*/
package jalview.io;
-import static org.testng.AssertJUnit.assertTrue;
-
import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignedCodonFrame;
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
+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.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @DataProvider(name = "initialAccessions")
+ static Object[][] getAccessions()
+ {
+ return new String[][] { { "UNIPROT", "P00338" },
+ { "UNIPROT", "Q8Z9G6" },
+ { "ENSEMBLGENOMES", "CAD01290" } };
+ }
+
/**
- * test store and recovery of expanded views
+ * 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" }, enabled = true)
- public void testRetrieveAndShowCrossref() throws Exception
+ @Test(
+ groups =
+ { "Operational" },
+ dataProvider = "initialAccessions",
+ enabled = true)
+ public void testRetrieveAndShowCrossref(String forSource,
+ String forAccession) throws Exception
{
+
+ 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
// . codonframes
//
//
- HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
- List<String> keyseq = new ArrayList<String>();
- HashMap<String, File> savedProjects = new HashMap<String, File>();
-
- for (String[] did : new String[][] { { "UNIPROT", "P01731" } })
+ 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
{
- // 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
+ 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)
{
- String first = did[0] + " " + did[1];
- AlignFrame af = null;
- boolean dna;
- AlignmentI retral;
- AlignmentI dataset;
- SequenceI[] seqs;
- List<String> ptypes = null;
- if (pass1 == 0)
- {
- // retrieve dbref
-
- keyseq.add(first);
+ // retrieve dbref
- af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
- .get(0);
- assertTrue("Didn't retrieve " + first, af != null);
+ 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();
- // verify references for retrieved data
- AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
- .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
- + pass3 + "): Fetch " + first + ":");
- dna = af.getViewport().getAlignment().isNucleotide();
- retral = af.getViewport().getAlignment();
- dataset = retral.getDataset();
- seqs = retral.getSequencesArray();
+ }
+ else
+ {
+ 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 + ":");
- }
- else
- {
- Desktop.instance.closeAll_actionPerformed(null);
- // recover stored project
- af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), FormatAdapter.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 + ":");
+ }
- }
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
- // 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);
- ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
- seqs, dataset).findXrefSourcesForSequences(dna);
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
+ {
- // start of pass2: retrieve each cross-ref for fetched or restored
- // project.
- pass2 = 0;
- do // second cross ref and recover crossref loop
+ for (String db : ptypes)
{
-
- 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
{
- // 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<AlignmentViewPanel>();
- CrossRefAction cra = null;
- if (pass2 == 0)
- { // retrieve and show cross-refs in this thread
- cra = new CrossRefAction(af, seqs, dna, db);
- cra.run();
- Assert.assertTrue(cra.getXrefViews().size() > 0,
- "No crossrefs retrieved for " + db);
- cra_views = cra.getXrefViews();
+ 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;
}
- else
+
+ // 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())
{
- Desktop.instance.closeAll_actionPerformed(null);
- // recover stored project
- AlignFrame af2 = new FileLoader(false)
- .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), FormatAdapter.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());
+ // top view, then bottom
+ cra_views.add(af2.getViewport().getAlignPanel());
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
- }
}
- HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
- // first save/verify views.
