From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 4 Apr 2006 09:35:34 +0000 (+0000)
Subject: Autocalculate consensus
X-Git-Tag: Release_2_08~78
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9ef2d2b865889e9f75faf8e14597c8f508d0ce1;p=jalview.git

Autocalculate consensus
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b2c8901..9d2cf0f 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();
@@ -1196,7 +1204,10 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-    if (viewport.getAlignment().padGaps())
+
+    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);
   }
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a92517c..2c8172b 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -86,6 +86,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -99,6 +100,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bddc504..f0e5e67 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -110,7 +110,7 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenu jMenu2 = new JMenu();
-  JMenuItem padGapsMenuitem = new JMenuItem();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
@@ -124,6 +124,7 @@ public class GAlignFrame
 
 
   JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
 
@@ -977,6 +978,15 @@ public class GAlignFrame
         associatedData_actionPerformed(e);
       }
     });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState(true);
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -1063,6 +1073,7 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
     webService.add(webServiceNoServices);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
@@ -1373,11 +1384,6 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
-  {
-
-  }
-
   public void featureSettings_actionPerformed(ActionEvent e)
   {
 
@@ -1407,4 +1413,9 @@ public class GAlignFrame
   {
 
   }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
 }