Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index fabd0c6..837462f 100755 (executable)
--- 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());
@@ -129,7 +129,7 @@ public class SeqsetUtils
     {
       if (sfeatures != null)
       {
-        System.err.println(
+        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);
@@ -244,7 +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");
           }
         }
@@ -252,7 +252,7 @@ public class SeqsetUtils
     }
     if (unmatched.size() > 0 && !quiet)
     {
-      System.err.println("Did not find matches for :");
+      jalview.bin.Console.errPrintln("Did not find matches for :");
       for (Enumeration i = unmatched.elements(); i
               .hasMoreElements(); System.out
                       .println(((SequenceI) i.nextElement()).getName()))