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JAL-1355
[jalview.git] / src / jalview / jbgui / GPreferences.java
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index d11d046..eb0e1c7 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -133,9 +133,11 @@ public class GPreferences extends JPanel
 
   JPanel jPanel1 = new JPanel();
 
-  TitledBorder titledBorder1 = new TitledBorder(MessageManager.getString("label.proxy_server"));
+  TitledBorder titledBorder1 = new TitledBorder(
+          MessageManager.getString("label.proxy_server"));
 
-  TitledBorder titledBorder2 = new TitledBorder(MessageManager.getString("label.file_output"));
+  TitledBorder titledBorder2 = new TitledBorder(
+          MessageManager.getString("label.file_output"));
 
   GridBagLayout gridBagLayout2 = new GridBagLayout();
 
@@ -302,9 +304,11 @@ public class GPreferences extends JPanel
     quality.setHorizontalTextPosition(SwingConstants.LEFT);
     quality.setSelected(true);
     quality.setText(MessageManager.getString("label.quality"));
-    visualTab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
+    visualTab.setBorder(new TitledBorder(MessageManager
+            .getString("action.open_new_aligmnent")));
     visualTab.setLayout(null);
-    visual2Tab.setBorder(new TitledBorder(MessageManager.getString("action.open_new_aligmnent")));
+    visual2Tab.setBorder(new TitledBorder(MessageManager
+            .getString("action.open_new_aligmnent")));
     visual2Tab.setLayout(new FlowLayout());
     fullScreen.setFont(verdana11);
     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -325,17 +329,20 @@ public class GPreferences extends JPanel
     showGroupbits.setFont(verdana11);
     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
-    showGroupbits.setText(MessageManager.getString("action.show_group") + ":");
+    showGroupbits.setText(MessageManager.getString("action.show_group")
+            + ":");
     showConsensbits.setFont(verdana11);
     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
-    showConsensbits.setText(MessageManager.getString("label.consensus") + ":");
+    showConsensbits.setText(MessageManager.getString("label.consensus")
+            + ":");
     showConsensHistogram.setEnabled(false);
     showConsensHistogram.setFont(verdana11);
     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
     showConsensHistogram.setSelected(true);
-    showConsensHistogram.setText(MessageManager.getString("label.histogram"));
+    showConsensHistogram.setText(MessageManager
+            .getString("label.histogram"));
     showConsensLogo.setEnabled(false);
     showConsensLogo.setFont(verdana11);
     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -353,19 +360,22 @@ public class GPreferences extends JPanel
     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
     showGroupConservation.setSelected(true);
-    showGroupConservation.setText(MessageManager.getString("label.conservation"));
+    showGroupConservation.setText(MessageManager
+            .getString("label.conservation"));
     showNpTooltip.setEnabled(true);
     showNpTooltip.setFont(verdana11);
     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
     showNpTooltip.setSelected(true);
-    showNpTooltip.setText(MessageManager.getString("label.non_positional_features"));
+    showNpTooltip.setText(MessageManager
+            .getString("label.non_positional_features"));
     showDbRefTooltip.setEnabled(true);
     showDbRefTooltip.setFont(verdana11);
     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
     showDbRefTooltip.setSelected(true);
-    showDbRefTooltip.setText(MessageManager.getString("label.database_references"));
+    showDbRefTooltip.setText(MessageManager
+            .getString("label.database_references"));
     annotations.setFont(verdana11);
     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
     annotations.setHorizontalTextPosition(SwingConstants.LEADING);
@@ -397,7 +407,8 @@ public class GPreferences extends JPanel
     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
     showUnconserved.setSelected(true);
-    showUnconserved.setText(MessageManager.getString("action.show_unconserved"));
+    showUnconserved.setText(MessageManager
+            .getString("action.show_unconserved"));
     showUnconserved.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -410,13 +421,15 @@ public class GPreferences extends JPanel
     shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
     shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
     shareSelections.setSelected(true);
-    shareSelections.setText(MessageManager.getString("label.share_selection_across_views"));
+    shareSelections.setText(MessageManager
+            .getString("label.share_selection_across_views"));
     followHighlight.setFont(verdana11);
     followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
     followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
     // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
     followHighlight.setSelected(true);
-    followHighlight.setText(MessageManager.getString("label.scroll_highlighted_regions"));
+    followHighlight.setText(MessageManager
+            .getString("label.scroll_highlighted_regions"));
 
