JAL-281 added string label for loading from database

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index bf87e5e..290066b 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -299,7 +299,7 @@ label.show_distances = Show distances
 label.mark_unassociated_leaves = Mark Unassociated Leaves
 label.fit_to_window = Fit To Window
 label.newick_format = Newick Format
-label.select_newick_like_tree_file = Select a newick-like tree file
+label.select_tree_file = Select a tree file
 label.colours = Colours
 label.view_mapping = View Mapping
 label.wireframe = Wireframe
@@ -389,6 +389,7 @@ label.sequences_selection_not_aligned = Sequences in selection are not aligned
 label.problem_reading_tree_file =  Problem reading tree file
 label.possible_problem_with_tree_file = Possible problem with tree file
 label.tree_url_example = Please enter a complete URL, \"for example http://purl.org/phylo/treebase/phylows/study/TB2:S15480?format=nexus\"
+label.from_database = From Database...
 label.load_tree_url = Tree from URL
 label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation = Please select at least three bases in at least one sequence in order to perform a cDNA translation.
 label.translation_failed = Translation Failed
@@ -561,10 +562,10 @@ label.select_copy_raw_html = Select this if you want to copy raw html
 label.share_data_vamsas_applications = Share data with other vamsas applications
 label.connect_to = Connect to
 label.join_existing_vamsas_session = Join an existing vamsas session
-label.from_url = from URL
+label.from_url = From URL
 label.any_trees_calculated_or_loaded_alignment_automatically_sort = When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment
 label.sort_with_new_tree = Sort With New Tree
-label.from_textbox = from Textbox
+label.from_textbox = From Textbox
 label.window = Window
 label.preferences = Preferences
 label.tools = Tools

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index f6d9fd6..4a49734 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -130,7 +130,7 @@ public final class AptxInit
 
   public static MainFrame createInstanceFromUrl(URL treeUrl,
           AlignmentViewport viewport)
-          throws FileNotFoundException, IOException
+          throws FileNotFoundException, IOException, RuntimeException
   {
     
     Phylogeny[] trees = AptxUtil.readPhylogeniesFromUrl(treeUrl,
@@ -154,7 +154,6 @@ public final class AptxInit
 
     return bindFrameToJalview(aptxApp);
 
-
   }
 
 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f5e8521..8408bcb 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3878,27 +3878,53 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return seqs;
   }
-public void chooseTreeFile() {
-  // Pick the tree file
-  JalviewFileChooser chooser = new JalviewFileChooser(
-          jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-  chooser.setFileView(new JalviewFileView());
-  chooser.setDialogTitle(
-          MessageManager.getString("label.select_newick_like_tree_file")); // modify
-  chooser.setToolTipText(
-            MessageManager.getString("label.load_tree_for_sequence_set"));
-  for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
-          .values())
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
+  {
+    chooseTreeFile();
+  }
+
+  @Override
+  protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
   {
-    chooser.setFileFilter(treeFormat.getTreeFilter());
+    chooseTreeUrl();
   }
 
-  int value = chooser.showOpenDialog(null);
+  @Override
+  protected void loadTreeDbItem_actionPerformed(ActionEvent e)
+  {
+    chooseTreeDb();
+  }
 
-  if (value == JalviewFileChooser.APPROVE_OPTION)
+  public void chooseTreeFile()
   {
-    String filePath = chooser.getSelectedFile().getPath();
-    Cache.setProperty("LAST_DIRECTORY", filePath);
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_tree_file")); // modify
+    chooser.setToolTipText(
+            MessageManager.getString("label.load_tree_for_sequence_set"));
+    for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter
+            .values())
+    {
+      chooser.setFileFilter(treeFormat.getTreeFilter());
+    }
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String filePath = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", filePath);
 
       TreeParser treeParser = new TreeParser(filePath);
       treeParser.loadTree(viewport);
@@ -3907,7 +3933,7 @@ public void chooseTreeFile() {
   }
 
   /**
-   * Move to TreeParser?
+   * Break up and move to TreeParser?
    */
   public void chooseTreeUrl()
   {
@@ -3930,14 +3956,14 @@ public void chooseTreeFile() {
     StringTokenizer st;
 
     if (historyItems != null)
-    {
+      {
       st = new StringTokenizer(historyItems, "\t");
 
       while (st.hasMoreTokens())
       {
         history.addItem(st.nextToken());
       }
-    }
+      }
 
     int reply = JvOptionPane.showInternalConfirmDialog(this, panel,
             MessageManager.getString("label.load_tree_url"),
@@ -3958,15 +3984,13 @@ public void chooseTreeFile() {
         treeUrl = new URL(urlString);
         AptxInit.createInstanceFromUrl(treeUrl, viewport);
 
-      } catch (IOException e)
+      } catch (IOException | RuntimeException e)
       {
-        JvOptionPane.showMessageDialog(this,
-                MessageManager.formatMessage(
-                        "exception.failed_to_read_data_from_source",
-                        new String[]
-                        { urlString }),
-                MessageManager.getString("label.url_not_found")
-         , JvOptionPane.ERROR_MESSAGE);
+        JvOptionPane.showMessageDialog(this, MessageManager.formatMessage(
+                "exception.failed_to_read_data_from_source", new String[]
+                { urlString }),
+                MessageManager.getString("label.url_not_found"),
+                JvOptionPane.ERROR_MESSAGE);
         e.printStackTrace();
       }
     }
@@ -3974,42 +3998,11 @@ public void chooseTreeFile() {
     {
 
     }
-
-
-
-
-    // final String url_string = JOptionPane
-    // .showInputDialog( this,
-    // message,
-    // "Use URL/webservice to obtain a phylogeny",
-    // JOptionPane.QUESTION_MESSAGE );
-    // boolean nhx_or_nexus = false;
-    // if ( ( url_string != null ) && ( url_string.length() > 0 ) ) {
-    // try {
-    // url = new URL( url_string );
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
+  public void chooseTreeDb()
   {
-    chooseTreeFile();
-  }
 
-  @Override
-  protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
-  {
-    chooseTreeUrl();
-  }
-
-  @Override
-  protected void loadTreeDbItem_actionPerformed(ActionEvent e)
-  {
 
   }
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 954721e..0672136 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1101,7 +1101,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem loadTreeDb = new JMenuItem(
-            MessageManager.getString("FIX ME"));
+            MessageManager.getString("label.from_database"));
     loadTreeDb.addActionListener(new ActionListener()
     {
       @Override