JAL-1517 fix copyright for 2.8.2

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6974d96..038477f 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -6,14 +6,16 @@
  * 
  * 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.
+ * 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/>.
+ * 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;
@@ -32,7 +34,7 @@ import jalview.io.*;
 import jalview.schemes.*;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.MessageManager;\r
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
 /**
@@ -286,7 +288,7 @@ public class PopupMenu extends JPopupMenu
             final String rnastruc = aa[i].getRNAStruc();
             final String structureLine = aa[i].label;
             menuItem = new JMenuItem();
-            menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
+            menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
             menuItem.addActionListener(new java.awt.event.ActionListener()
             
             {
@@ -324,7 +326,7 @@ public class PopupMenu extends JPopupMenu
 
               // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
-              menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
+              menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
               menuItem.addActionListener(new java.awt.event.ActionListener()
               {
                 public void actionPerformed(ActionEvent e)
@@ -343,7 +345,7 @@ public class PopupMenu extends JPopupMenu
 
       }
 
-      menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
+      menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
       menuItem.addActionListener(new java.awt.event.ActionListener()
       {
         public void actionPerformed(ActionEvent e)
@@ -356,7 +358,7 @@ public class PopupMenu extends JPopupMenu
       if (ap.av.getSelectionGroup() != null
               && ap.av.getSelectionGroup().getSize() > 1)
       {
-        menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
+        menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
         menuItem.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -374,7 +376,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.av.adjustForHiddenSeqs(index)
                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
         {
-          menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
+          menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
           menuItem.addActionListener(new ActionListener()
           {
             public void actionPerformed(ActionEvent e)
@@ -394,7 +396,7 @@ public class PopupMenu extends JPopupMenu
     if (ap.av.hasHiddenRows())
     {
       {
-        menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
+        menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
         menuItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -417,8 +419,8 @@ public class PopupMenu extends JPopupMenu
 
     if (sg != null && sg.getSize() > 0)
     {      
-      groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
-      groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
+      groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
+      groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
 
       if (sg.cs instanceof ZappoColourScheme)
       {
@@ -520,13 +522,13 @@ public class PopupMenu extends JPopupMenu
         final JMenuItem gpdbview,rpdbview;
         if (pdbe.size() == 1)
         {
-          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
+          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
         }
         else
         {
-          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));          \r
+          structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));          
         }
-        gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
+        gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
         gpdbview.addActionListener(new ActionListener()
         {
 
@@ -562,11 +564,11 @@ public class PopupMenu extends JPopupMenu
     {
       createGroupMenuItem.setVisible(true);
       unGroupMenuItem.setVisible(false);
-      jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
+      jMenu1.setText(MessageManager.getString("action.edit_new_group"));
     } else {
       createGroupMenuItem.setVisible(false);
       unGroupMenuItem.setVisible(true);
-      jMenu1.setText(MessageManager.getString("action.edit_group"));\r
+      jMenu1.setText(MessageManager.getString("action.edit_group"));
     }
 
     if (seq == null)
@@ -578,7 +580,7 @@ public class PopupMenu extends JPopupMenu
     if (links != null && links.size() > 0)
     {
 