     gapLabel.setFont(verdana11);
     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -425,7 +438,8 @@ public class GPreferences extends JPanel
     colour.setBounds(new Rectangle(172, 225, 155, 21));
     colourLabel.setFont(verdana11);
     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    colourLabel.setText(MessageManager.getString("label.alignment_colour") + " ");
+    colourLabel.setText(MessageManager.getString("label.alignment_colour")
+            + " ");
     fontLabel.setFont(verdana11);
     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     fontLabel.setText(MessageManager.getString("label.font"));
@@ -493,18 +507,22 @@ public class GPreferences extends JPanel
     portLabel.setText(MessageManager.getString("label.port"));
     browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
-    browserLabel.setText(MessageManager.getString("label.default_browser_unix"));
+    browserLabel.setText(MessageManager
+            .getString("label.default_browser_unix"));
     defaultBrowser.setFont(verdana11);
     defaultBrowser.setText("");
-    usagestats.setText(MessageManager.getString("label.send_usage_statistics"));
+    usagestats.setText(MessageManager
+            .getString("label.send_usage_statistics"));
     usagestats.setFont(verdana11);
     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
-    questionnaire.setText(MessageManager.getString("label.check_for_questionnaires"));
+    questionnaire.setText(MessageManager
+            .getString("label.check_for_questionnaires"));
     questionnaire.setFont(verdana11);
     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
-    versioncheck.setText(MessageManager.getString("label.check_for_latest_version"));
+    versioncheck.setText(MessageManager
+            .getString("label.check_for_latest_version"));
     versioncheck.setFont(verdana11);
     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
@@ -552,7 +570,8 @@ public class GPreferences extends JPanel
     });
 
     linkScrollPane.setBorder(null);
-    linkPanel.setBorder(new TitledBorder(MessageManager.getString("label.url_linkfrom_sequence_id")));
+    linkPanel.setBorder(new TitledBorder(MessageManager
+            .getString("label.url_linkfrom_sequence_id")));
     linkPanel.setLayout(borderLayout2);
     editLinkButtons.setLayout(gridLayout1);
     gridLayout1.setRows(3);
@@ -609,7 +628,7 @@ public class GPreferences extends JPanel
     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
     blcjv.setText(MessageManager.getString("label.blc") + "     ");
     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
-    msfjv.setText(MessageManager.getString("label.msf")+ "     ");
+    msfjv.setText(MessageManager.getString("label.msf") + "     ");
     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
     msfjv.setFont(verdana11);
@@ -640,24 +659,25 @@ public class GPreferences extends JPanel
     smoothFont.setText(MessageManager.getString("label.smooth_font"));
     calcTab.setLayout(null);
     autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());
-    autoCalculateConsCheck.setText(MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculateConsCheck.setText(MessageManager
+            .getString("label.autocalculate_consensus"));
     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
     padGaps.setFont(JvSwingUtils.getLabelFont());
     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
     sortByTree.setFont(JvSwingUtils.getLabelFont());
-    sortByTree.setText(MessageManager.getString("label.sort_with_new_tree"));
     sortByTree
-            .setToolTipText(MessageManager.getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
+            .setText(MessageManager.getString("label.sort_with_new_tree"));
+    sortByTree
+            .setToolTipText(MessageManager
+                    .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 
     autoIdWidth.setFont(JvSwingUtils.getLabelFont());
-    autoIdWidth.setText(MessageManager.getString("label.automatically_set_id_width"));
+    autoIdWidth.setText(MessageManager
+            .getString("label.automatically_set_id_width"));
     autoIdWidth
-            .setToolTipText("<html>"
-                    + JvSwingUtils
-                            .wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")
-                    + "</html>");
+            .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.adjusts_width_generated_eps_png")));
     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
     autoIdWidth.addActionListener(new ActionListener()
     {
@@ -669,17 +689,12 @@ public class GPreferences extends JPanel
       }
     });
     userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
-    userIdWidthlabel.setText(MessageManager.getString("label.figure_id_column_width"));
+    userIdWidthlabel.setText(MessageManager
+            .getString("label.figure_id_column_width"));
     userIdWidth
-            .setToolTipText("<html>"
-                    + JvSwingUtils
-                            .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
-                    + "</html>");
+            .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.manually_specify_width_left_column")));
     userIdWidthlabel
-            .setToolTipText("<html>"
-                    + JvSwingUtils
-                            .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")
-                    + "</html>");
+            .setToolTipText(JvSwingUtils.wrapTooltip(MessageManager.getString("label.manually_specify_width_left_column")));
     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
     userIdWidth.setText("");
@@ -694,7 +709,8 @@ public class GPreferences extends JPanel
       }
     });
     modellerOutput.setFont(JvSwingUtils.getLabelFont());
-    modellerOutput.setText(MessageManager.getString("label.use_modeller_output"));
+    modellerOutput.setText(MessageManager
+            .getString("label.use_modeller_output"));
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 
     dasPanel.setLayout(borderLayout4);
@@ -711,9 +727,11 @@ public class GPreferences extends JPanel
     idItalics.setFont(JvSwingUtils.getLabelFont());
     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
-    idItalics.setText(MessageManager.getString("label.sequence_name_italics"));
+    idItalics.setText(MessageManager
+            .getString("label.sequence_name_italics"));
     openoverv.setFont(JvSwingUtils.getLabelFont());
-    openoverv.setActionCommand(MessageManager.getString("label.open_overview"));
+    openoverv.setActionCommand(MessageManager
+            .getString("label.open_overview"));
     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
     openoverv.setText(MessageManager.getString(("label.open_overview")));
@@ -767,24 +785,26 @@ public class GPreferences extends JPanel
     autoAnnotSettings3.add(showConsensLogo);
 
