X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ccf7303f35160d152b5f9854d58296cc4b07c7fb;hb=b2319fcc38be5c500ed7cafc014cf9da96a4ce98;hp=b2c890160329bac9f5ed309d03b5e8a4ea0d904d;hpb=0ad0cc7fe1de5c299363b0dc9b4b032d5d199275;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b2c8901..ccf7303 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -263,7 +263,7 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);
       }
 
-      Jalview2XML.SaveAlignment(this, file, shortName);
+      new Jalview2XML().SaveAlignment(this, file, shortName);
 
       // USE Jalview2XML to save this file
       return true;
@@ -912,6 +912,11 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
@@ -1134,7 +1139,10 @@ public class AlignFrame
 
  public void alignmentChanged()
  {
-   if(viewport.vconsensus!=null)
+   if(viewport.padGaps)
+     viewport.getAlignment().padGaps();
+
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
    {
      viewport.updateConsensus();
      viewport.updateConservation();
@@ -1196,8 +1204,11 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-    if (viewport.getAlignment().padGaps())
-      alignmentChanged();
+
+    viewport.padGaps = padGapsMenuitem.isSelected();
+
+   // if (viewport.padGaps)
+    alignmentChanged();
   }
 
   /**
@@ -1928,6 +1939,13 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1977,7 +1995,7 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
         (viewport.getSelectionGroup().getSize() > 3))
@@ -2029,7 +2047,6 @@ public class AlignFrame
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2725,10 +2742,10 @@ public void drop(DropTargetDropEvent evt)
 }
 
   // This method will attempt to load a "dropped" file first by testing
-  // whether its and Annotation file, then group file. If both are
+  // whether its and Annotation file, then features file. If both are
   // false then the user may have dropped an alignment file onto this
   // AlignFrame
-   void loadJalviewDataFile(String file)
+   public void loadJalviewDataFile(String file)
   {
     try{
       boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.