*/
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.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenSequences;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.AlignmentTest;
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 jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.testng.Assert;
-import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
- @Test(groups = { "Functional" })
- public void testRNAStructureRecovery() throws Exception
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- 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);
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @Test(groups = { "Functional" })
- public void testTCoffeeScores() throws Exception
+ @DataProvider(name = "initialAccessions")
+ static Object[][] getAccessions()
{
- 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.");
+ return new String[][] { { "UNIPROT", "P00338" },
+ { "UNIPROT", "Q8Z9G6" },
+ { "ENSEMBLGENOMES", "CAD01290" } };
}
- @Test(groups = { "Functional" })
- public void testColourByAnnotScores() throws Exception
+ /**
+ * test store and recovery of all reachable cross refs from all reachable
+ * crossrefs for one or more fetched db refs. Currently, this test has a known
+ * failure case.
+ *
+ * @throws Exception
+ */
+ @Test(
+ groups =
+ { "Operational" },
+ dataProvider = "initialAccessions",
+ enabled = true)
+ public void testRetrieveAndShowCrossref(String forSource,
+ String forAccession) 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++)
+
+ List<String> failedDBRetr = new ArrayList<>();
+ List<String> failedXrefMenuItems = new ArrayList<>();
+ List<String> failedProjectRecoveries = new ArrayList<>();
+ // only search for ensembl or Uniprot crossrefs
+ List<String> limit = Arrays
+ .asList(new String[]
+ { DBRefUtils.getCanonicalName("ENSEMBL"),
+ DBRefUtils.getCanonicalName("Uniprot") });
+ // 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
+ //
+ //
+ Map<String, String> dbtoviewBit = new HashMap<>();
+ List<String> keyseq = new ArrayList<>();
+ Map<String, File> savedProjects = new HashMap<>();
+
+ // for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+ // {
+ // pass counters - 0 - first pass, 1 means retrieve project rather than
+ // perform action
+ int pass1 = 0, pass2 = 0, pass3 = 0;
+ // each do loop performs two iterations in the first outer loop pass, but
+ // only performs one iteration on the second outer loop
+ // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
+ // { pass 2 = 0 { pass 3 = 0 } }
+ do
{
- if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
- .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+ String first = forSource + " " + forAccession;// did[0] + " " + did[1];
+ AlignFrame af = null;
+ boolean dna;
+ AlignmentI retral;
+ AlignmentI dataset;
+ SequenceI[] seqs;
+ List<String> ptypes = null;
+ if (pass1 == 0)
{
- diffseqcols = true;
+ // retrieve dbref
+
+ SequenceFetcher sf = new SequenceFetcher(Desktop.getInstance(),
+ forSource, forAccession);
+ sf.run();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ if (afs.length == 0)
+ {
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
+ }
+ keyseq.add(first);
+ af = afs[0];
+
+ // verify references for retrieved data
+ AlignmentTest.assertAlignmentDatasetRefs(
+ af.getViewport().getAlignment(), "Pass (" + pass1 + ","
+ + pass2 + "," + pass3 + "): Fetch " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ af.getViewport().getAlignment(), "Pass (" + pass1 + ","
+ + pass2 + "," + pass3 + "): Fetch " + first + ":");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
+
}
- }
- 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]))
+ else
{
- diffgseqcols = true;
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ // recover stored project
+ af = new FileLoader(false).LoadFileWaitTillLoaded(
+ savedProjects.get(first).toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + first + "' from '"
+ + savedProjects.get(first).toString() + "'");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
+
+ // verify references for recovered data
+ AlignmentTest.assertAlignmentDatasetRefs(
+ af.getViewport().getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
+ + first + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ af.getViewport().getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
+ + first + ":");
+
}
- }
- 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);
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
- }
+ ptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
+ filterDbRefs(ptypes, limit);
- @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())
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
+ {
+
+ for (String db : ptypes)
+ {
+ // counter for splitframe views retrieved via crossref
+ int firstcr_ap = 0;
+ // build next key so we an retrieve all views
+ String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
+ // perform crossref action, or retrieve stored project
+ List<AlignmentViewPanel> cra_views = new ArrayList<>();
+ CrossRefAction cra = null;
+
+ if (pass2 == 0)
+ { // retrieve and show cross-refs in this thread
+ cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
+ cra.run();
+ cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views.size() == 0)
+ {
+ failedXrefMenuItems.add(
+ "No crossrefs retrieved for " + first + " -> " + db);
+ continue;
+ }
+ assertNucleotide(cra_views.get(0),
+ "Nucleotide panel included proteins for " + first
+ + " -> " + db);
+ assertProtein(cra_views.get(1),
+ "Protein panel included nucleotides for " + first
+ + " -> " + db);
+ }
+ else
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ pass3 = 0;
+ // recover stored project
+ File storedProject = savedProjects.get(nextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries
+ .add("Failed to store a view for '" + nextxref + "'");
+ continue;
+ }
+
+ // recover stored project
+ AlignFrame af2 = new FileLoader(false).LoadFileWaitTillLoaded(
+ savedProjects.get(nextxref).toString(),
+ DataSourceType.FILE);
+ System.out
+ .println("Recovered view for '" + nextxref + "' from '"
+ + savedProjects.get(nextxref).toString() + "'");
+ // gymnastics to recover the alignPanel/Complementary alignPanel
+ if (af2.getViewport().isNucleotide())
+ {
+ // top view, then bottom
+ cra_views.add(af2.getViewport().getAlignPanel());
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+
+ }
+ else
+ {
+ // bottom view, then top
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+ cra_views.add(af2.getViewport().getAlignPanel());
+
+ }
+ }
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
+ // first save/verify views.
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+ assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+
+ SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+
+ List<String> _xrptypes = (seqs == null || seqs.length == 0)
+ ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(
+ avp.getAlignViewport().isNucleotide());
+
+ stringify(dbtoviewBit, savedProjects, nextxref, avp);
+ xrptypes.put(nextxref, _xrptypes);
+
+ }
+
+ // now do the second xref pass starting from either saved or just
+ // recovered split pane, in sequence
+ do // retrieve second set of cross refs or recover and verify
+ {
+ firstcr_ap = 0;
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
+ {
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
+ int q = 0;
+ String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
+ + "}";
+
+ if (pass3 == 0)
+ {
+ SequenceI[] xrseqs = avp.getAlignment()
+ .getSequencesArray();
+ AlignFrame nextaf = Desktop
+ .getAlignFrameFor(avp.getAlignViewport());
+
+ cra = CrossRefAction.getHandlerFor(xrseqs,
+ avp.getAlignViewport().isNucleotide(), xrefdb,
+ nextaf);
+ cra.run();
+ cra_views2 = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views2.size() == 0)
+ {
+ failedXrefMenuItems.add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ continue;
+ }
+ assertNucleotide(cra_views2.get(0),
+ "Nucleotide panel included proteins for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ assertProtein(cra_views2.get(1),
+ "Protein panel included nucleotides for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+
+ }
+ else
+ {
+ Desktop.getInstance().closeAll_actionPerformed(null);
+ // recover stored project
+ File storedProject = savedProjects.get(nextnextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries
+ .add("Failed to store a view for '"
+ + nextnextxref + "'");
+ continue;
+ }
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(savedProjects
+ .get(nextnextxref).toString(),
+ DataSourceType.FILE);
+ System.out
+ .println("Recovered view for '" + nextnextxref
+ + "' from '" + savedProjects
+ .get(nextnextxref).toString()
+ + "'");
+ // gymnastics to recover the alignPanel/Complementary
+ // alignPanel
+ if (af2.getViewport().isNucleotide())
+ {
+ // top view, then bottom
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+
+ }
+ else
+ {
+ // bottom view, then top
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ }
+ Assert.assertEquals(cra_views2.size(), 2);
+ Assert.assertNotNull(cra_views2.get(0));
+ Assert.assertNotNull(cra_views2.get(1));
+ }
+
+ for (AlignmentViewPanel nextavp : cra_views2)
+ {
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
+
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(
+ nextavp.getAlignment(),
+ "" + "Pass (" + pass1 + "," + pass2 + "): For "
+ + nextnextxref + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ nextavp.getAlignment(),
+ "" + "Pass (" + pass1 + "," + pass2 + "): For "
+ + nextnextxref + ":");
+
+ stringify(dbtoviewBit, savedProjects, nextnextxref,
+ nextavp);
+ keyseq.add(nextnextxref);
+ }
+ } // end of loop around showing all xrefdb for crossrf2
+
+ } // end of loop around all viewpanels from crossrf1
+ } while (pass2 == 2 && pass3++ < 2);
+ // fetchdb->crossref1->crossref-2->verify for xrefs we
+ // either loop twice when pass2=0, or just once when pass2=1
+ // (recovered project from previous crossref)
+
+ } // end of loop over db-xrefs for crossref-2
+
+ // fetchdb-->crossref1
+ // for each xref we try to retrieve xref, store and verify when
+ // pass1=0, or just retrieve and verify when pass1=1
+ } while (pass1 == 1 && pass2++ < 2);
+ // fetchdb
+ // for each ref we
+ // loop twice: first, do the retrieve, second recover from saved project
+
+ // increment pass counters, so we repeat traversal starting from the
+ // oldest saved project first.
