import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
-import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.ScoreModelI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
import jalview.io.TCoffeeScoreFile;
-import jalview.io.gff.SequenceOntologyI;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
-import jalview.ws.SequenceFetcher;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.jabaws2.Jws2Instance;
protected void showProductsFor(final SequenceI[] sel,
final boolean _odna, final String source)
{
- Runnable foo = new Runnable()
- {
-
- @Override
- public void run()
- {
- final long sttime = System.currentTimeMillis();
- AlignFrame.this.setProgressBar(MessageManager.formatMessage(
- "status.searching_for_sequences_from",
- new Object[] { source }), sttime);
- try
- {
- AlignmentI alignment = AlignFrame.this.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)
- {
- 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.this.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,
- DEFAULT_WIDTH, 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"), getTitle());
- newFrame.setTitle(newtitle);
-
- if (copyAlignment == null)
- {
- /*
- * split frame display is turned off in preferences file
- */
- Desktop.addInternalFrame(newFrame, newtitle, DEFAULT_WIDTH,
- DEFAULT_HEIGHT);
- return; // via finally clause
- }
- AlignFrame copyThis = new AlignFrame(copyAlignment,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- copyThis.setTitle(AlignFrame.this.getTitle());
-
- boolean showSequenceFeatures = viewport.isShowSequenceFeatures();
- newFrame.setShowSeqFeatures(showSequenceFeatures);
- copyThis.setShowSeqFeatures(showSequenceFeatures);
- FeatureRenderer myFeatureStyling = 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();
- } catch (OutOfMemoryError e)
- {
- new OOMWarning("whilst fetching crossreferences", e);
- } catch (Throwable e)
- {
- Cache.log.error("Error when finding crossreferences", e);
- } finally
- {
- AlignFrame.this.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;
- }
-
- };
- Thread frunner = new Thread(foo);
- frunner.start();
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ .start();
}
/**
--- /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;
+
+/**
+ * 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)
+ {
+ 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);
+ }
+
+}
*/
package jalview.io;
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.api.AlignViewportI;
+import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
-import jalview.api.ViewStyleI;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.structure.StructureImportSettings;
-import jalview.viewmodel.AlignmentViewport;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.IdentityHashMap;
import java.util.List;
-import java.util.Map;
import org.testng.Assert;
-import org.testng.AssertJUnit;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
- @Test(groups = { "Functional" })
- public void testRNAStructureRecovery() throws Exception
- {
- String inFile = "examples/RF00031_folded.stk";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- int olddsann = countDsAnn(af.getViewport());
- assertTrue("Didn't find any dataset annotations", olddsann > 0);
- af.rnahelicesColour_actionPerformed(null);
- assertTrue(
- "Couldn't apply RNA helices colourscheme",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
- int newdsann = countDsAnn(af.getViewport());
- assertTrue(
- "Differing numbers of dataset sequence annotation\nOriginally "
- + olddsann + " and now " + newdsann,
- olddsann == newdsann);
- System.out
- .println("Read in same number of annotations as originally present ("
- + olddsann + ")");
- assertTrue(
- "RNA helices colourscheme was not applied on import.",
- af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
- }
-
- @Test(groups = { "Functional" })
- public void testTCoffeeScores() throws Exception
- {
- String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
- assertTrue(
- "Didn't set T-coffee colourscheme",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
- assertTrue(
- "Recognise T-Coffee score from string",
- jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
- .getAlignment(),
- jalview.schemes.ColourSchemeProperty.getColourName(af
- .getViewport().getGlobalColourScheme())) != null);
-
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
- assertTrue(
- "Didn't set T-coffee colourscheme for imported project.",
- af.getViewport().getGlobalColourScheme().getClass()
- .equals(jalview.schemes.TCoffeeColourScheme.class));
- System.out
- .println("T-Coffee score shading successfully recovered from project.");
- }
-
- @Test(groups = { "Functional" })
- public void testColourByAnnotScores() throws Exception
- {
- String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
