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

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index ab2c00a..9f8ac4e 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -150,7 +150,7 @@ public class JPredFile extends AlignFile
   @Override
   public void parse() throws IOException
   {
-    // JBPNote log.System.out.println("all read in ");
+    // JBPNote log.jalview.bin.Console.outPrintln("all read in ");
     String line;
     QuerySeqPosition = -1;
     noSeqs = 0;
@@ -240,7 +240,7 @@ public class JPredFile extends AlignFile
       }
       else if (id.equals("jnetconf"))
       {
-        // log.debug System.out.println("here");
+        // log.debug jalview.bin.Console.outPrintln("here");
         id = "Prediction Confidence";
         this.conf = new Vector(numSymbols);
 
@@ -377,14 +377,14 @@ public class JPredFile extends AlignFile
 
       for (int i = 0; i < jpred.seqs.size(); i++)
       {
-        System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName()
+        jalview.bin.Console.outPrintln(((Sequence) jpred.seqs.elementAt(i)).getName()
                 + "\n"
                 + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
                 + "\n");
       }
     } catch (java.io.IOException e)
     {
-      System.err.println("Exception " + e);
+      jalview.bin.Console.errPrintln("Exception " + e);
       // e.printStackTrace(); not java 1.1 compatible!
     }
   }
@@ -447,6 +447,6 @@ public class JPredFile extends AlignFile
  * out = BLCFile.print(s);
  * 
  * AlignFrame af = new AlignFrame(null, s); af.resize(700, 500); af.show();
- * System.out.println(out); } catch (java.io.IOException e) {
- * System.out.println("Exception " + e); } } }
+ * jalview.bin.Console.outPrintln(out); } catch (java.io.IOException e) {
+ * jalview.bin.Console.outPrintln("Exception " + e); } } }
  */