- for (AlignmentViewPanel avp : cra_views)
+ else
{
- nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
- // verify references for this panel
- AlignmentTest.assertAlignmentDatasetRefs(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);
+ // bottom view, then top
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+ cra_views.add(af2.getViewport().getAlignPanel());
}
- // now do the next xref pass starting from either saved or just
- // recovered split pane, in sequence
- pass3 = 0;
- do // 3rd cross ref and recover crossref loop, for each view from
- // second xref view set or recover viewset
+ }
+ 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)
{
- firstcr_ap = 0;
- for (AlignmentViewPanel avp : cra_views)
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
{
- nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
- for (String xrefdb : xrptypes.get(nextxref))
- {
- List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
- int q = 0;
- String nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q + "}";
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
+ int q = 0;
+ String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
+ + "}";
- if (pass3 == 0)
+ 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)
{
-
- SequenceI[] xrseqs = avp.getAlignment()
- .getSequencesArray();
- 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 '" + nextnextxref
- + "' to " + xrefdb + " via '"
- + nextaf.getTitle() + "'");
- cra_views2 = cra.getXrefViews();
+ failedXrefMenuItems.add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ continue;
}
- else
+ 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)
{
- Desktop.instance.closeAll_actionPerformed(null);
- // recover stored project
- AlignFrame af2 = new FileLoader(false)
- .LoadFileWaitTillLoaded(
- savedProjects.get(nextnextxref)
- .toString(), FormatAdapter.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));
+ 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());
- for (AlignmentViewPanel nextavp : cra_views2)
+ }
+ else
{
- nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q++ + "}";
-
- // verify references for this panel
- AlignmentTest.assertAlignmentDatasetRefs(
- nextavp.getAlignment(), "" + "Pass (" + pass1
- + "," + pass2 + "): For "
- + nextnextxref + ":");
-
- stringify(dbtoviewBit, savedProjects, nextnextxref,
- nextavp);
- keyseq.add(nextnextxref);
+ // bottom view, then top
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views2.add(af2.getViewport().getAlignPanel());
}
- } // end of loop around showing all xrefdb for crossrf2
+ 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);
- } // end of loop around all viewpanels from crossrf1
- } while (pass3++ < 2 && pass2 < 1);
- // 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)
+ if (failedXrefMenuItems.size() > 0)
+ {
+ for (String s : failedXrefMenuItems)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
+ + " counts)");
+ }
+ if (failedProjectRecoveries.size() > 0)
+ {
- }
- // 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 (pass2++ < 2 && pass1 < 1);
- // fetchdb
- // for each ref we
- // loop twice: first, do the retrieve, second recover from saved project
- } while (pass1++ < 2);
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail(
+ "Didn't recover projects for some retrievals (did they retrieve ?) ("
+ + failedProjectRecoveries.size() + " counts)");
+ }
+ if (failedDBRetr.size() > 0)
+ {
+ for (String s : failedProjectRecoveries)
+ {
+ System.err.println(s);
+ }
+ Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
+ + failedDBRetr.size() + " counts)");
+ }
+ }
+
+ private void filterDbRefs(List<String> ptypes, List<String> limit)
+ {
+ if (limit != null)
+ {
+ int p = 0;
+ while (ptypes.size() > p)
+ {
+ if (!limit.contains(ptypes.get(p)))
+ {
+ ptypes.remove(p);
+ }
+ else
+ {
+ p++;
+ }
+ }
+ }
+ }
+
+ /**
+ * wrapper to trap known defect for AH002001 testcase
+ *
+ * @param alignment
+ * @param string
+ */
+ private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
+ String message)
+ {
+ try
+ {
+ AlignmentTest.assertDatasetIsNormalised(al, message);
+ } catch (AssertionError ae)
+ {
+ if (!ae.getMessage().endsWith("EMBL|AH002001"))
+ {
+ throw ae;
+ }
+ else
+ {
+ System.out.println("Ignored exception for known defect: JAL-2179 : "
+ + message);
+ }
+
+ }
+ }
+
+ private void assertProtein(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(true, alignmentViewPanel, message);
+ }
+
+ private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
+ String message)
+ {
+ assertType(false, alignmentViewPanel, message);
+ }
+
+ private void assertType(boolean expectProtein,
+ AlignmentViewPanel alignmentViewPanel, String message)
+ {
+ 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() + " ]");
}
}
* viewpanel needs to be called with a distinct xrefpath to ensure
* each one's strings are compared)
*/
- private void stringify(HashMap<String, String> dbtoviewBit,
- HashMap<String, File> savedProjects, String xrefpath,
+ private void stringify(Map<String, String> dbtoviewBit,
+ Map<String, File> savedProjects, String xrefpath,
AlignmentViewPanel avp)
{
if (savedProjects != null)
}
else
{
- Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
- + xrefpath);
+ Assert.assertEquals(sbr.toString(), dbt,
+ "stringify mismatch for " + xrefpath);
}
}
}
git://source.jalview.org / jalview.git / blobdiff