Autocalculate consensus

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b2c8901..9d2cf0f 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -263,7 +263,7 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);\r
       }\r
 \r
-      Jalview2XML.SaveAlignment(this, file, shortName);\r
+      new Jalview2XML().SaveAlignment(this, file, shortName);\r
 \r
       // USE Jalview2XML to save this file\r
       return true;\r
@@ -912,6 +912,11 @@ public class AlignFrame
    */\r
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
+    if(viewport.cursorMode)\r
+    {\r
+      alignPanel.seqPanel.keyboardNo1 = null;\r
+      alignPanel.seqPanel.keyboardNo2 = null;\r
+    }\r
     viewport.setSelectionGroup(null);\r
     viewport.getColumnSelection().clear();\r
     viewport.setSelectionGroup(null);\r
@@ -1134,7 +1139,10 @@ public class AlignFrame
 \r
  public void alignmentChanged()\r
  {\r
-   if(viewport.vconsensus!=null)\r
+   if(viewport.padGaps)\r
+     viewport.getAlignment().padGaps();\r
+\r
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)\r
    {\r
      viewport.updateConsensus();\r
      viewport.updateConservation();\r
@@ -1196,7 +1204,10 @@ public class AlignFrame
   {\r
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
                                    HistoryItem.HIDE));\r
-    if (viewport.getAlignment().padGaps())\r
+\r
+    viewport.padGaps = padGapsMenuitem.isSelected();\r
+\r
+    if (viewport.padGaps)\r
       alignmentChanged();\r
   }\r
 \r
@@ -1928,6 +1939,13 @@ public class AlignFrame
      new PCAPanel(viewport);\r
   }\r
 \r
+\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+  }\r
+\r
+\r
   /**\r
    * DOCUMENT ME!\r
    *\r
@@ -1977,7 +1995,7 @@ public class AlignFrame
    */\r
   void NewTreePanel(String type, String pwType, String title)\r
   {\r
-    final TreePanel tp;\r
+    TreePanel tp;\r
 \r
     if ( (viewport.getSelectionGroup() != null) &&\r
         (viewport.getSelectionGroup().getSize() > 3))\r
@@ -2029,7 +2047,6 @@ public class AlignFrame
     }\r
 \r
     addTreeMenuItem(tp, title);\r
-    viewport.setCurrentTree(tp.getTree());\r
 \r
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
   }\r