     JPanel tooltipSettings = new JPanel();
-    tooltipSettings.setBorder(new TitledBorder(MessageManager.getString("label.sequence_id_tooltip")));
+    tooltipSettings.setBorder(new TitledBorder(MessageManager
+            .getString("label.sequence_id_tooltip")));
     tooltipSettings.setBounds(173, 130, 200, 62);
     tooltipSettings.setLayout(new GridLayout(2, 1));
     tooltipSettings.add(showDbRefTooltip);
     tooltipSettings.add(showNpTooltip);
     visualTab.add(tooltipSettings);
     visualTab.add(jPanel2);
-    JvSwingUtils.addtoLayout(visual2Tab,
-           MessageManager.getString("label.default_colour_scheme_for_alignment"), colourLabel, colour);
+    JvSwingUtils.addtoLayout(visual2Tab, MessageManager
+            .getString("label.default_colour_scheme_for_alignment"),
+            colourLabel, colour);
     JPanel annotationShding = new JPanel();
-    annotationShding.setBorder(new TitledBorder(
-            MessageManager.getString("label.annotation_shading_default")));
+    annotationShding.setBorder(new TitledBorder(MessageManager
+            .getString("label.annotation_shading_default")));
     annotationShding.setLayout(new GridLayout(1, 2));
-    JvSwingUtils.addtoLayout(annotationShding,
-            MessageManager.getString("label.default_minimum_colour_annotation_shading"),
+    JvSwingUtils.addtoLayout(annotationShding, MessageManager
+            .getString("label.default_minimum_colour_annotation_shading"),
             mincolourLabel, minColour);
-    JvSwingUtils.addtoLayout(annotationShding,
-            MessageManager.getString("label.default_maximum_colour_annotation_shading"),
+    JvSwingUtils.addtoLayout(annotationShding, MessageManager
+            .getString("label.default_maximum_colour_annotation_shading"),
             maxcolourLabel, maxColour);
     visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 
@@ -848,7 +868,8 @@ public class GPreferences extends JPanel
 
     tabbedPane.add(visualTab, MessageManager.getString("label.visual"));
     tabbedPane.add(visual2Tab, MessageManager.getString("label.colours"));
-    tabbedPane.add(connectTab, MessageManager.getString("label.connections"));
+    tabbedPane.add(connectTab,
+            MessageManager.getString("label.connections"));
     tabbedPane.add(exportTab, MessageManager.getString("label.output"));
     jPanel11.add(jLabel1);
     jPanel11.add(blcjv);
@@ -867,7 +888,8 @@ public class GPreferences extends JPanel
     calcTab.add(padGaps);
     calcTab.add(sortByTree);
 
-    tabbedPane.add(dasPanel, MessageManager.getString("label.das_settings"));
+    tabbedPane
+            .add(dasPanel, MessageManager.getString("label.das_settings"));
     tabbedPane.add(wsPanel, MessageManager.getString("label.web_services"));
 
     exportTab.add(epsLabel);