JAL-4089 selected columns are reported in absolute column numbers, not visible columns

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 32d295a..7a5d5bc 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -174,7 +174,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (name == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
@@ -387,7 +387,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sf.getType() == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "SequenceFeature type may not be null: " + sf.toString());
       return false;
     }
@@ -1754,6 +1754,13 @@ public class Sequence extends ASequence implements SequenceI
       transferAnnotation(entry.getDatasetSequence(), mp);
       return;
     }
+    // transfer from entry to sequence
+    // if entry has a description and sequence doesn't, then transfer
+    if (entry.getDescription()!=null && (description==null || description.trim().length()==0))
+    {
+      description = entry.getDescription();
+    }
+    
     // transfer any new features from entry onto sequence
     if (entry.getSequenceFeatures() != null)
     {