*/
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 / blobdiff