--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.SequenceFetcher;
+
+import java.util.ArrayList;
+import java.util.List;
+
++import javax.swing.JOptionPane;
++
+/**
+ * Factory constructor and runnable for discovering and displaying
+ * cross-references for a set of aligned sequences
+ *
+ * @author jprocter
+ *
+ */
+public class CrossRefAction implements Runnable
+{
+ private AlignFrame alignFrame;
+
+ private SequenceI[] sel;
+
+ private boolean _odna;
+
+ private String source;
+
+ List<AlignmentViewPanel> xrefViews = new ArrayList<AlignmentViewPanel>();
+
+ public List<jalview.api.AlignmentViewPanel> getXrefViews()
+ {
+ return xrefViews;
+ }
+
+ @Override
+ public void run()
+ {
+ final long sttime = System.currentTimeMillis();
+ alignFrame.setProgressBar(
+ MessageManager.formatMessage(
+ "status.searching_for_sequences_from",
+ new Object[] { source }), sttime);
+ try
+ {
+ AlignmentI alignment = alignFrame.getViewport().getAlignment();
+ AlignmentI dataset = alignment.getDataset() == null ? alignment
+ : alignment.getDataset();
+ boolean dna = alignment.isNucleotide();
+ if (_odna != dna)
+ {
+ System.err
+ .println("Conflict: showProducts for alignment originally "
+ + "thought to be " + (_odna ? "DNA" : "Protein")
+ + " now searching for " + (dna ? "DNA" : "Protein")
+ + " Context.");
+ }
+ AlignmentI xrefs = new CrossRef(sel, dataset).findXrefSequences(
+ source, dna);
+ if (xrefs == null)
+ {
+ return;
+ }
+ /*
+ * get display scheme (if any) to apply to features
+ */
+ FeatureSettingsModelI featureColourScheme = new SequenceFetcher()
+ .getFeatureColourScheme(source);
+
+ AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
+ xrefs);
+ if (!dna)
+ {
+ xrefsAlignment = AlignmentUtils.makeCdsAlignment(
+ xrefsAlignment.getSequencesArray(), dataset, sel);
+ xrefsAlignment.alignAs(alignment);
+ }
+
+ /*
+ * If we are opening a splitframe, make a copy of this alignment (sharing the same dataset
+ * sequences). If we are DNA, drop introns and update mappings
+ */
+ AlignmentI copyAlignment = null;
+
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+ {
+ boolean copyAlignmentIsAligned = false;
+ if (dna)
+ {
+ copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
+ xrefsAlignment.getSequencesArray());
+ if (copyAlignment.getHeight() == 0)
+ {
++ JOptionPane.showMessageDialog(alignFrame,
++ MessageManager.getString("label.cant_map_cds"),
++ MessageManager.getString("label.operation_failed"),
++ JOptionPane.OK_OPTION);
+ System.err.println("Failed to make CDS alignment");
+ }
+
+ /*
+ * pending getting Embl transcripts to 'align',
+ * we are only doing this for Ensembl
+ */
+ // TODO proper criteria for 'can align as cdna'
+ if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+ || AlignmentUtils.looksLikeEnsembl(alignment))
+ {
+ copyAlignment.alignAs(alignment);
+ copyAlignmentIsAligned = true;
+ }
+ }
+ else
+ {
+ copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
+ xrefs.getSequencesArray(), dataset);
+ }
+ copyAlignment
+ .setGapCharacter(alignFrame.viewport.getGapCharacter());
+
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+
+ /*
+ * register any new mappings for sequence mouseover etc
+ * (will not duplicate any previously registered mappings)
+ */
+ ssm.registerMappings(dataset.getCodonFrames());
+
+ if (copyAlignment.getHeight() <= 0)
+ {
+ System.err.println("No Sequences generated for xRef type "
+ + source);
+ return;
+ }
+ /*
+ * align protein to dna
+ */
+ if (dna && copyAlignmentIsAligned)
+ {
+ xrefsAlignment.alignAs(copyAlignment);
+ }
+ else
+ {
+ /*
+ * align cdna to protein - currently only if
+ * fetching and aligning Ensembl transcripts!