+ if (pass1 == 0)
+ {
+ // verify stored projects for first set of cross references
+ pass1 = 1;
+ // and verify cross-references retrieved from stored projects
+ pass2 = 0;
+ pass3 = 0;
+ }
+ else
+ {
+ pass1++;
+ }
+ } while (pass1 < 3);
+
+ if (failedXrefMenuItems.size() > 0)
{
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+ for (String s : failedXrefMenuItems)
{
- sps = ap;
- break;
+ System.err.println(s);
}
+ Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+ + " counts)");
}
- 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 (failedProjectRecoveries.size() > 0)
{
- if (ra.graph != 0)
+
+ for (String s : failedProjectRecoveries)
{
- refan = ra;
- break;
+ System.err.println(s);
}
+ Assert.fail(
+ "Didn't recover projects for some retrievals (did they retrieve ?) ("
+ + failedProjectRecoveries.size() + " counts)");
}
- 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())
+ if (failedDBRetr.size() > 0)
{
- AlignmentAnnotation alaa;
- sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
- alaa.adjustForAlignment();
- if (ala.graph == refan.graph)
+ for (String s : failedProjectRecoveries)
{
- 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]);
- }
- }
+ System.err.println(s);
}
+ Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+ + failedDBRetr.size() + " counts)");
}
-
}
- @Test(groups = { "Functional" })
- public void testCopyViewSettings() throws Exception
+ private void filterDbRefs(List<String> ptypes, List<String> limit)
{
- 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 (limit != null)
{
- if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
- {
- sps = ap;
- }
- if (ap.getViewName().contains("MAFFT"))
+ int p = 0;
+ while (ptypes.size() > p)
{
- groups = ap;
+ if (!limit.contains(ptypes.get(p)))
+ {
+ ptypes.remove(p);
+ }
+ else
+ {
+ p++;
+ }
}
}
- 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
+ * wrapper to trap known defect for AH002001 testcase
*
- * @throws Exception
+ * @param alignment
+ * @param string
*/
- @Test(groups = { "Functional" }, enabled = true)
- public void testStoreAndRecoverExpandedviews() throws Exception
+ private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
+ String message)
{
- 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)
+ AlignmentTest.assertDatasetIsNormalised(al, message);
+ } catch (AssertionError ae)
{
- 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);
+ if (!ae.getMessage().endsWith("EMBL|AH002001"))
+ {
+ throw ae;
+ }
+ else
+ {
+ System.out.println("Ignored exception for known defect: JAL-2179 : "
+ + message);
+ }
+
}
- 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
+ private void assertProtein(AlignmentViewPanel alignmentViewPanel,
+ String message)
{
- 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();
+ assertType(true, alignmentViewPanel, message);
+ }
- 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.");
- }
+ private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(false, alignmentViewPanel, message);
}
- @Test(groups = { "Functional" })
- public void testIsVersionStringLaterThan()
+ private void assertType(boolean expectProtein,
+ AlignmentViewPanel alignmentViewPanel, String message)
{
- /*
- * 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"));
+ List<SequenceI> nonType = new ArrayList<>();
+ for (SequenceI sq : alignmentViewPanel.getAlignViewport().getAlignment()
+ .getSequences())
+ {
+ if (sq.isProtein() != expectProtein)
+ {
+ nonType.add(sq);
+ }
+ }
+ if (nonType.size() > 0)
+ {
+ Assert.fail(message + " [ "
+ + (expectProtein ? "nucleotides were " : "proteins were ")
+ + nonType.toString() + " ]");
+ }
}
/**
- * Test save and reload of a project with a different sequence group (and
- * representative sequence) in each view.
+ * first time called, record strings derived from alignment and
+ * alignedcodonframes, and save view to a project file. Second time called,
+ * compare strings to existing ones. org.testng.Assert.assertTrue on
+ * stringmatch
*
- * @throws Exception
+ * @param dbtoviewBit
+ * map between xrefpath and view string
+ * @param savedProjects
+ * - map from xrefpath to saved project filename (createTempFile)
+ * @param xrefpath
+ * - xrefpath - unique ID for this context (composed of sequence of
+ * db-fetch/cross-ref actions preceeding state)
+ * @param avp
+ * - viewpanel to store (for viewpanels in splitframe, the same
+ * project should be written for both panels, only one needs
+ * recovering for comparison on the next stringify call, but each
+ * viewpanel needs to be called with a distinct xrefpath to ensure
+ * each one's strings are compared)
*/
- @Test(groups = { "Functional" })
- public void testStoreAndRecoverGroupRepSeqs() throws Exception
+ private void stringify(Map<String, String> dbtoviewBit,
+ Map<String, File> savedProjects, String xrefpath,
+ AlignmentViewPanel avp)
{
- 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))
+ if (savedProjects != null)
{
- 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);
-
- /*
- * have rep sequence represent itself and the one before it
- * this hides the group (except for the rep seq)
- */
- 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());
-
- /*
- * represent group with sequence adds to a map of hidden rep sequences
- * (it does not create a group on the alignment)
- */
- ((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++;
+ if (savedProjects.get(xrefpath) == null)
+ {
+ // write a project file for this view. On the second pass, this will be
+ // recovered and cross-references verified
+ try
+ {
+ File prfile = File.createTempFile("crossRefTest", ".jvp");
+ AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
+ new Jalview2XML(false).saveAlignment(af, prfile.toString(),
+ af.getTitle());
+ System.out.println("Written view from '" + xrefpath + "' as '"
+ + prfile.getAbsolutePath() + "'");
+ savedProjects.put(xrefpath, prfile);
+ } catch (IOException q)
+ {
+ Assert.fail("Unexpected IO Exception", q);
+ }
+ }
+ else
+ {
+ System.out.println("Stringify check on view from '" + xrefpath
+ + "' [ possibly retrieved from '"
+ + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
+
+ }
}
- File tfile = File
- .createTempFile("testStoreAndRecoverGroupReps", ".jvp");
- try
- {
- new Jalview2XML(false).saveState(tfile);
- } catch (Throwable e)
+
+ StringBuilder sbr = new StringBuilder();
+ sbr.append(avp.getAlignment().toString());
+ sbr.append("\n");
+ sbr.append("<End of alignment>");
+ sbr.append("\n");
+ sbr.append(avp.getAlignment().getDataset());
+ sbr.append("\n");
+ sbr.append("<End of dataset>");
+ sbr.append("\n");
+ int p = 0;
+ if (avp.getAlignment().getCodonFrames() != null)
{
- Assert.fail("Didn't save the expanded view state", e);
+ for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
+ {
+ sbr.append("<AlignedCodonFrame " + p++ + ">");
+ sbr.append("\n");
+ sbr.append(ac.toString());
+ sbr.append("\n");
+ }
}
- Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ String dbt = dbtoviewBit.get(xrefpath);
+ if (dbt == null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ dbtoviewBit.put(xrefpath, sbr.toString());
}
-
- af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
- FormatAdapter.FILE);
- afid = af.getViewport().getSequenceSetId();
-
- for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
+ else
{
- 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));
-
- /*
- * 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());
+ Assert.assertEquals(sbr.toString(), dbt,
+ "stringify mismatch for " + xrefpath);
}
}
}
git://source.jalview.org / jalview.git / blobdiff