JAL-1355

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 5c0c9c5..50086dc 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -647,7 +647,7 @@ label.edit_sequence_name_description = Edit Sequence Name/Description
 label.spaces_converted_to_backslashes = Spaces have been converted to _\r
 label.no_spaces_allowed_sequence_name = No spaces allowed in Sequence Name\r
 label.select_outline_colour = Select Outline Colour\r
-label.web_browser_not_found_unix = Unixers: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."\r
+label.web_browser_not_found_unix = Unixers\: Couldn't find default web browser.\nAdd the full path to your browser in Preferences."\r
 label.web_browser_not_found = Web browser not found\r
 label.select_pdb_file_for = Select a PDB file for {0}\r
 label.html = HTML\r
@@ -1064,13 +1064,13 @@ warn.input_is_too_big = Input is too big!
 warn.invalid_job_param_set = Invalid job parameter set!\r
 info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}\r
 info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}\r
-info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service!\n\r
+info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n\r
 info.no_jobs_ran = No jobs ran\r
-info.failed_to_submit_prediction = Failed to submit the prediction:\n{0} {1}\r
-info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data!\n{2}\r
+info.failed_to_submit_prediction = Failed to submit the prediction\:\n{0} {1}\r
+info.invalid_jnet_job_result_data ={0}\n{1}\nInvalid JNet job result data\!\n{2}\r
 info.failed_to_submit_sequences_for_alignment = Failed to submit sequences for alignment.\nIt is most likely that there is a problem with the server.\nJust close the window\n\r
 info.alignment_object_method_notes = \nAlignment Object Method Notes\n\r
-info.server_exception = \n{0} Server exception!\n{1}\r
+info.server_exception = \n{0} Server exception\!\n{1}\r
 status.processing_commandline_args = Processing commandline arguments...\r
 status.das_features_being_retrived = DAS features being retrieved...\r
 status.searching_for_sequences_from = Searching for sequences from {0}\r
@@ -1099,8 +1099,8 @@ status.fetching_db_refs = Fetching db refs
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data\r
 label.error_loading_file_params = Error loading file {0}\r
 label.error_loading_jalview_file = Error loading Jalview file\r
-warn.out_of_memory_when_action = Out of memory when {0}!!\nSee help files for increasing Java Virtual Machine memory.\r
-warn.out_of_memory_loading_file = Out of memory loading file {0}!!\nSee help files for increasing Java Virtual Machine memory.\r
+warn.out_of_memory_when_action = Out of memory when {0}\!\!\nSee help files for increasing Java Virtual Machine memory.\r
+warn.out_of_memory_loading_file = Out of memory loading file {0}\!\!\nSee help files for increasing Java Virtual Machine memory.\r
 label.out_of_memory = Out of memory\r
 label.invalid_id_column_width = Invalid ID Column width\r
 warn.user_defined_width_requirements = The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.\r
@@ -1111,4 +1111,16 @@ warn.url_must_contain = Sequence URL must contain $SEQUENCE_ID$ or a regex $SEQU
 info.validate_jabaws_server = Validate JabaWS Server ?\n(Look in console output for results)\r
 label.test_server = Test Server?\r
 info.you_want_jalview_to_find_uniprot_accessions = Do you want Jalview to find\nUniprot Accession ids for given sequence names?\r
-label.find_uniprot_accession_ids = Find Uniprot Accession Ids
\ No newline at end of file
+label.find_uniprot_accession_ids = Find Uniprot Accession Ids\r
+label.new_sequence_fetcher = New Sequence Fetcher\r
+label.additional_sequence_fetcher = Additional Sequence Fetcher\r
+label.select_database_retrieval_source = Select Database Retrieval Source\r
+label.overwrite_existing_file = Overwrite existing file?\r
+label.file_already_exists = File exists\r
+label.edit_jabaws_url = Edit JABAWS URL\r
+label.add_jabaws_url = Add new JABAWS URL\r
+label.news_from_jalview = News from http://www.jalview.org\r
+label.cut_paste_alignmen_file = Cut & Paste Alignment File\r
+label.enter_redundancy_thereshold = Enter the redundancy thereshold\r
+label.select_dark_light_set_thereshold = <html><i>Select a dark and light text colour, then set the threshold to<br>switch between colours, based on background colour</i></html>\r
+label.select_feature_colour = Select Feature Colour
\ No newline at end of file