-      JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
+      JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
       Vector linkset = new Vector();
       for (int i = 0; i < links.size(); i++)
       {
@@ -705,10 +707,10 @@ public class PopupMenu extends JPopupMenu
     // menu appears asap
     // sequence only URLs
     // ID/regex match URLs
-    groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+    groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
     JMenu[] linkMenus = new JMenu[]
-    { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
-        new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
+    { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
+        new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
                                           // created.
     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
@@ -831,7 +833,7 @@ public class PopupMenu extends JPopupMenu
     }
     if (addMenu)
     {
-      groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
+      groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
       for (int m = 0; m < linkMenus.length; m++)
       {
         if (linkMenus[m] != null
@@ -857,7 +859,7 @@ public class PopupMenu extends JPopupMenu
   private void addshowLink(JMenu linkMenu, String label, final String url)
   {
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
+    item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -892,8 +894,8 @@ public class PopupMenu extends JPopupMenu
           final GroupUrlLink urlgenerator, final Object[] urlstub)
   {
     JMenuItem item = new JMenuItem(label);
-    item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
-    // TODO: put in info about what is being sent.\r
+    item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
+    // TODO: put in info about what is being sent.
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -926,9 +928,9 @@ public class PopupMenu extends JPopupMenu
    */
   private void jbInit() throws Exception
   {
-    groupMenu.setText(MessageManager.getString("label.group"));\r
-    groupMenu.setText(MessageManager.getString("label.selection"));\r
-    groupName.setText(MessageManager.getString("label.name"));\r
+    groupMenu.setText(MessageManager.getString("label.group"));
+    groupMenu.setText(MessageManager.getString("label.selection"));
+    groupName.setText(MessageManager.getString("label.name"));
     groupName.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -936,8 +938,8 @@ public class PopupMenu extends JPopupMenu
         groupName_actionPerformed();
       }
     });
-    sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
-    sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
+    sequenceMenu.setText(MessageManager.getString("label.sequence"));
+    sequenceName.setText(MessageManager.getString("label.edit_name_description"));
     sequenceName.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -945,7 +947,7 @@ public class PopupMenu extends JPopupMenu
         sequenceName_actionPerformed();
       }
     });
-    sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+    sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
     sequenceDetails.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -953,7 +955,7 @@ public class PopupMenu extends JPopupMenu
         sequenceDetails_actionPerformed();
       }
     });
-    sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
+    sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
     sequenceSelDetails
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -963,7 +965,7 @@ public class PopupMenu extends JPopupMenu
               }
             });
     PIDColour.setFocusPainted(false);
-    unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
+    unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -971,7 +973,7 @@ public class PopupMenu extends JPopupMenu
         unGroupMenuItem_actionPerformed();
       }
     });
-    createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
+    createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -980,7 +982,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    outline.setText(MessageManager.getString("action.border_colour"));\r
+    outline.setText(MessageManager.getString("action.border_colour"));
     outline.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -988,7 +990,7 @@ public class PopupMenu extends JPopupMenu
         outline_actionPerformed();
       }
     });
-    nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
+    nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
     nucleotideMenuItem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -996,8 +998,8 @@ public class PopupMenu extends JPopupMenu
         nucleotideMenuItem_actionPerformed();
       }
     });
-    colourMenu.setText(MessageManager.getString("label.group_colour"));\r
-    showBoxes.setText(MessageManager.getString("action.boxes"));\r
+    colourMenu.setText(MessageManager.getString("label.group_colour"));
+    showBoxes.setText(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
     showBoxes.addActionListener(new ActionListener()
     {
@@ -1006,7 +1008,7 @@ public class PopupMenu extends JPopupMenu
         showBoxes_actionPerformed();
       }
     });
-    showText.setText(MessageManager.getString("action.text"));\r
+    showText.setText(MessageManager.getString("action.text"));
     showText.setState(true);
     showText.addActionListener(new ActionListener()
     {
@@ -1015,7 +1017,7 @@ public class PopupMenu extends JPopupMenu
         showText_actionPerformed();
       }
     });
-    showColourText.setText(MessageManager.getString("label.colour_text"));\r
+    showColourText.setText(MessageManager.getString("label.colour_text"));
     showColourText.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1023,7 +1025,7 @@ public class PopupMenu extends JPopupMenu
         showColourText_actionPerformed();
       }
     });
-    displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
+    displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
     displayNonconserved.setState(true);
     displayNonconserved.addActionListener(new ActionListener()
     {
@@ -1032,8 +1034,8 @@ public class PopupMenu extends JPopupMenu
         showNonconserved_actionPerformed();
       }
     });
-    editMenu.setText(MessageManager.getString("action.edit"));\r
-    cut.setText(MessageManager.getString("action.cut"));\r
+    editMenu.setText(MessageManager.getString("action.edit"));
+    cut.setText(MessageManager.getString("action.cut"));
     cut.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1041,7 +1043,7 @@ public class PopupMenu extends JPopupMenu
         cut_actionPerformed();
       }
     });
-    upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
+    upperCase.setText(MessageManager.getString("label.to_upper_case"));
     upperCase.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1049,7 +1051,7 @@ public class PopupMenu extends JPopupMenu
         changeCase(e);
       }
     });
-    copy.setText(MessageManager.getString("action.copy"));\r
+    copy.setText(MessageManager.getString("action.copy"));
     copy.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1057,7 +1059,7 @@ public class PopupMenu extends JPopupMenu
         copy_actionPerformed();
       }
     });
-    lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
+    lowerCase.setText(MessageManager.getString("label.to_lower_case"));
     lowerCase.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1065,7 +1067,7 @@ public class PopupMenu extends JPopupMenu
         changeCase(e);
       }
     });
-    toggle.setText(MessageManager.getString("label.toggle_case"));\r
+    toggle.setText(MessageManager.getString("label.toggle_case"));
     toggle.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1073,8 +1075,8 @@ public class PopupMenu extends JPopupMenu
         changeCase(e);
       }
     });
-    pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
-    pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
+    pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
+    pdbFromFile.setText(MessageManager.getString("label.from_file"));
     pdbFromFile.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1108,7 +1110,7 @@ public class PopupMenu extends JPopupMenu
 //             }
 //      }   
 //    });
-    enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
+    enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
     enterPDB.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1116,7 +1118,7 @@ public class PopupMenu extends JPopupMenu
         enterPDB_actionPerformed();
       }
     });
-    discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
+    discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
     discoverPDB.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1124,8 +1126,8 @@ public class PopupMenu extends JPopupMenu
         discoverPDB_actionPerformed();
       }
     });
-    outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
-    sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
+    outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
+    sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
     sequenceFeature.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1133,7 +1135,7 @@ public class PopupMenu extends JPopupMenu
         sequenceFeature_actionPerformed();
       }
     });
-    textColour.setText(MessageManager.getString("label.text_colour"));\r
+    textColour.setText(MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1141,11 +1143,11 @@ public class PopupMenu extends JPopupMenu
         textColour_actionPerformed();
       }
     });
-    jMenu1.setText(MessageManager.getString("label.group"));\r
-    structureMenu.setText(MessageManager.getString("label.structure"));\r
-    viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
+    jMenu1.setText(MessageManager.getString("label.group"));
+    structureMenu.setText(MessageManager.getString("label.structure"));
+    viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
     // colStructureMenu.setText("Colour By Structure");
-    editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
+    editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
     editSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -1238,7 +1240,7 @@ public class PopupMenu extends JPopupMenu
     structureMenu.add(pdbMenu);
     structureMenu.add(viewStructureMenu);
     // structureMenu.add(colStructureMenu);
-    noColourmenuItem.setText(MessageManager.getString("label.none"));\r
+    noColourmenuItem.setText(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1247,7 +1249,7 @@ public class PopupMenu extends JPopupMenu
       }
     });
 