+ */
+ // TODO: generalise for other sources of locus/transcript/cds data
+ if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+ {
+ copyAlignment.alignAs(xrefsAlignment);
+ }
+ }
+ }
+ /*
+ * build AlignFrame(s) according to available alignment data
+ */
+ AlignFrame newFrame = new AlignFrame(xrefsAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ newFrame.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ }
+ String newtitle = String.format("%s %s %s", MessageManager
+ .getString(dna ? "label.proteins" : "label.nucleotides"),
+ MessageManager.getString("label.for"), alignFrame.getTitle());
+ newFrame.setTitle(newtitle);
+
+ if (copyAlignment == null)
+ {
+ /*
+ * split frame display is turned off in preferences file
+ */
+ Desktop.addInternalFrame(newFrame, newtitle,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ xrefViews.add(newFrame.alignPanel);
+ return; // via finally clause
+ }
+ AlignFrame copyThis = new AlignFrame(copyAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyThis.setTitle(alignFrame.getTitle());
+
+ boolean showSequenceFeatures = alignFrame.getViewport()
+ .isShowSequenceFeatures();
+ newFrame.setShowSeqFeatures(showSequenceFeatures);
+ copyThis.setShowSeqFeatures(showSequenceFeatures);
+ FeatureRenderer myFeatureStyling = alignFrame.alignPanel
+ .getSeqPanel().seqCanvas.getFeatureRenderer();
+
+ /*
+ * copy feature rendering settings to split frame
+ */
+ newFrame.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(myFeatureStyling);
+ copyThis.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(myFeatureStyling);
+
+ /*
+ * apply 'database source' feature configuration
+ * if any was found
+ */
+ // TODO is this the feature colouring for the original
+ // alignment or the fetched xrefs? either could be Ensembl
+ newFrame.getViewport().applyFeaturesStyle(featureColourScheme);
+ copyThis.getViewport().applyFeaturesStyle(featureColourScheme);
+
+ SplitFrame sf = new SplitFrame(dna ? copyThis : newFrame,
+ dna ? newFrame : copyThis);
+ newFrame.setVisible(true);
+ copyThis.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+ Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+ sf.adjustDivider();
+
+ // finally add the top, then bottom frame to the view list
+ xrefViews.add(dna ? copyThis.alignPanel : newFrame.alignPanel);
+ xrefViews.add(!dna ? copyThis.alignPanel : newFrame.alignPanel);
+
+ } catch (OutOfMemoryError e)
+ {
+ new OOMWarning("whilst fetching crossreferences", e);
+ } catch (Throwable e)
+ {
+ Cache.log.error("Error when finding crossreferences", e);
+ } finally
+ {
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.finished_searching_for_sequences_from",
+ new Object[] { source }), sttime);
+ }
+ }
+
+ /**
+ * Makes an alignment containing the given sequences, and adds them to the
+ * given dataset, which is also set as the dataset for the new alignment
+ *
+ * TODO: refactor to DatasetI method
+ *
+ * @param dataset
+ * @param seqs
+ * @return
+ */
+ protected AlignmentI makeCrossReferencesAlignment(AlignmentI dataset,
+ AlignmentI seqs)
+ {
+ SequenceI[] sprods = new SequenceI[seqs.getHeight()];
+ for (int s = 0; s < sprods.length; s++)
+ {
+ sprods[s] = (seqs.getSequenceAt(s)).deriveSequence();
+ if (dataset.getSequences() == null
+ || !dataset.getSequences().contains(
+ sprods[s].getDatasetSequence()))
+ {
+ dataset.addSequence(sprods[s].getDatasetSequence());
+ }
+ sprods[s].updatePDBIds();
+ }
+ Alignment al = new Alignment(sprods);
+ al.setDataset(dataset);
+ return al;
+ }
+
+ public CrossRefAction(AlignFrame alignFrame, SequenceI[] sel,
+ boolean _odna, String source)
+ {
+ this.alignFrame = alignFrame;
+ this.sel = sel;
+ this._odna = _odna;
+ this.source = source;
+ }
+
+ public static CrossRefAction showProductsFor(final SequenceI[] sel,
+ final boolean _odna, final String source,
+ final AlignFrame alignFrame)
+ {
+ return new CrossRefAction(alignFrame, sel, _odna, source);
+ }
+
+}
--- /dev/null
+package jalview.io;
+
+import jalview.bin.Cache;
++import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+
- import java.time.Instant;
+import java.util.Date;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+
+public class Jalview2xmlBase
+{
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/io/testProps_nodas.jvprops" });
- jalview.bin.Cache.setProperty(
- "JALVIEW_NEWS_RSS_LASTMODIFIED",
- Cache.date_format.format(Date.from(Instant.now().plusSeconds(
- 3600))));
++ /*
++ * use read-only test properties file
++ */
++ Cache.loadProperties("test/jalview/io/testProps.jvprops");
++
++ /*
++ * set news feed last read to a future time to ensure no
++ * 'unread' news item is displayed
++ */
++ Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
++ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
++
++ Jalview.main(new String[] {});
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @AfterClass(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public static void clearDesktop()
+ {
+ if (Desktop.instance != null && Desktop.getAlignFrames() != null)
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+ }
+
+ public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+ {
+ int numdsann = 0;
+ for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+ {
+ if (sq.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation dssa : sq.getAnnotation())
+ {
+ if (dssa.isValidStruc())
+ {
+ numdsann++;
+ }
+ }
+ }
+ }
+ return numdsann;
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff