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

[jalview.git] / src / jalview / analysis / StructureFrequency.java

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index cc97be0..3f5099b 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -148,7 +148,7 @@ public class StructureFrequency
           {
             if (sequences[j] == null)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
@@ -226,14 +226,14 @@ public class StructureFrequency
           maxResidue = "{";
         }
       }
-      residueHash.put(MAXCOUNT, new Integer(count));
+      residueHash.put(MAXCOUNT, Integer.valueOf(count));
       residueHash.put(MAXRESIDUE, maxResidue);
 
       percentage = ((float) count * 100) / jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
+      residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
       percentage = ((float) count * 100) / nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
+      residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
       if (result[i] == null)
       {
@@ -260,14 +260,14 @@ public class StructureFrequency
           residueHash.put(PAIRPROFILE, pairs);
         }
 
-        residueHash.put(MAXCOUNT, new Integer(count));
+        residueHash.put(MAXCOUNT, Integer.valueOf(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
         percentage = ((float) count * 100) / jSize;
-        residueHash.put(PID_GAPS, new Float(percentage));
+        residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
         percentage = ((float) count * 100) / nongap;
-        residueHash.put(PID_NOGAPS, new Float(percentage));
+        residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
         result[bpEnd] = residueHash;
       }