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;
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- omitHidden = viewport.getViewAsString(false);
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
}
int[] alignmentStartEnd = new int[2];
alignmentToExport = viewport.getAlignment();
alignmentStartEnd = viewport.getAlignment()
.getVisibleStartAndEndIndex(
- viewport
- .getColumnSelection().getHiddenColumns());
+ viewport.getColumnSelection().getHiddenColumns());
}
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
-
/**
* DOCUMENT ME!
*
{
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);
}
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;
return showp;
}
+ /**
+ * Finds and displays cross-references for the selected sequences (protein
+ * products for nucleotide sequences, dna coding sequences for peptides).
+ *
+ * @param sel
+ * the sequences to show cross-references for
+ * @param dna
+ * true if from a nucleotide alignment (so showing proteins)
+ * @param source
+ * the database to show cross-references for
+ */
protected void showProductsFor(final SequenceI[] sel, final boolean dna,
final String source)
{
{
AlignmentI alignment = AlignFrame.this.getViewport()
.getAlignment();
- AlignmentI xrefs = CrossRef.findXrefSequences(sel, dna, source,
+ AlignmentI xrefs = CrossRefs.findXrefSequences(sel, dna, source,
alignment);
if (xrefs != null)
{
System.err.println("Failed to make CDS alignment");
}
al.getCodonFrames().clear();
- al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
/*
* pending getting Embl transcripts to 'align',
{
copyAlignment = AlignmentUtils.makeCopyAlignment(
sequenceSelection, xrefs.getSequencesArray());
- copyAlignment.getCodonFrames().addAll(cf);
+ copyAlignment.addCodonFrames(cf);
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
}
copyAlignment.setGapCharacter(AlignFrame.this.viewport
.getGapCharacter());
}
} catch (Exception e)
{
- Cache.log.error(
- "Exception when finding crossreferences", e);
+ Cache.log.error("Exception when finding crossreferences", e);
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences",
- e);
+ Cache.log.error("Error when finding crossreferences", e);
} finally
{
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
.getString("label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
- + MessageManager.getString("translation_failed");
+ + MessageManager.getString("label.translation_failed");
JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
AlignFrame.this.setMenusForViewport();
}
});
- dbRefFetcher
- .fetchDBRefs(false);
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
-
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+ viewport.getAlignment()));
} catch (Exception ex)
{
System.err.println(ex.getMessage());