new savestate method

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63b3787..846ab24 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -82,8 +82,7 @@ public class AlignFrame extends GAlignFrame
         String shortName = title.replace('/', '_');
         title = title.replace('\\', '_');
         String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
-                              choice);
+        Jalview2XML.SaveState(this, choice, shortName);
         // USE Jalview2XML to save this file
         return;
       }
@@ -237,7 +236,6 @@ public class AlignFrame extends GAlignFrame
           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
           if(restore.getLength()==0)
           {
-            System.out.println(hi.getHidden().elementAt(i));
             restore.setSequence(hi.getHidden().elementAt(i).toString());
             viewport.alignment.getSequences().insertElementAt(
                restore,
@@ -545,6 +543,7 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment,
                                    HistoryItem.HIDE));
+
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();