Merge branch 'develop' into features/JAL-2316

Conflicts (resolved):
	resources/lang/Messages.properties
	resources/lang/Messages_es.properties
	src/jalview/gui/Preferences.java

diff --cc help/html/webServices/urllinks.html
Simple merge

diff --cc resources/lang/Messages.properties
index bee4809,6360dc7..7833903
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1272,18 -1274,4 +1274,19 @@@ label.SEQUENCE_ID_no_longer_used = $SEQ
  label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window:
  label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'.
  label.do_not_display_again = Do not display this message again
 -label.output_seq_details = Output Sequence Details to list all database references
 +exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
 +exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line
 +label.filter = Filter text:
 +action.customfilter = Custom only
 +action.showall = Show All
 +label.insert = Insert:
 +action.seq_id = $SEQUENCE_ID$
 +action.db_acc = $DB_ACCESSION$
 +label.default = On Click
 +label.inmenu = In Menu
 +label.id = ID
 +label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
 +label.edit_sequence_url_link = Edit sequence URL link
 +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids
- label.invalid_name = Invalid Name !
++label.invalid_name = Invalid Name !
++label.output_seq_details = Output Sequence Details to list all database references

diff --cc resources/lang/Messages_es.properties
index 99aeed5,e5b5e27..88fb0a4
--- 1/resources/lang/Messages_es.properties
--- 2/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@@ -1273,18 -1275,4 +1275,19 @@@ label.SEQUENCE_ID_no_longer_used = $SEQ
  label.SEQUENCE_ID_for_DB_ACCESSION1 = Por favor, revise sus URLs en la pestaña 'Conexiones' de la ventana de Preferencias:
  label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'.
  label.do_not_display_again = No mostrar este mensaje de nuevo
 -label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
 +exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name
 +exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link
 +label.filter = Filter text:
 +action.customfilter = Custom only
 +action.showall = Show All
 +label.insert = Insert:
 +action.seq_id = $SEQUENCE_ID$
 +action.db_acc = $DB_ACCESSION$
 +label.default = On Click
 +label.inmenu = In Menu
 +label.id = ID
 +label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option
 +label.edit_sequence_url_link = Edit sequence URL link
 +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids
- label.invalid_name = Invalid Name !
++label.invalid_name = Invalid Name !
++label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas

diff --cc src/jalview/gui/DasSourceBrowser.java
Simple merge

diff --cc src/jalview/gui/Desktop.java
Simple merge

diff --cc src/jalview/gui/IdPanel.java
Simple merge

diff --cc src/jalview/gui/Preferences.java
index b46ae10,0b65c1b..00b2a38
--- 1/src/jalview/gui/Preferences.java
--- 2/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@@ -54,20 -56,7 +55,19 @@@ import javax.help.HelpSetException
  import javax.swing.JColorChooser;
  import javax.swing.JFileChooser;
  import javax.swing.JInternalFrame;
- import javax.swing.JOptionPane;
  import javax.swing.JPanel;
 +import javax.swing.ListSelectionModel;
 +import javax.swing.RowFilter;
 +import javax.swing.RowSorter;
 +import javax.swing.SortOrder;
 +import javax.swing.event.DocumentEvent;
 +import javax.swing.event.DocumentListener;
 +import javax.swing.event.ListSelectionEvent;
 +import javax.swing.event.ListSelectionListener;
 +import javax.swing.table.TableCellRenderer;
 +import javax.swing.table.TableColumn;
 +import javax.swing.table.TableModel;
 +import javax.swing.table.TableRowSorter;
  
  import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  
@@@ -907,9 -795,10 +908,9 @@@ public class Preferences extends GPrefe
      boolean valid = false;
      while (!valid)
      {
-       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 -
+       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 -              MessageManager.getString("label.new_sequence_url_link"),
 +              MessageManager.getString("label.edit_sequence_url_link"),
-               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+               JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
        {
          if (link.checkValid())
          {

diff --cc src/jalview/gui/WsPreferences.java
Simple merge

diff --cc src/jalview/jbgui/GSequenceLink.java
index 93b7935,dbce5f3..ab3ea2c
--- 1/src/jalview/jbgui/GSequenceLink.java
--- 2/src/jalview/jbgui/GSequenceLink.java
+++ b/src/jalview/jbgui/GSequenceLink.java
@@@ -35,9 -35,7 +36,8 @@@ import java.awt.event.KeyAdapter
  import java.awt.event.KeyEvent;
  
  import javax.swing.BorderFactory;
 +import javax.swing.JButton;
  import javax.swing.JLabel;
- import javax.swing.JOptionPane;
  import javax.swing.JPanel;
  import javax.swing.JTextField;
  import javax.swing.SwingConstants;
@@@ -225,13 -163,25 +225,13 @@@ public class GSequenceLink extends JPan
      return false;
    }
  
 -  JTextField nameTB = new JTextField();
 -
 -  JTextField urlTB = new JTextField();
 -
 -  JLabel jLabel1 = new JLabel();
 -
 -  JLabel jLabel2 = new JLabel();
 -
 -  JLabel jLabel3 = new JLabel();
 -
 -  JLabel jLabel4 = new JLabel();
 -
 -  JLabel jLabel5 = new JLabel();
 -
 -  JLabel jLabel6 = new JLabel();
 -
 -  JPanel jPanel1 = new JPanel();
 -
 -  GridBagLayout gridBagLayout1 = new GridBagLayout();
 +  public void notifyDuplicate()
 +  {
-     JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
++    JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
 +            MessageManager.getString("warn.name_cannot_be_duplicate"),
 +            MessageManager.getString("label.invalid_name"),
-             JOptionPane.WARNING_MESSAGE);
++            JvOptionPane.WARNING_MESSAGE);
 +  }
  
    public void nameTB_keyTyped(KeyEvent e)
    {