- String tfile = File.createTempFile("JalviewTest", ".jvp")
- .getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, FormatAdapter.FILE);
- assertTrue("Didn't read input file " + inFile, af != null);
- af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
- AlignmentAnnotation[] aa = af.getViewport().getAlignment()
- .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
- assertTrue(
- "Didn't find any IUPred annotation to use to shade alignment.",
- aa != null && aa.length > 0);
- AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
- aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
- AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
- aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
- cs.setSeqAssociated(true);
- gcs.setSeqAssociated(true);
- af.changeColour(cs);
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(57);
- sg.setEndRes(92);
- sg.cs = gcs;
- af.getViewport().getAlignment().addGroup(sg);
- sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
- sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
- af.alignPanel.alignmentChanged();
- assertTrue("Failed to store as a project.",
- af.saveAlignment(tfile, "Jalview"));
- af.closeMenuItem_actionPerformed(true);
- af = null;
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
- FormatAdapter.FILE);
- assertTrue("Failed to import new project", af != null);
-
- // check for group and alignment colourschemes
-
- ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
- ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
- .get(0).cs;
- assertTrue("Didn't recover global colourscheme", _rcs != null);
- assertTrue("Didn't recover annotation colour global scheme",
- _rcs instanceof AnnotationColourGradient);
- AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
- assertTrue("Annotation colourscheme wasn't sequence associated",
- __rcs.isSeqAssociated());
-
- boolean diffseqcols = false, diffgseqcols = false;
- SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
- {
- if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
- .findColour(sqs[5].getCharAt(p), p, sqs[5]))
- {
- diffseqcols = true;
- }
- }
- assertTrue("Got Different sequence colours", diffseqcols);
- System.out
- .println("Per sequence colourscheme (Background) successfully applied and recovered.");
-
- assertTrue("Didn't recover group colourscheme", _rgcs != null);
- assertTrue("Didn't recover annotation colour group colourscheme",
- _rgcs instanceof AnnotationColourGradient);
- __rcs = (AnnotationColourGradient) _rgcs;
- assertTrue("Group Annotation colourscheme wasn't sequence associated",
- __rcs.isSeqAssociated());
-
- for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
- {
- if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
- .findColour(sqs[2].getCharAt(p), p, sqs[2]))
- {
- diffgseqcols = true;
- }
- }
- assertTrue("Got Different group sequence colours", diffgseqcols);
- System.out
- .println("Per sequence (Group) colourscheme successfully applied and recovered.");
- }
-
- @Test(groups = { "Functional" })
- public void gatherViewsHere() throws Exception
- {
- int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
- .getAlignFrames().length;
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- assertTrue("Didn't gather the views in the example file.",
- Desktop.getAlignFrames().length == 1 + origCount);
-
- }
-
- @Test(groups = { "Functional" })
- public void viewRefPdbAnnotation() throws Exception
- {
- // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER
- // StructureImportSettings
- // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
- StructureImportSettings.setProcessSecondaryStructure(true);
- StructureImportSettings.setVisibleChainAnnotation(true);
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- AlignmentViewPanel sps = null;
- for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
- {
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- break;
- }
- }
- assertTrue("Couldn't find the structure view", sps != null);
- SequenceI sq = sps.getAlignment().findName("1A70|");
- AlignmentAnnotation refan = null;
- for (AlignmentAnnotation ra : sps.getAlignment()
- .getAlignmentAnnotation())
- {
- if (ra.graph != 0)
- {
- refan = ra;
- break;
- }
- }
- assertTrue("Annotation secondary structure not found.", refan != null);
- assertTrue("Couldn't find 1a70 null chain", sq != null);
- // compare the manually added temperature factor annotation
- // to the track automatically transferred from the pdb structure on load
- for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
- {
- AlignmentAnnotation alaa;
- sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
- alaa.adjustForAlignment();
- if (ala.graph == refan.graph)
- {
- for (int p = 0; p < ala.annotations.length; p++)
- {
- sq.findPosition(p);
- try
- {
- assertTrue(
- "Mismatch at alignment position " + p,
- (alaa.annotations[p] == null && refan.annotations[p] == null)
- || alaa.annotations[p].value == refan.annotations[p].value);
- } catch (NullPointerException q)
- {
- Assert.fail("Mismatch of alignment annotations at position "
- + p + " Ref seq ann: " + refan.annotations[p]
- + " alignment " + alaa.annotations[p]);
- }
- }
- }
- }
-
- }
-
- @Test(groups = { "Functional" })
- public void testCopyViewSettings() throws Exception
- {
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- AlignmentViewPanel sps = null, groups = null;
- for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
- {
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- }
- if (ap.getViewName().contains("MAFFT"))
- {
- groups = ap;
- }
- }
- assertTrue("Couldn't find the structure view", sps != null);
- assertTrue("Couldn't find the MAFFT view", groups != null);
-
- ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
- ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
- AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
-
- groups.getAlignViewport().setViewStyle(structureStyle);
- AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
- Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
- .getViewStyle()));
-
- }
-
/**
* test store and recovery of expanded views
*
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = true)
- public void testStoreAndRecoverExpandedviews() throws Exception
- {
- Desktop.instance.closeAll_actionPerformed(null);
-
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- Assert.assertEquals(Desktop.getAlignFrames().length, 1);
- String afid = af.getViewport().getSequenceSetId();
-
- // check FileLoader returned a reference to the one alignFrame that is
- // actually on the Desktop
- assertTrue(
- "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
- af == Desktop.getAlignFrameFor(af.getViewport()));
-
- Desktop.explodeViews(af);
-
- int oldviews = Desktop.getAlignFrames().length;
- Assert.assertEquals(Desktop.getAlignFrames().length,
- Desktop.getAlignmentPanels(afid).length);
- File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
- try
- {
- new Jalview2XML(false).saveState(tfile);
- } catch (Error e)
- {
- Assert.fail("Didn't save the expanded view state", e);
- } catch (Exception e)
- {
- Assert.fail("Didn't save the expanded view state", e);
- }
- Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
- {
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
- }
- af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- tfile.getAbsolutePath(), FormatAdapter.FILE);
- Assert.assertNotNull(af);
- Assert.assertEquals(
- Desktop.getAlignFrames().length,
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- oldviews,
- Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
- }
-
- /**
- * Test save and reload of a project with a different representative sequence
- * in each view.
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testStoreAndRecoverReferenceSeqSettings() throws Exception
- {
- Desktop.instance.closeAll_actionPerformed(null);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- String afid = af.getViewport().getSequenceSetId();
-
- // remember reference sequence for each panel
- Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
-
- /*
- * mark sequence 2, 3, 4.. in panels 1, 2, 3...
- * as reference sequence for itself and the preceding sequence
- */
- int n = 1;
- for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
- {
- AlignViewportI av = ap.getAlignViewport();
- AlignmentI alignment = ap.getAlignment();
- int repIndex = n % alignment.getHeight();
- SequenceI rep = alignment.getSequenceAt(repIndex);
- refseqs.put(ap.getViewName(), rep);
-
- // code from mark/unmark sequence as reference in jalview.gui.PopupMenu
- // todo refactor this to an alignment view controller
- av.setDisplayReferenceSeq(true);
- av.setColourByReferenceSeq(true);
- av.getAlignment().setSeqrep(rep);
-
- n++;
- }
- File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq",
- ".jvp");
- try
- {
- new Jalview2XML(false).saveState(tfile);
- } catch (Throwable e)
- {
- Assert.fail("Didn't save the expanded view state", e);
- }
- Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
- {
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
- }
-
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- FormatAdapter.FILE);
- afid = af.getViewport().getSequenceSetId();
-
- for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
- {
- // check representative
- AlignmentI alignment = ap.getAlignment();
- SequenceI rep = alignment.getSeqrep();
- Assert.assertNotNull(rep,
- "Couldn't restore sequence representative from project");
- // can't use a strong equals here, because by definition, the sequence IDs
- // will be different.
- // could set vamsas session save/restore flag to preserve IDs across
- // load/saves.
