Merge branch 'features/JAL-1723_sequenceReport' into develop

 Conflicts:
	resources/lang/Messages.properties
	resources/lang/Messages_es.properties
	src/jalview/io/SequenceAnnotationReport.java
reconciled refactored report/ellipsis code with refactored URLLink code for generating dynamic links with ACCESSION_ID tokens

diff --cc resources/lang/Messages.properties
index 49a0456,1c52b63..01ba0ff
--- 1/resources/lang/Messages.properties
--- 2/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@@ -1268,7 -1268,4 +1268,8 @@@ status.exporting_alignment_as_x_file = 
  label.column = Column
  label.cant_map_cds = Unable to map CDS to protein\nCDS missing or incomplete
  label.operation_failed = Operation failed
 +label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB accessions
 +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

diff --cc resources/lang/Messages_es.properties
index 96c8ef2,8009ae9..9c2436c
--- 1/resources/lang/Messages_es.properties
--- 2/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@@ -1269,7 -1269,4 +1269,8 @@@ status.exporting_alignment_as_x_file = 
  label.column = Columna
  label.cant_map_cds = No se pudo mapear CDS a proteína\nDatos CDS faltantes o incompletos
  label.operation_failed = Operación fallada
 +label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ no se utiliza más para accesiones DB
 +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.do_not_display_again = No mostrar este mensaje de nuevo
+ label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas

diff --cc src/jalview/appletgui/APopupMenu.java
Simple merge

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

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

diff --cc src/jalview/io/SequenceAnnotationReport.java
index 89f1068,59daa87..850b1dc
--- 1/src/jalview/io/SequenceAnnotationReport.java
--- 2/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@@ -24,11 -25,13 +25,13 @@@ import jalview.datamodel.DBRefSource
  import jalview.datamodel.SequenceFeature;
  import jalview.datamodel.SequenceI;
  import jalview.io.gff.GffConstants;
 -import jalview.util.DBRefUtils;
+ import jalview.util.MessageManager;
  import jalview.util.UrlLink;
  
--import java.util.ArrayList;
+ import java.util.Arrays;
 +import java.util.Collection;
+ import java.util.Comparator;
 +import java.util.LinkedHashMap;
  import java.util.List;
  import java.util.Map;
  
@@@ -248,13 -307,115 +307,13 @@@ public class SequenceAnnotationRepor
        System.err.println(urlLink.getInvalidMessage());
        return null;
      }
 -    final String target = urlLink.getTarget(); // link.substring(0,
 -    // link.indexOf("|"));
 -    final String label = urlLink.getLabel();
 -    if (seq != null && urlLink.isDynamic())
 -    {
 -      urlSets.addAll(createDynamicLinks(seq, urlLink, uniques));
 -    }
 -    else
 -    {
 -      String unq = label + "|" + urlLink.getUrl_prefix();
 -      if (!uniques.contains(unq))
 -      {
 -        uniques.add(unq);
 -        urlSets.add(new String[] { target, label, null,
 -            urlLink.getUrl_prefix() });
 -      }
 -    }
 -
 -    return urlSets.toArray(new String[][] {});
 -  }
  
 -  /**
 -   * Formats and returns a list of dynamic href links
 -   * 
 -   * @param seq
 -   * @param urlLink
 -   * @param uniques
 -   */
 -  List<String[]> createDynamicLinks(SequenceI seq, UrlLink urlLink,
 -          List<String> uniques)
 -  {
 -    List<String[]> result = new ArrayList<String[]>();
 -    final String target = urlLink.getTarget();
 -    final String label = urlLink.getLabel();
 +    urlLink.createLinksFromSeq(seq, urlSets);
  
 -    // collect matching db-refs
 -    DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
 -            new String[] { target });
 -    // collect id string too
 -    String id = seq.getName();
 -    String descr = seq.getDescription();
 -    if (descr != null && descr.length() < 1)
 -    {
 -      descr = null;
 -    }
 -    if (dbr != null)
 -    {
 -      for (int r = 0; r < dbr.length; r++)
 -      {
 -        if (id != null && dbr[r].getAccessionId().equals(id))
 -        {
 -          // suppress duplicate link creation for the bare sequence ID
 -          // string with this link
 -          id = null;
 -        }
 -        // create Bare ID link for this URL
 -        String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
 -        if (urls != null)
 -        {
 -          for (int u = 0; u < urls.length; u += 2)
 -          {
 -            String unq = urls[u] + "|" + urls[u + 1];
 -            if (!uniques.contains(unq))
 -            {
 -              result.add(new String[] { target, label, urls[u], urls[u + 1] });
 -              uniques.add(unq);
 -            }
 -          }
 -        }
 -      }
 -    }
 -    if (id != null)
 -    {
 -      // create Bare ID link for this URL
 -      String[] urls = urlLink.makeUrls(id, true);
 -      if (urls != null)
 -      {
 -        for (int u = 0; u < urls.length; u += 2)
 -        {
 -          String unq = urls[u] + "|" + urls[u + 1];
 -          if (!uniques.contains(unq))
 -          {
 -            result.add(new String[] { target, label, urls[u], urls[u + 1] });
 -            uniques.add(unq);
 -          }
 -        }
 -      }
 -    }
 -    if (descr != null && urlLink.getRegexReplace() != null)
 -    {
 -      // create link for this URL from description only if regex matches
 -      String[] urls = urlLink.makeUrls(descr, true);
 -      if (urls != null)
 -      {
 -        for (int u = 0; u < urls.length; u += 2)
 -        {
 -          String unq = urls[u] + "|" + urls[u + 1];
 -          if (!uniques.contains(unq))
 -          {
 -            result.add(new String[] { target, label, urls[u], urls[u + 1] });
 -            uniques.add(unq);
 -          }
 -        }
 -      }
 -    }
 -    return result;
 +    return urlSets.values();
    }
  
-   public void createSequenceAnnotationReport(final StringBuffer tip,
+   public void createSequenceAnnotationReport(final StringBuilder tip,
            SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
            Map<String, float[][]> minmax)
    {