X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=70306374540c6bbad68feb559544884f985535df;hb=7dd9c4874042f584dc1feb6a345fe929a8509e2b;hp=83870895d0bd2d61b0d09396f28c0e852b4d2e82;hpb=37b210ecad3c132b87c525f84e3b754a4edf12a6;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8387089..7030637 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -144,7 +144,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
     alignPanel.alabels.addKeyListener(this);
     createAlignFrameWindow(embedded, title);
-    alignPanel.validate();
+
+    validate();
     alignPanel.adjustAnnotationHeight();
     alignPanel.paintAlignment(true);
   }
@@ -1031,7 +1032,7 @@ 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();
@@ -1064,12 +1065,25 @@ 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;
@@ -2573,7 +2587,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
   protected void documentation_actionPerformed()
   {
-    showURL("http://www.jalview.org/help.html", "HELP");
+    alignPanel.av.applet.openJalviewHelpUrl();
   }
 
   protected void about_actionPerformed()
@@ -2644,45 +2658,7 @@ 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);
     }
   }
 
@@ -3580,4 +3556,18 @@ 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();
+  }
 }