X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=759075a46a1b723a133a69bc0879f81f9a1f49b5;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=8f8ac5a027be59dd45a684cde4a8b7e04401e3b1;hpb=f0ed39b35bf7581ff35bfeb52bb2403c179060c0;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8f8ac5a..759075a 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -601,6 +601,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.autocalculateConsensus = autoCalculate.getState();
     }
+    else if (evt.getSource() == sortByTree)
+    {
+      viewport.sortByTree = sortByTree.getState();
+    }
     else if (evt.getSource() == this.centreColumnLabelFlag)
     {
       centreColumnLabelFlag_stateChanged();
@@ -1032,7 +1036,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   private Hashtable getDisplayedFeatureCols()
   {
-    if (alignPanel.getFeatureRenderer() != null)
+    if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
     {
       FeatureRenderer fr = alignPanel.getFeatureRenderer();
       Hashtable fcols = new Hashtable();
@@ -1065,12 +1069,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (displayTextbox)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      boolean frimport=false;
+      if (features==null || features.equals("No Features Visible"))
+      {
+        features = "# No features visible - paste some and import them here.";
+        frimport=true;
+      }
+      
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+      if (frimport)
+      {
+        cap.setAnnotationImport();
+      }
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
-
       cap.setText(features);
+    } else {
+      if (features==null)
+        features = "";
     }
 
     return features;
@@ -2538,7 +2555,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         sortByTree(treePanel, title); // treePanel.getTitle());
       }
     });
-
+    
     treePanel.addWindowListener(new WindowAdapter()
     {
       public void windowOpened(WindowEvent e)
@@ -2572,6 +2589,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
     return true;
   }
+
   protected void documentation_actionPerformed()
   {
     alignPanel.av.applet.openJalviewHelpUrl();
@@ -2805,6 +2823,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
           "Autocalculate Consensus", true);
 
+  CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+          "Sort Alignment With New Tree", true);
+
   Menu sortByTreeMenu = new Menu();
 
   Menu sort = new Menu();
@@ -3000,6 +3021,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sort.setLabel("Sort");
     calculate.setLabel("Calculate Tree");
     autoCalculate.addItemListener(this);
+    sortByTree.addItemListener(this);
     inputText.setLabel("Input from textbox");
     inputText.addActionListener(this);
     centreColumnLabelFlag.setLabel("Centre column labels");
@@ -3144,6 +3166,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
     this.add(statusBar, BorderLayout.SOUTH);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
@@ -3543,4 +3566,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     alignPanel.seqPanel.scrollTo(row, column);    
   }
+  public void scrollToRow(int row)
+  {
+    alignPanel.seqPanel.scrollToRow(row);    
+  }
+  public void scrollToColumn(int column)
+  {
+    alignPanel.seqPanel.scrollToColumn(column);    
+  }
+  /**
+   * @return the alignments unique ID.
+   */
+  public String getSequenceSetId() {
+    return viewport.getSequenceSetId();
+  }
 }