import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
import java.awt.Color;
+import java.awt.Rectangle;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.HiddenSequences;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PopupMenu;
+import jalview.gui.Preferences;
import jalview.gui.SliderPanel;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.util.matcher.Condition;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
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 for patch release versions
+ */
+ assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
+ assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4"));
+ assertFalse(
+ Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0"));
+ assertFalse(
+ Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2"));
+
}
/**
acg.setPredefinedColours(true);
af.changeColour(acg);
Color seqcol[] = new Color[3];
- for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
- seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+ for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++)
+ {
+ seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas
+ .getSequenceRenderer()
+ .getResidueColour(fsq, iStart + i, null);
}
/*
* save project, close windows, reload project, verify
"testStoreAndRecoverAnnotRowElemColors", ".jvp");
tfile.deleteOnExit();
new Jalview2XML(false).saveState(tfile);
- //Desktop.instance.closeAll_actionPerformed(null);
+ // Desktop.instance.closeAll_actionPerformed(null);
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af, "Failed to reload project");
* verify alignment annotation has colors
*/
av = af.getViewport();
-
+
ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
- Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+ Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,
+ "Didn't apply Annotation colour gradient");
acg = (AnnotationColourGradient) loadedCscheme;
assertTrue(acg.isSeqAssociated());
assertTrue(acg.isPredefinedColours());
for (int iStart = al.getSequenceAt(0)
.findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
{
- Assert.assertTrue(ala.annotations[i].colour!=null);
+ Assert.assertTrue(ala.annotations[i].colour != null);
Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
- Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
- Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+ Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas
+ .getSequenceRenderer()
+ .getResidueColour(fsq, iStart + i, null);
+ Assert.assertTrue(seqcol[i].equals(newseqcol),
+ "Sequence shading is different");
}
-
+
}
/**
}
/**
+ * test store and recovery of Overview windows
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverOverview() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ Cache.setProperty(Preferences.USE_LEGACY_GAP, "false");
+ Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green);
+ Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow);
+ Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true");
+
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", DataSourceType.FILE);
+
+ /*
+ * open and resize / reposition overview
+ */
+ af.overviewMenuItem_actionPerformed(null);
+ OverviewPanel ov1 = af.alignPanel.getOverviewPanel();
+ assertNotNull(ov1);
+ ov1.setFrameBounds(20, 30, 200, 400);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa");
+ assertTrue(ov1.isShowHiddenRegions());
+
+ /*
+ * open a New View and its Overview and reposition it
+ */
+ af.newView_actionPerformed(null);
+ af.overviewMenuItem_actionPerformed(null);
+ OverviewPanel ov2 = af.alignPanel.getOverviewPanel();
+ assertNotNull(ov2);
+ assertNotSame(ov1, ov2);
+ ov2.setFrameBounds(25, 35, 205, 405);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+ assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+
+ File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ /*
+ * change preferences (should _not_ affect reloaded Overviews)
+ */
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ Cache.setProperty(Preferences.USE_LEGACY_GAP, "true");
+ Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue);
+ Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange);
+ Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false");
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+
+ /*
+ * workaround: explicitly select View 1 (not in focus after restore)
+ */
+ af.tabSelectionChanged(1);
+
+ /*
+ * verify restored overview for View 1
+ */
+ ov2 = af.alignPanel.getOverviewPanel();
+ assertEquals(ov2.getCanvas().getGapColour(), Color.green);
+ // 'non-legacy' colouring uses white for non-gapped residues
+ assertEquals(ov2.getCanvas().getResidueColour(), Color.white);
+ assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow);
+ assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+ assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405));
+ assertTrue(ov2.isShowHiddenRegions());
+
+ /*
+ * verify restored overview for Original view
+ */
+ af.tabSelectionChanged(0);
+ ov1 = af.alignPanel.getOverviewPanel();
+ assertEquals(ov1.getCanvas().getGapColour(), Color.green);
+ // 'non-legacy' colouring uses white for non-gapped residues
+ assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
+ assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
+ assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+ assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+ assertTrue(ov1.isShowHiddenRegions());
+ }
+
+ /**
+ * Test that a view with no Overview is restored with no Overview, even if
+ * 'Open Overview' is selected in Preferences
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testStoreAndRecoverNoOverview() throws Exception
+ {
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+
+ File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+
+ assertNull(af.alignPanel.getOverviewPanel());
+ }
+
+ /**
+ * Test that a view from an older version of Jalview is restored with Overview
+ * automatically shown when the preference is set
+ *
+ * @throws Exception
+ */
+ @Test(groups = { "Functional" }, enabled = true)
+ public void testAutoShowOverviewForLegacyProjects() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ Cache.setProperty("SHOW_OVERVIEW", "true");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+
+ Cache.setProperty("SHOW_OVERVIEW", "false");
+ assertNotNull(af.alignPanel.getOverviewPanel());
+ }
+
+ /**
* Test that loading example.jvp, doing some stuff, then hitting reload
* doesn't leave the modified window still open
*
+ * See JAL-4127 - interactively performing the same actions and reloading
+ * works fine, but programmatically they do not
+ *
* @throws Exception
*/
- @Test(groups = { "Functional" }, enabled = true)
+ @Test(groups = { "Functional" }, enabled = false)
public void testReloadActuallyReloads() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
// af exists still but isn't shown
assertTrue(af.isClosed());
}
+
+ @Test(groups = { "Functional" })
+ public void testPAEsaveRestore() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+ AlignmentI al = af.getViewport().getAlignment();
+ // PAE matrices are added as reference annotation to the dataset sequence
+ // at least for now.
+ SequenceI sq = al.getSequenceAt(0).getDatasetSequence();
+ int i = sq.getLength();
+ float[][] paevals = new float[i][i];
+ for (i = i - 1; i >= 0; i--)
+ {
+ for (int j = 0; j <= i; j++)
+ {
+ paevals[i][j] = ((i - j < 2)
+ || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+ paevals[j][i] = paevals[i][j];
+ }
+ }
+ PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+ String content = ContactMatrix.contactToFloatString(dummyMat);
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4],paevals[3][4]);
+ dummyMat.makeGroups(0.5f, false);
+ Assert.assertNotSame(dummyMat.getNewick(), "");
+ AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
+ al.addAnnotation(paeCm);
+ File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
+ ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ AlignmentI newAl = af.getViewport().getAlignment();
+ SequenceI newSeq = newAl.getSequenceAt(0).getDatasetSequence();
+ // check annotation of the expected type exists
+ Assert.assertEquals(newSeq.getAnnotation().length, 1);
+ Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph);
+
+ // check a contact matrix was recovered
+ Assert.assertEquals(newSeq.getContactMaps().size(), 1);
+ // and can be found for the annotation on the sequence
+ ContactMatrixI restoredMat = newSeq
+ .getContactMatrixFor(newSeq.getAnnotation()[0]);
+ Assert.assertNotNull(restoredMat);
+ for (i = sq.getLength() - 1; i >= 0; i--)
+ {
+ ContactListI oldCM = dummyMat.getContactList(i),
+ newCM = restoredMat.getContactList(i);
+ for (int j = oldCM.getContactHeight(); j >= 0; j--)
+ {
+ Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
+ }
+ }
+ Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
+ Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
+ Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
+ Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
+
+
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff