Autocalculate consensus

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a92517c..2c8172b 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -86,6 +86,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;\r
     AlignmentAnnotation conservation;\r
     AlignmentAnnotation quality;\r
+    boolean autoCalculateConsensus = true;\r
 \r
     /** DOCUMENT ME!! */\r
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
@@ -99,6 +100,8 @@ public class AlignViewport
 \r
     boolean antiAlias = false;\r
 \r
+    boolean padGaps = false;\r
+\r
 \r
     public AlignViewport(AlignmentI al, boolean dataset)\r
     {\r

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bddc504..f0e5e67 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -110,7 +110,7 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
   JMenu jMenu2 = new JMenu();\r
-  JMenuItem padGapsMenuitem = new JMenuItem();\r
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
   protected ButtonGroup colours = new ButtonGroup();\r
   JMenuItem vamsasStore = new JMenuItem();\r
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
@@ -124,6 +124,7 @@ public class GAlignFrame
 \r
 \r
   JMenuItem associatedData = new JMenuItem();\r
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
 \r
@@ -977,6 +978,15 @@ public class GAlignFrame
         associatedData_actionPerformed(e);\r
       }\r
     });\r
+    autoCalculate.setText("Autocalculate Consensus");\r
+    autoCalculate.setState(true);\r
+    autoCalculate.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        autoCalculate_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -1063,6 +1073,7 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.addSeparator();\r
     calculateMenu.add(showTranslation);\r
+    calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
     webService.add(webServiceNoServices);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
@@ -1373,11 +1384,6 @@ public class GAlignFrame
 \r
   }\r
 \r
-  public void tabSelected()\r
-  {\r
-\r
-  }\r
-\r
   public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -1407,4 +1413,9 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r