- Assert.assertEquals(refseqs.get(ap.getViewName()).toString(),
- rep.toString(),
- "Representative wasn't the same when recovered.");
- Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(),
- "Display reference sequence view setting not set.");
- Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(),
- "Colour By Reference Seq view setting not set.");
- }
- }
-
- @Test(groups = { "Functional" })
- public void testIsVersionStringLaterThan()
- {
- /*
- * No version / development / test / autobuild is leniently assumed to be
- * compatible
- */
- assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
- assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3"));
- assertTrue(Jalview2XML.isVersionStringLaterThan(null,
- "Development Build"));
- assertTrue(Jalview2XML.isVersionStringLaterThan(null,
- "DEVELOPMENT BUILD"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
- "Development Build"));
- assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
- assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
- assertTrue(Jalview2XML
- .isVersionStringLaterThan(null, "Automated Build"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
- "Automated Build"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
- "AUTOMATED BUILD"));
-
- /*
- * same version returns true i.e. compatible
- */
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
-
- /*
- * later version returns true
- */
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
- assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
-
- /*
- * earlier version returns false
- */
- assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
- assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
- assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
- assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
- assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
- }
-
- /**
- * Test save and reload of a project with a different sequence group (and
- * representative sequence) in each view.
- *
- * @throws Exception
- */
- @Test(groups = { "Functional" })
- public void testStoreAndRecoverGroupRepSeqs() throws Exception
+ @Test(groups = { "Operational" }, enabled = true)
+ public void testRetrieveAndShowCrossref() throws Exception
{
- Desktop.instance.closeAll_actionPerformed(null);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", FormatAdapter.FILE);
- assertTrue("Didn't read in the example file correctly.", af != null);
- String afid = af.getViewport().getSequenceSetId();
- // make a second view of the alignment
- af.newView_actionPerformed(null);
-
- /*
- * remember representative and hidden sequences marked
- * on each panel
- */
- Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
- Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
-
- /*
- * mark sequence 2, 3, 4.. in panels 1, 2, 3...
- * as reference sequence for itself and the preceding sequence
- */
- int n = 1;
- for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
- {
- AlignViewportI av = ap.getAlignViewport();
- AlignmentI alignment = ap.getAlignment();
- int repIndex = n % alignment.getHeight();
- // ensure at least one preceding sequence i.e. index >= 1
- repIndex = Math.max(repIndex, 1);
- SequenceI repSeq = alignment.getSequenceAt(repIndex);
- repSeqs.put(ap.getViewName(), repSeq);
- List<String> hiddenNames = new ArrayList<String>();
- hiddenSeqNames.put(ap.getViewName(), hiddenNames);
-
+ // for every set of db queries
+ // retrieve db query
+ // verify presence of expected xrefs
+ // show xrefs - verify expected type of frame is shown for each xref
+ // show xrefs again
+ // - verify original -> xref -> xref(original) recovers frame containing at
+ // least the first retrieved sequence
+ // store
+ // 1. whole project
+ // 2. individual frames
+ // 3. load each one back and verify
+ // . aligned sequences (.toString() )
+ // . xrefs (.toString() )
+ // . codonframes
+ //
+ //
+ for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+ {
+ AlignFrame af = jalview.gui.SequenceFetcher.fetchAndShow(did[0],
+ did[1]).get(0);
+ assertTrue("Didn't read in the example file correctly.", af != null);
+ boolean dna = af.getViewport().getAlignment().isNucleotide();
+ AlignmentI retral = af.getViewport().getAlignment();
+ AlignmentI dataset = retral.getDataset();
+ SequenceI[] seqs = retral.getSequencesArray();