-    clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
+    clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1255,7 +1257,7 @@ public class PopupMenu extends JPopupMenu
         clustalColour_actionPerformed();
       }
     });
-    zappoColour.setText(MessageManager.getString("label.zappo"));\r
+    zappoColour.setText(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1263,7 +1265,7 @@ public class PopupMenu extends JPopupMenu
         zappoColour_actionPerformed();
       }
     });
-    taylorColour.setText(MessageManager.getString("label.taylor"));\r
+    taylorColour.setText(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1271,7 +1273,7 @@ public class PopupMenu extends JPopupMenu
         taylorColour_actionPerformed();
       }
     });
-    hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
+    hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
     hydrophobicityColour
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1280,7 +1282,7 @@ public class PopupMenu extends JPopupMenu
                 hydrophobicityColour_actionPerformed();
               }
             });
-    helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
+    helixColour.setText(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1288,7 +1290,7 @@ public class PopupMenu extends JPopupMenu
         helixColour_actionPerformed();
       }
     });
-    strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
+    strandColour.setText(MessageManager.getString("label.strand_propensity"));
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1296,7 +1298,7 @@ public class PopupMenu extends JPopupMenu
         strandColour_actionPerformed();
       }
     });
-    turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
+    turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1304,7 +1306,7 @@ public class PopupMenu extends JPopupMenu
         turnColour_actionPerformed();
       }
     });
-    buriedColour.setText(MessageManager.getString("label.buried_index"));\r
+    buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1312,7 +1314,7 @@ public class PopupMenu extends JPopupMenu
         buriedColour_actionPerformed();
       }
     });
-    abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
+    abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
     abovePIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1320,7 +1322,7 @@ public class PopupMenu extends JPopupMenu
         abovePIDColour_actionPerformed();
       }
     });
-    userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
+    userDefinedColour.setText(MessageManager.getString("action.user_defined"));
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1328,7 +1330,7 @@ public class PopupMenu extends JPopupMenu
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
+    PIDColour.setText(MessageManager.getString("label.percentage_identity"));
     PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1336,7 +1338,7 @@ public class PopupMenu extends JPopupMenu
         PIDColour_actionPerformed();
       }
     });
-    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
+    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1344,7 +1346,7 @@ public class PopupMenu extends JPopupMenu
         BLOSUM62Colour_actionPerformed();
       }
     });
-    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
+    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
     purinePyrimidineColour
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1361,7 +1363,7 @@ public class PopupMenu extends JPopupMenu
      * covariationColour_actionPerformed(); } });
      */
 
