X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=837462f081896d35563a60a04da172422a9a7daa;hb=e75315ad5faf541f6943e9395c81a078369f2f63;hp=27b3041f2d50c84d07da01a1ca30c51c6827428e;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 27b3041..837462f 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -45,8 +45,8 @@ public class SeqsetUtils
   {
     Hashtable sqinfo = new Hashtable();
     sqinfo.put("Name", seq.getName());
-    sqinfo.put("Start", new Integer(seq.getStart()));
-    sqinfo.put("End", new Integer(seq.getEnd()));
+    sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+    sqinfo.put("End", Integer.valueOf(seq.getEnd()));
     if (seq.getDescription() != null)
     {
       sqinfo.put("Description", seq.getDescription());
@@ -124,14 +124,13 @@ public class SeqsetUtils
     {
       sq.setDescription(description);
     }
-    if ((seqds != null)
-            && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
-                    .getLength() == 0))
+    if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+            && seqds.getLength() == 0))
     {
       if (sfeatures != null)
       {
-        System.err
-                .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+        jalview.bin.Console.errPrintln(
+                "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
       }
       sq.setDatasetSequence(seqds);
     }
@@ -245,7 +244,7 @@ public class SeqsetUtils
         {
           if (!quiet)
           {
-            System.err.println("Can't find '" + ((String) key)
+            jalview.bin.Console.errPrintln("Can't find '" + ((String) key)
                     + "' in uniquified alignment");
           }
         }
@@ -253,9 +252,10 @@ public class SeqsetUtils
     }
     if (unmatched.size() > 0 && !quiet)
     {
-      System.err.println("Did not find matches for :");
-      for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
-              .println(((SequenceI) i.nextElement()).getName()))
+      jalview.bin.Console.errPrintln("Did not find matches for :");
+      for (Enumeration i = unmatched.elements(); i
+              .hasMoreElements(); System.out
+                      .println(((SequenceI) i.nextElement()).getName()))
       {
         ;
       }