Merge branch 'develop' into features/JAL-2110_makeSenseOfCrossRef

diff --combined src/jalview/gui/AlignFrame.java
index 477d113,7ab8311..39e4bcd
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -23,7 -23,6 +23,7 @@@ package jalview.gui
  import jalview.analysis.AlignmentSorter;
  import jalview.analysis.AlignmentUtils;
  import jalview.analysis.CrossRef;
 +import jalview.analysis.CrossRefs;
  import jalview.analysis.Dna;
  import jalview.analysis.ParseProperties;
  import jalview.analysis.SequenceIdMatcher;
@@@ -1326,10 -1325,10 +1326,10 @@@ public class AlignFrame extends GAlignF
      else
      {
        alignmentToExport = viewport.getAlignment();
-       alignmentStartEnd = viewport.getAlignment()
-               .getVisibleStartAndEndIndex(
-                       viewport.getColumnSelection().getHiddenColumns());
      }
+     alignmentStartEnd = alignmentToExport
+             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+                     .getHiddenColumns());
      AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
              omitHidden, alignmentStartEnd, settings);
      return ed;
@@@ -4648,21 -4647,24 +4648,21 @@@
      {
        showProducts.removeAll();
        final boolean dna = viewport.getAlignment().isNucleotide();
 -      String[] ptypes = (selection == null || selection.length == 0) ? null
 -              : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
 +      List<String> ptypes = (selection == null || selection.length == 0) ? null
 +              : CrossRef.findXrefSourcesForSequences(dna, selection, dataset);
  
 -      for (int t = 0; ptypes != null && t < ptypes.length; t++)
 +      for (final String source : ptypes)
        {
          showp = true;
          final AlignFrame af = this;
 -        final String source = ptypes[t];
 -        JMenuItem xtype = new JMenuItem(ptypes[t]);
 +        JMenuItem xtype = new JMenuItem(source);
          xtype.addActionListener(new ActionListener()
          {
 -
            @Override
            public void actionPerformed(ActionEvent e)
            {
              showProductsFor(af.viewport.getSequenceSelection(), dna, source);
            }
 -
          });
          showProducts.add(xtype);
        }
@@@ -4670,7 -4672,7 +4670,7 @@@
        showProducts.setEnabled(showp);
      } catch (Exception e)
      {
 -      jalview.bin.Cache.log
 +      Cache.log
                .warn("canShowProducts threw an exception - please report to help@jalview.org",
                        e);
        return false;
@@@ -4706,7 -4708,7 +4706,7 @@@
          {
            AlignmentI alignment = AlignFrame.this.getViewport()
                    .getAlignment();
 -          AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
 +          AlignmentI xrefs = CrossRefs.findXrefSequences(sel, dna, source,
                    alignment);
            if (xrefs != null)
            {