sequence groups carry their own conservation and consensus annotation rows

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9b21f60..5f2a977 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -79,6 +79,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
+  CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+
   Menu editMenu = new Menu("Edit");
 
   MenuItem copy = new MenuItem("Copy (Jalview Only)");
@@ -150,6 +152,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
+      displayNonconserved.setState(sg.getShowunconserved());
       if (!ap.av.alignment.getGroups().contains(sg))
       {
         groupMenu.remove(unGroupMenuItem);
@@ -176,7 +179,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
           continue;
         }
         final String target = urlLink.getTarget(); // link.substring(0,
-                                                    // link.indexOf("|"));
+        // link.indexOf("|"));
         final String label = urlLink.getLabel();
         if (urlLink.isDynamic())
         {
@@ -188,7 +191,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
-          if (descr!=null && descr.length()<1)
+          if (descr != null && descr.length() < 1)
           {
             descr = null;
           }
@@ -227,8 +230,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
             }
             // addshowLink(linkMenu, target, url_pref + id + url_suff);
           }
-          // Now construct URLs from description but only try to do it for regex URL links
-          if (descr != null && urlLink.getRegexReplace()!=null)
+          // Now construct URLs from description but only try to do it for regex
+          // URL links
+          if (descr != null && urlLink.getRegexReplace() != null)
           {
             // create link for this URL from description only if regex matches
             String[] urls = urlLink.makeUrls(descr, true);
@@ -249,11 +253,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
          * final String url;
          * 
          * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
-         * string and any matching database reference accessions String url_pref =
-         * link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$"));
+         * string and any matching database reference accessions String url_pref
+         * = link.substring(link.indexOf("|") + 1,
+         * link.indexOf("$SEQUENCE_ID$"));
          * 
          * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
-         *  // collect matching db-refs DBRefEntry[] dbr =
+         * // collect matching db-refs DBRefEntry[] dbr =
          * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
          * String[]{target}); // collect id string too String id =
          * seq.getName(); if (id.indexOf("|") > -1) { id =
@@ -268,14 +273,16 @@ public class APopupMenu extends java.awt.PopupMenu implements
          * link.substring(link.lastIndexOf("|")+1)); }
          */
       }
-
-      if (seq != null)
-      {
-        seqMenu.add(linkMenu);
-      }
-      else
+      if (linkMenu.getItemCount() > 0)
       {
-        add(linkMenu);
+        if (seq != null)
+        {
+          seqMenu.add(linkMenu);
+        }
+        else
+        {
+          add(linkMenu);
+        }
       }
     }
     if (seq != null)
@@ -298,10 +305,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
    * add a show URL menu item to the given linkMenu
    * 
    * @param linkMenu
-   * @param target -
-   *                menu label string
-   * @param url -
-   *                url to open
+   * @param target
+   *          - menu label string
+   * @param url
+   *          - url to open
    */
   private void addshowLink(Menu linkMenu, final String target,
           final String url)
@@ -313,12 +320,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
    * add a show URL menu item to the given linkMenu
    * 
    * @param linkMenu
-   * @param target -
-   *                URL target window
-   * @param label -
-   *                menu label string
-   * @param url -
-   *                url to open
+   * @param target
+   *          - URL target window
+   * @param label
+   *          - menu label string
+   * @param url
+   *          - url to open
    */
   private void addshowLink(Menu linkMenu, final String target,
           final String label, final String url)
@@ -352,6 +359,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
     {
       showBoxes_itemStateChanged();
     }
+    else if (evt.getSource() == displayNonconserved)
+    {
+      this.showNonconserved_itemStateChanged();
+    }
   }
 
   public void actionPerformed(ActionEvent evt)
@@ -677,7 +688,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     showBoxes.setState(true);
     showBoxes.addItemListener(this);
     sequenceName.addActionListener(this);
-
+    displayNonconserved.setLabel("Show Nonconserved");
+    displayNonconserved.setState(false);
+    displayNonconserved.addItemListener(this);
     showText.setLabel("Text");
     showText.addItemListener(this);
     showColourText.setLabel("Colour Text");
@@ -766,6 +779,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     menu1.add(showBoxes);
     menu1.add(showText);
     menu1.add(showColourText);
+    menu1.add(displayNonconserved);
     toggleCase.addActionListener(this);
     pdb.addActionListener(this);
     hideSeqs.addActionListener(this);
@@ -966,6 +980,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     refresh();
   }
 
+  public void showNonconserved_itemStateChanged()
+  {
+    getGroup().setShowunconserved(this.displayNonconserved.getState());
+    refresh();
+  }
+
   public void showBoxes_itemStateChanged()
   {
     getGroup().setDisplayBoxes(showBoxes.getState());