import jalview.analysis.CrossRef;
import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.List;
// . 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" } })
{
- 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);
- /*
- * map between a view, and views generated after retrieving xrefs
- */
- IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
- /*
- * map between a particular view and it's originating dbref path
- */
- IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();
-
- String first = did[0] + " " + did[1];
- viewsourcedb.put(af.alignPanel, first);
- for (String db : ptypes)
+ // 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
{
- // 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())
+ String first = did[0] + " " + did[1];
+ AlignFrame af = null;
+ if (pass1 == 0)
+ {
+ // retrieve dbref
+
+ keyseq.add(first);
+
+ af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1])
+ .get(0);
+ assertTrue("Didn't retrieve " + first, af != null);
+ // store project to recover on next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+ }
+ else
{
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
+ .get(first).toString(), FormatAdapter.FILE);
+ }
- 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)
+ 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);
+
+ /*
+ * map between a view, and views generated after retrieving xrefs
+ */
+ IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>> viewxrefview = new IdentityHashMap<AlignmentViewPanel, List<AlignmentViewPanel>>();
+ /*
+ * map between a particular view and it's originating dbref path
+ */
+ IdentityHashMap<AlignmentViewPanel, String> viewsourcedb = new IdentityHashMap<AlignmentViewPanel, String>();
+
+ viewsourcedb.put(af.alignPanel, first);
+ for (String db : ptypes)
+ {
+ pass2 = 0;
+ do // second cross ref and recover crossref loop
{
- 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())
+ // counter for splitframe views retrieved via crossref
+ int p = 0;
+ // build next key so we an retrieve all views
+ String nextxref = first + " -> " + db + "{" + p + "}";
+ // 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();
+ viewxrefview.put(af.alignPanel, cra.getXrefViews());
+ }
+ else
{
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(savedProjects.get(first)
+ .toString(), FormatAdapter.FILE);
+ // 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());
- viewsourcedb.put(nextavp, nextxref + " -> " + xrefdb);
+ }
}
- }
+ for (AlignmentViewPanel avp : cra_views)
+ {
+
+ SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+ nextxref = first + " -> " + db + "{" + p++ + "}";
+
+ viewsourcedb.put(avp, nextxref);
+ stringify(dbtoviewBit, savedProjects, nextxref, avp);
+ keyseq.add(nextxref);
+
+ List<String> xrptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(avp
+ .getAlignViewport().isNucleotide());
+ for (String xrefdb : xrptypes)
+ {
+ pass3 = 0;
+ do // 3rd cross ref and recover crossref loop
+ {
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+ int q = 0;
+ String nextnextxref = "{" + p + "}" + nextxref + " -> "
+ + xrefdb + "{" + q + "}";
+
+ AlignFrame nextaf = Desktop.getAlignFrameFor(avp
+ .getAlignViewport());
+ if (pass3 == 0)
+ {
+
+ 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()
+ + "'");
+ cra_views2 = cra.getXrefViews();
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(
+ savedProjects.get(nextnextxref)
+ .toString(), FormatAdapter.FILE);
+ // 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 = "{" + p + "}" + nextxref + " -> "
+ + xrefdb + "{" + q++ + "}";
+ viewsourcedb.put(nextavp, nextnextxref);
+ stringify(dbtoviewBit, savedProjects, nextnextxref,
+ nextavp);
+ keyseq.add(nextnextxref);
+ }
+ } while (pass3++ < 2 && pass2 < 1);
+ }
+ }
+ } while (pass2++ < 2 && pass1 < 1);
}
- }
+ } while (++pass1 < 2);
}
- Thread.sleep(50000);
}
+ /**
+ * 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
+ *
+ * @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)
+ */
+ private void stringify(HashMap<String, String> dbtoviewBit,
+ HashMap<String, File> savedProjects, String xrefpath,
+ AlignmentViewPanel avp)
+ {
+ if (savedProjects != null)
+ {
+ 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() + "' ]");
+
+ }
+ }
+
+ 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)
+ {
+ for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
+ {
+ sbr.append("<AlignedCodonFrame " + p++ + ">");
+ sbr.append("\n");
+ sbr.append(ac.toString());
+ sbr.append("\n");
+ }
+ }
+ String dbt = dbtoviewBit.get(xrefpath);
+ if (dbt == null)
+ {
+ dbtoviewBit.put(xrefpath, sbr.toString());
+ }
+ else
+ {
+ Assert.assertEquals(sbr.toString(), dbt,
+ "stringify mismatch for " + xrefpath);
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff