X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=d133624a3dc9a22f4a13065abc3b837b34b86481;hp=80b01d0ce2da74bb150583837d7d1c96fb40b8d1;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hpb=9740e237ec7a9accfd02aa6d21fd9be34847e214

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 80b01d0..d133624 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, J Engelhardt, LM Lui, 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)
@@ -2572,9 +2589,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.paintAlignment(true);
     return true;
   }
+
   protected void documentation_actionPerformed()
   {
-    showURL("http://www.jalview.org/help.html", "HELP");
+    alignPanel.av.applet.openJalviewHelpUrl();
   }
 
   protected void about_actionPerformed()
@@ -2645,45 +2663,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      try
-      {
-        if (url.indexOf(":") == -1)
-        {
-          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
-          // form valid URL
-          // Should really use docbase, not codebase.
-          if (url.indexOf("/") == 0)
-          {
-            String codebase = viewport.applet.getCodeBase().toString();
-            url = codebase.substring(0, codebase.length()
-                    - viewport.applet.getCodeBase().getFile().length())
-                    + url;
-          }
-          else
-          {
-            url = viewport.applet.getCodeBase() + url;
-          }
-          System.out.println("Show url (prepended codebase): " + url);
-        }
-        else
-        {
-          System.out.println("Show url: " + url);
-        }
-        if (url.indexOf("javascript:") == 0)
-        {
-          // no target for the javascript context
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url));
-        }
-        else
-        {
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url), target);
-        }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      viewport.applet.showURL(url, target);
     }
   }
 
@@ -2843,6 +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();
@@ -3038,6 +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");
@@ -3182,6 +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);
@@ -3581,4 +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();
+  }
 }