JAL-1620 version bump and release notes

[jalview.git] / src / jalview / gui / JDatabaseTree.java

diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 53fc35c..0f240d6 100644 (file)
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -1,6 +1,27 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 import jalview.bin.Cache;
+import jalview.util.MessageManager;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -31,6 +52,7 @@ import javax.swing.tree.DefaultMutableTreeNode;
 import javax.swing.tree.DefaultTreeCellRenderer;
 import javax.swing.tree.DefaultTreeModel;
 import javax.swing.tree.TreeCellRenderer;
+import javax.swing.tree.TreeNode;
 import javax.swing.tree.TreePath;
 import javax.swing.tree.TreeSelectionModel;
 
@@ -40,7 +62,8 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
 
   JButton getDatabaseSelectorButton()
   {
-    final JButton viewdbs = new JButton("--- Select Database ---");
+    final JButton viewdbs = new JButton(
+            MessageManager.getString("action.select_ddbb"));
     viewdbs.addActionListener(new ActionListener()
     {
 
@@ -63,7 +86,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
 
   public JDatabaseTree(jalview.ws.SequenceFetcher sfetch)
   {
-    initDialogFrame(this, true, false, "Select Database Retrieval Source",
+    initDialogFrame(this, true, false, MessageManager.getString("label.select_database_retrieval_source"),
             650, 490);
     /*
      * Dynamically generated database list will need a translation function from
@@ -74,7 +97,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<String, DefaultMutableTreeNode>();
     sfetcher = sfetch;
     String dbs[] = sfetch.getSupportedDb();
-    Hashtable<String,String> ht = new Hashtable<String,String>();
+    Hashtable<String, String> ht = new Hashtable<String, String>();
     for (int i = 0; i < dbs.length; i++)
     {
       tn = source.get(dbs[i]);
@@ -117,6 +140,8 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
       }
       root.add(tn);
     }
+    // and sort the tree
+    sortTreeNodes(root);
     svp = new JScrollPane();
     // svp.setAutoscrolls(true);
     dbviews = new JTree(new DefaultTreeModel(root, false));
@@ -165,6 +190,46 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     validate();
   }
 
+  private void sortTreeNodes(DefaultMutableTreeNode root)
+  {
+    if (root.getChildCount() == 0)
+    {
+      return;
+    }
+    int count = root.getChildCount();
+    String[] names = new String[count];
+    DefaultMutableTreeNode[] nodes = new DefaultMutableTreeNode[count];
+    for (int i = 0; i < count; i++)
+    {
+      TreeNode node = root.getChildAt(i);
+      if (node instanceof DefaultMutableTreeNode)
+      {
+        DefaultMutableTreeNode child = (DefaultMutableTreeNode) node;
+        nodes[i] = child;
+        if (child.getUserObject() instanceof DbSourceProxy)
+        {
+          names[i] = ((DbSourceProxy) child.getUserObject()).getDbName()
+                  .toLowerCase();
+        }
+        else
+        {
+          names[i] = ((String) child.getUserObject()).toLowerCase();
+          sortTreeNodes(child);
+        }
+      }
+      else
+      {
+        throw new Error(MessageManager.getString("error.implementation_error_cant_reorder_tree"));
+      }
+    }
+    jalview.util.QuickSort.sort(names, nodes);
+    root.removeAllChildren();
+    for (int i = count - 1; i >= 0; i--)
+    {
+      root.add(nodes[i]);
+    }
+  }
+
   private class DbTreeRenderer extends DefaultTreeCellRenderer implements
           TreeCellRenderer
   {
@@ -300,21 +365,9 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
             }
             else
             {
-              if ((admt = dmt.getFirstLeaf()) != null
-                      && admt.getUserObject() != null)
-              {
-                // modify db selection to just first leaf.
-                if (admt.getUserObject() instanceof DbSourceProxy)
-                {
-                  srcs.add((DbSourceProxy) admt.getUserObject());
-                }
-                else
-                {
-                  srcs.add(sfetcher.getSourceProxy(
-                          (String) admt.getUserObject()).get(0));
-                }
-                forcedFirstChild = true;
-              }
+              srcs.add(sfetcher
+                      .getSourceProxy((String) dmt.getUserObject()).get(0));
+              forcedFirstChild = true;
             }
           }
         }
@@ -356,23 +409,27 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
 
     if (allowMultiSelections)
     {
-      dbstatus.setText("Selected "
-              + srcs.size()
-              + " database"
-              + (srcs.size() == 1 ? "" : "s")
-              + " to fetch from"
-              + (srcs.size() > 0 ? " with " + x + " test quer"
-                      + (x == 1 ? "y" : "ies") : "."));
+      dbstatus.setText(MessageManager.formatMessage(
+              "label.selected_database_to_fetch_from", new String[]
+              {
+                  Integer.valueOf(srcs.size()).toString(),
+                  (srcs.size() == 1 ? "" : "s"),
+                  (srcs.size() > 0 ? " with " + x + " test quer"
+                          + (x == 1 ? "y" : "ies") : ".") }));
       dbstatex.setText(" ");
     }
     else
     {
       if (nm.length() > 0)
       {
-        dbstatus.setText("Database: " + nm);
+        dbstatus.setText(MessageManager.formatMessage(
+                "label.database_param", new String[]
+                { nm }));
         if (qr.length() > 0)
         {
-          dbstatex.setText("Example: " + qr);
+          dbstatex.setText(MessageManager.formatMessage(
+                  "label.example_param", new String[]
+                  { qr }));
         }
         else
         {