+ List<String> ptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
/*
- * have rep sequence represent itself and the one before it
- * this hides the group (except for the rep seq)
+ * map between a view, and views generated after retrieving xrefs
*/
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(repSeq, false);
- SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1);
- sg.addSequence(precedingSeq, false);
- sg.setSeqrep(repSeq);
- assertTrue(sg.getSequences().contains(repSeq));
- assertTrue(sg.getSequences().contains(precedingSeq));
- av.setSelectionGroup(sg);
- assertSame(repSeq, sg.getSeqrep());
-
+ IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
/*
- * represent group with sequence adds to a map of hidden rep sequences
- * (it does not create a group on the alignment)
+ * map between a particular view and it's originating dbref path
*/
- ((AlignmentViewport) av).hideSequences(repSeq, true);
- assertSame(repSeq, sg.getSeqrep());
- assertTrue(sg.getSequences().contains(repSeq));
- assertTrue(sg.getSequences().contains(precedingSeq));
- assertTrue("alignment has groups", alignment.getGroups().isEmpty());
- Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
- .getHiddenRepSequences();
- assertNotNull(hiddenRepSeqsMap);
- assertEquals(1, hiddenRepSeqsMap.size());
- assertSame(sg, hiddenRepSeqsMap.get(repSeq));
- assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq));
- assertFalse(alignment.getHiddenSequences().isHidden(repSeq));
- hiddenNames.add(precedingSeq.getName());
-
- n++;
- }
- File tfile = File
- .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
- try
- {
- new Jalview2XML(false).saveState(tfile);
- } catch (Throwable e)
- {
- Assert.fail("Didn't save the expanded view state", e);
- }
- Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
- {
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
- }
-
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- FormatAdapter.FILE);
- afid = af.getViewport().getSequenceSetId();
+ IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();
- for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
- {
- String viewName = ap.getViewName();
- AlignViewportI av = ap.getAlignViewport();
- AlignmentI alignment = ap.getAlignment();
- List<SequenceGroup> groups = alignment.getGroups();
- assertNotNull(groups);
- assertTrue("Alignment has groups", groups.isEmpty());
- Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
- .getHiddenRepSequences();
- assertNotNull("No hidden represented sequences", hiddenRepSeqsMap);
- assertEquals(1, hiddenRepSeqsMap.size());
- assertEquals(repSeqs.get(viewName).getDisplayId(true),
- hiddenRepSeqsMap.keySet().iterator().next()
- .getDisplayId(true));
+ String first = did[0] + " " + did[1];
+ viewsourcedb.put(af.alignPanel, first);
+ for (String db : ptypes)
+ {
+ // retrieve and show cross-refs in this thread
+ CrossRefAction cra = new CrossRefAction(af, seqs, dna, db);
+ cra.run();
+ Assert.assertTrue(cra.getXrefViews().size() > 0,
+ "No crossrefs retrieved for " + db);
+ viewxrefview.put(af.alignPanel, cra.getXrefViews());
+
+ for (AlignmentViewPanel avp : cra.getXrefViews())
+ {
- /*
- * verify hidden sequences in restored panel
- */
- List<String> hidden = hiddenSeqNames.get(ap.getViewName());
- HiddenSequences hs = alignment.getHiddenSequences();
- assertEquals(
- "wrong number of restored hidden sequences in "
- + ap.getViewName(), hidden.size(), hs.getSize());
+ SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+ String nextxref = first + " -> " + db;
+ viewsourcedb.put(avp, nextxref);
+ List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(avp
+ .getAlignViewport().isNucleotide());
+ for (String xrefdb : xrptypes)
+ {
+ AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+ .getAlignViewport());
+ cra = new CrossRefAction(nextaf, xrseqs, avp.getAlignViewport()
+ .isNucleotide(), xrefdb);
+ cra.run();
+ Assert.assertTrue(cra.getXrefViews().size() > 0,
+ "No crossrefs found for '" + nextxref + "' to "
+ + xrefdb + " via '" + nextaf.getTitle() + "'");
+ // save views for analysis
+ viewxrefview.put(avp, cra.getXrefViews());
+ for (AlignmentViewPanel nextavp : cra.getXrefViews())
+ {
+
+ viewsourcedb.put(nextavp, nextxref + " -> " + xrefdb);
+ }
+ }
+ }
+ }
}
+ Thread.sleep(50000);
}
+
}
git://source.jalview.org / jalview.git / commitdiff