X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=1801674431aa4c5ac04ae6d6adbe73aec4aa0241;hb=95600b03ceeaf7162219dfa9b0a6bed432228b60;hp=0f3edfd8c9a9fc3bd65ac6e938d10780caca3d78;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 0f3edfd..1801674 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -453,8 +453,8 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
-                + nSeq
+        jalview.bin.Console.errPrintln("WARNING: tmp.size()=" + tmp.size()
+                + " != nseq=" + nSeq
                 + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
@@ -548,7 +548,9 @@ public class AlignmentSorter
 
     if ((left == null) && (right == null))
     {
-      if (!(node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()) && (node.element() != null))
+      if (!(node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())
+              && (node.element() != null))
       {
         if (node.element() instanceof SequenceI)
         {
@@ -712,7 +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;
     }
 
@@ -830,7 +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]);
           }
@@ -845,7 +847,8 @@ 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);