X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=b0373366166692a6032455e38775f935e24489fd;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=b02d49c773fd1fcad9365938caa532f9c1c8df8a;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b02d49c..b037336 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -453,7 +453,7 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+        jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size() + " != nseq="
                 + nSeq
                 + " in getOrderByTree - tree contains sequences not in alignment");
       }
@@ -714,7 +714,7 @@ public class AlignmentSorter
       String msg = String.format(
               "Implementation Error - sortByFeature method must be either '%s' or '%s'",
               FEATURE_SCORE, FEATURE_DENSITY);
-      System.err.println(msg);
+      jalview.bin.Console.errPrintln(msg);
       return;
     }
 
@@ -832,7 +832,7 @@ public class AlignmentSorter
           {
             // int nf = (feats[i] == null) ? 0
             // : ((SequenceFeature[]) feats[i]).length;
-            // // System.err.println("Sorting on Score: seq " +
+            // // jalview.bin.Console.errPrintln("Sorting on Score: seq " +
             // seqs[i].getName()
             // + " Feats: " + nf + " Score : " + scores[i]);
           }
@@ -847,7 +847,7 @@ public class AlignmentSorter
         int featureCount = feats[i] == null ? 0
                 : ((SequenceFeature[]) feats[i]).length;
         scores[i] = featureCount;
-        // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+        // jalview.bin.Console.errPrintln("Sorting on Density: seq "+seqs[i].getName()+
         // " Feats: "+featureCount+" Score : "+scores[i]);
       }
       QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);