -1075,7 +1075,7 @@ public class AnnotationFile
             {
               // TODO: specify and implement duplication of alignment annotation
               // for multiple group references.
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Ignoring 1:many group reference mappings for group name '"
                               + groupRef + "'");
             }
@@ -1368,7 +1368,7 @@ public class AnnotationFile
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Couldn't combine annotations. None are added to alignment yet!");
     }
   }
@@ -1385,7 +1385,7 @@ public class AnnotationFile
       value = Float.valueOf(nextToken);
     } catch (NumberFormatException e)
     {
-      System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+      jalview.bin.Console.errPrintln("line " + nlinesread + ": Threshold '" + nextToken
               + "' invalid, setting to zero");
     }
     String label = st.hasMoreTokens() ? st.nextToken() : null;
@@ -1435,7 +1435,7 @@ public class AnnotationFile
       }
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
                       + rng + "' - assuming alignment width for group.");
       // assume group is full width