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index e112b2a..3dd567e 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -28,6 +28,7 @@ import java.awt.*;
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
 import jalview.io.FileParse;
+import jalview.util.MessageManager;
 
 public class PDBfile extends jalview.io.AlignFile
 {

diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index 3757415..c527308 100644 (file)
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -20,6 +20,8 @@
  */
 package jalview.appletgui;
 
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.FlowLayout;

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 11ca86a..29c3ac5 100644 (file)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -353,8 +353,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       }
     }
 
-    String title = newFeatures ? "Create New Sequence Feature(s)"
-            : "Amend/Delete Features for " + sequences[0].getName();
+    String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
+            : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 
     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
             240);
@@ -901,7 +901,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         return ((GraduatedColor) fc).getMaxColor();
       }
     }
-    throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass(),featureType}));
+    throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),featureType}));
   }
 
   /**

diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index c7835a5..7a1065d 100644 (file)
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -331,7 +331,7 @@ public class BlogReader extends JPanel
         {
           createDialog();
           bounds = new Rectangle(5, 5, 550, 350);
-          jd.initDialogFrame(me, false, false, "News from www.jalview.org",
+          jd.initDialogFrame(me, false, false, MessageManager.getString("label.news_from_jalview"),
                   bounds.width, bounds.height);
           jd.frame.setModalExclusionType(ModalExclusionType.NO_EXCLUDE);
           Cache.log.info("Displaying news.");

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index a3cec98..123aed2 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1039,7 +1039,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewport);
-    Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
+    Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), 600, 500);
   }
 
   /*

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index b04aa85..d2d9c9c 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1024,7 +1024,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
         if (fcol instanceof Color)
         {
           Color col = JColorChooser.showDialog(Desktop.desktop,
-                  "Select Feature Colour", ((Color) fcol));
+                  MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
           if (col != null)
           {
             fcol = col;

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 577012b..1d8c116 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1062,8 +1062,8 @@ public class FeatureSettings extends JPanel
       }
     });
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-    tabbedPane.addTab("Feature Settings", settingsPane);
-    tabbedPane.addTab("DAS Settings", dasSettingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transbuttons.add(optimizeOrder);
     transbuttons.add(invert);

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 7f6ac85..39afd2c 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -29,6 +29,7 @@ import javax.swing.*;
 
 import jalview.datamodel.*;
 import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
 /**

diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 279662a..030e78a 100644 (file)
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -86,7 +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

diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 4a9b580..46ae664 100644 (file)
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -855,7 +855,7 @@ public class OptsAndParamsPage
       }
       else
       {
-        throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option}));
+        throw new Error(MessageManager.formatMessage("error.invalid_value_for_option", new String[]{string,option.getName()}));
       }
 
     }

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 91f2450..1fcd875 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -159,7 +159,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     progress.setVisible(false);
     progress = null;
 
-    label.setText("Enter the redundancy threshold");
+    label.setText(MessageManager.getString("label.enter_redundancy_thereshold"));
     slider.setVisible(true);
     applyButton.setEnabled(true);
     valueField.setVisible(true);

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 4506eaa..35bc29a 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -219,8 +219,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   private String getFrameTitle()
   {
-    return ((alignFrame == null) ? "New " : "Additional ")
-            + "Sequence Fetcher";
+    return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
   }
 
   private void jbInit() throws Exception

diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index bb2f295..6fe7660 100644 (file)
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -68,9 +68,7 @@ public class TextColourChooser
     JPanel panel = new JPanel();
     bigpanel.add(panel, BorderLayout.CENTER);
     bigpanel.add(
-            new JLabel(
-                    "<html><i>Select a dark and light text colour, then set the threshold to"
-                            + "<br>switch between colours, based on background colour</i></html>"),
+            new JLabel(MessageManager.getString("label.select_dark_light_set_thereshold")),
             BorderLayout.NORTH);
     panel.add(col1);
     panel.add(slider);

