JAL-629 null check and neatening code

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 891e295..837462f 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -84,20 +84,6 @@ public class SeqsetUtils
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
   {
-    return SeqCharacterUnhash(sq, sqinfo, false, false);
-  }
-
-  /**
-   * restore some characteristics for a sequence from its hash
-   * @param sq
-   * @param sqinfo
-   * @param excludeLimits - when true, start/end is left unmodified
-   * @param excludeFeatures - when true, features are not restored from stashed vector
-   * @return true if sequence's name was modified
-   */
-          
-  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo, boolean excludeLimits,boolean excludeFeatures)
-  {
     boolean namePresent = true;
     if (sqinfo == null)
     {
@@ -124,13 +110,13 @@ public class SeqsetUtils
       sq.setPDBId(pdbid);
     }
 
-    if (!excludeLimits && (start != null) && (end != null))
+    if ((start != null) && (end != null))
     {
       sq.setStart(start.intValue());
       sq.setEnd(end.intValue());
     }
-    // TODO: drop this completely since we should not manipulate sequenceFeatures as a vector any more
-    if (!excludeFeatures && sfeatures != null && !sfeatures.isEmpty())
+
+    if (sfeatures != null && !sfeatures.isEmpty())
     {
       sq.setSequenceFeatures(sfeatures);
     }
@@ -143,7 +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);
@@ -258,7 +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");
           }
         }
@@ -266,7 +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()))