-    conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
+    conservationMenuItem.setText(MessageManager.getString("label.conservation"));
     conservationMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
@@ -1389,7 +1391,7 @@ public class PopupMenu extends JPopupMenu
     StringBuffer contents = new StringBuffer();
     for (SequenceI seq : sequences)
     {
-      contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
+      contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
               + "</h2></p><p>");
       new SequenceAnnotationReport(null)
               .createSequenceAnnotationReport(
@@ -1404,8 +1406,8 @@ public class PopupMenu extends JPopupMenu
     }
     cap.setText("<html>" + contents.toString() + "</html>");
 
-    Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
-               ,500, 400);\r
+    Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
+               ,500, 400);
 
   }
 
@@ -1592,7 +1594,7 @@ public class PopupMenu extends JPopupMenu
   {
     SequenceGroup sg = getGroup();
 
-    if (e.getSource().equals(userDefinedColour))\r
+    if (e.getSource().equals(userDefinedColour))
     {
       new UserDefinedColours(ap, sg);
     }
@@ -1721,8 +1723,8 @@ public class PopupMenu extends JPopupMenu
 
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(),
-            sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",\r
-            MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
+            sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",
+            MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
             ap.alignFrame);
 
     if (!dialog.accept)
@@ -1761,8 +1763,8 @@ public class PopupMenu extends JPopupMenu
   void sequenceName_actionPerformed()
   {
     EditNameDialog dialog = new EditNameDialog(sequence.getName(),
-            sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",\r
-            MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
+            sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",
+            MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
             ap.alignFrame);
 
     if (!dialog.accept)
@@ -1775,8 +1777,8 @@ public class PopupMenu extends JPopupMenu
       if (dialog.getName().indexOf(" ") > -1)
       {
         JOptionPane.showMessageDialog(ap,
-                MessageManager.getString("label.spaces_converted_to_backslashes"),\r
-                MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
+                MessageManager.getString("label.spaces_converted_to_backslashes"),
+                MessageManager.getString("label.no_spaces_allowed_sequence_name"),
                 JOptionPane.WARNING_MESSAGE);
       }
 
@@ -1819,7 +1821,7 @@ public class PopupMenu extends JPopupMenu
   protected void outline_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
+    Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
             Color.BLUE);
 
     if (col != null)
@@ -1876,8 +1878,8 @@ public class PopupMenu extends JPopupMenu
       JOptionPane
               .showInternalMessageDialog(
                       Desktop.desktop,
-                      MessageManager.getString("label.web_browser_not_found_unix"),\r
-                      MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
+                      MessageManager.getString("label.web_browser_not_found_unix"),
+                      MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -1943,17 +1945,17 @@ public class PopupMenu extends JPopupMenu
 
       if (source == toggle)
       {
-        description = MessageManager.getString("label.toggle_case");\r
+        description = MessageManager.getString("label.toggle_case");
         caseChange = ChangeCaseCommand.TOGGLE_CASE;
       }
       else if (source == upperCase)
       {
-        description = MessageManager.getString("label.to_upper_case");\r
+        description = MessageManager.getString("label.to_upper_case");
         caseChange = ChangeCaseCommand.TO_UPPER;
       }
       else
       {
-        description = MessageManager.getString("label.to_lower_case");\r
+        description = MessageManager.getString("label.to_lower_case");
         caseChange = ChangeCaseCommand.TO_LOWER;
       }
 
@@ -1974,7 +1976,7 @@ public class PopupMenu extends JPopupMenu
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
     Desktop.addInternalFrame(cap,
-            MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
+            MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
 
     String[] omitHidden = null;
 
@@ -2005,8 +2007,8 @@ public class PopupMenu extends JPopupMenu
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
-    chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
+    chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
+    chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
 
     int value = chooser.showOpenDialog(null);
 
@@ -2034,7 +2036,7 @@ public class PopupMenu extends JPopupMenu
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
-            MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
+            MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
 
     if (id != null && id.length() > 0)
     {
@@ -2140,12 +2142,12 @@ public class PopupMenu extends JPopupMenu
 
       EditNameDialog dialog = new EditNameDialog(
               sequence.getSequenceAsString(sg.getStartRes(),
-                      sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
-                      MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
+                      sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
+                      MessageManager.getString("label.edit_sequence"), ap.alignFrame);
 
       if (dialog.accept)
       {
-        EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
+        EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
                 EditCommand.REPLACE, dialog.getName().replace(' ',
                         ap.av.getGapCharacter()),
                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),