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 1a5b9f8..876d157 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -274,7 +274,7 @@ public class WsPreferences extends GWsPreferences
     int sel = wsList.getSelectedRow();
     if (sel > -1)
     {
-      String url = editUrl(wsUrls.elementAt(sel), "Edit JABAWS URL");
+      String url = editUrl(wsUrls.elementAt(sel), MessageManager.getString("label.edit_jabaws_url"));
       if (url != null)
       {
         int present = wsUrls.indexOf(url);
@@ -516,7 +516,7 @@ public class WsPreferences extends GWsPreferences
   @Override
   protected void newWsUrl_actionPerformed(ActionEvent e)
   {
-    String url = editUrl(null, "Add new JABAWS URL");
+    String url = editUrl(null, MessageManager.getString("label.add_jabaws_url"));
     if (url != null)
     {
       if (!wsUrls.contains(url))

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 67559b9..ce15f0e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,6 +26,7 @@ import java.util.List;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.*;
+import jalview.util.MessageManager;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 470fd89..c84e542 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -205,7 +205,7 @@ public class JalviewFileChooser extends JFileChooser
             && getSelectedFile().exists())
     {
       int confirm = JOptionPane.showConfirmDialog(parent,
-              "Overwrite existing file?", "File exists",
+              MessageManager.getString("label.overwrite_existing_file"), MessageManager.getString("label.file_already_exists"),
               JOptionPane.YES_NO_OPTION);
 
       if (confirm != JOptionPane.YES_OPTION)

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 871c6d5..4f0d802 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -208,7 +208,7 @@ public class WSWUBlastClient
           imageIndex++;
           imageIndex %= 9;
           output.setFrameIcon(imageIcon[imageIndex]);
-          output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{jobsRunning}));
+          output.setTitle(MessageManager.formatMessage("label.blasting_for_unidentified_sequence_jobs_running", new String[]{Integer.valueOf(jobsRunning).toString()}));
         } catch (Exception ex)
         {
         }

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 0d0f047..5e8cb98 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -726,7 +726,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
         j.setAllowedServerExceptions(0);
         wsInfo.appendProgressText(j.getJobnum(),
-                MessageMAnager.getString("info.failed_to_submit_sequences_for_alignment"));
+                MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
       }
     }
   }

diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index e44fa6a..8916be9 100644 (file)
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.jws2;
 
+import jalview.util.MessageManager;
+
 import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.HashSet;

diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index 8ce4639..e78172e 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -26,6 +26,7 @@ import java.util.List;
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
 
+import jalview.util.MessageManager;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.ParameterUtils;

diff --git a/src/jalview/ws/rest/HttpResultSet.java b/src/jalview/ws/rest/HttpResultSet.java
index 47ad3b4..5af6b32 100644 (file)
--- a/src/jalview/ws/rest/HttpResultSet.java
+++ b/src/jalview/ws/rest/HttpResultSet.java
@@ -26,6 +26,7 @@ import jalview.io.packed.DataProvider;
 import jalview.io.packed.ParsePackedSet;
 import jalview.io.packed.SimpleDataProvider;
 import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.MessageManager;
 import jalview.ws.io.mime.JalviewMimeContentHandler;
 
 import java.io.BufferedReader;

diff --git a/src/jalview/ws/rest/params/Tree.java b/src/jalview/ws/rest/params/Tree.java
index 8af2071..2c58ed8 100644 (file)
--- a/src/jalview/ws/rest/params/Tree.java
+++ b/src/jalview/ws/rest/params/Tree.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.rest.params;
 
+import jalview.util.MessageManager;
 import jalview.ws.params.OptionI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.RestJob;