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.math.BigInteger;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.AlignViewportI;
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.GroupSet;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
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.MappableContactMatrixI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
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++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
@Test(groups = { "Functional" })
public void gatherViewsHere() throws Exception
{
- int origCount = Desktop.getAlignFrames() == null ? 0
- : Desktop.getAlignFrames().length;
+ int origCount = Desktop.getDesktopAlignFrames() == null ? 0
+ : Desktop.getDesktopAlignFrames().length;
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
- assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+ assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount,
"Didn't gather the views in the example file.");
}
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
- Assert.assertEquals(Desktop.getAlignFrames().length, 1);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1);
String afid = af.getViewport().getSequenceSetId();
// check FileLoader returned a reference to the one alignFrame that is
Desktop.explodeViews(af);
- int oldviews = Desktop.getAlignFrames().length;
- Assert.assertEquals(Desktop.getAlignFrames().length,
+ int oldviews = Desktop.getDesktopAlignFrames().length;
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
Desktop.getAlignmentPanels(afid).length);
File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
try
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af);
- Assert.assertEquals(Desktop.getAlignFrames().length,
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
Desktop.getAlignmentPanels(
af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(Desktop
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
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"));
+
}
/**
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
Assert.fail("Didn't save the state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
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");
}
-
+
}
/**
assertNotNull(af);
AlignmentI ds = null;
- for (AlignFrame alignFrame : Desktop.getAlignFrames())
+ for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
{
if (ds == null)
{
assertTrue(dbRef instanceof GeneLocus);
assertEquals(dbRef, dbref3);
}
+
+ /**
+ * 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 = false)
+ public void testReloadActuallyReloads() throws Exception
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/exampleFile.jvp", DataSourceType.FILE);
+ af.getViewport().getColumnSelection().addElement(3);
+ af.hideSelColumns_actionPerformed(null);
+ af.newView("new", true);
+ af.reload_actionPerformed(null);
+ Thread.sleep(30);
+ // af exists still but isn't shown
+ assertTrue(af.isClosed());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMatrixToFloatsAndBack()
+ {
+ int imax=2000;
+ int i=imax;
+ SequenceI sq = new Sequence("dummy","SEQ");
+ while (sq.getLength()<i)
+ {
+ sq.setSequence(sq.getSequenceAsString()+'Q');
+ }
+ float[][] paevals = new float[i][i];
+ for (i = imax - 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]);
+ assertEquals(vals[4][3], paevals[4][3]);
+
+ // test recovery
+ for (i=0;i<imax;i++)
+ {
+ for (int j=0;j<imax;j++)
+ {
+ assertEquals(vals[i][j],paevals[i][j]);
+ }
+ }
+ }
+ @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]);
+ assertEquals(vals[4][3], paevals[4][3]);
+ dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
+ Assert.assertNotSame(dummyMat.getNewick(), "");
+ AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
+ al.addAnnotation(paeCm);
+ // verify store/restore of group bitsets
+ for (BitSet gp : dummyMat.getGroups())
+ {
+ StringBuilder sb = new StringBuilder();
+ for (long val : gp.toLongArray())
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append(val);
+ }
+ String[] longvals = sb.toString().split(",");
+ long[] newlongvals = new long[longvals.length];
+ for (int lv = 0; lv < longvals.length; lv++)
+ {
+ try
+ {
+ newlongvals[lv] = Long.valueOf(longvals[lv]);
+ } catch (Exception x)
+ {
+ Assert.fail("failed to deserialise bitset element ");
+ }
+ }
+ BitSet newGp = BitSet.valueOf(newlongvals);
+ assertTrue(gp.equals(newGp));
+ }
+ 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);
+ MapList oldMap = ((MappableContactMatrixI) dummyMat).getMapFor(sq);
+ MapList newMap = ((MappableContactMatrixI) restoredMat)
+ .getMapFor(newSeq);
+ Assert.assertEquals(oldMap.getFromRanges(), newMap.getFromRanges());
+ Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
+ Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
+ Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
+ 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--)
+ {
+ double old_j = oldCM.getContactAt(j);
+ double new_j = newCM.getContactAt(j);
+ Assert.assertEquals(old_j, new_j);
+ }
+ }
+ Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
+ Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
+ Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
+ Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
+ // verify no duplicate PAE matrix data when new view created and saved
+
+ // add reference annotations to view first, then copy
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
+
+ AlignmentViewPanel newview = af.newView("copy of PAE", true);
+
+ // redundant asserts here check all is good with the new view firest...
+ AlignmentI newviewAl = newview.getAlignment();
+ SequenceI newviewSeq = newviewAl.getSequenceAt(0);
+ // check annotation of the expected type exists
+ Assert.assertEquals(newviewSeq.getAnnotation().length, 1);
+ Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
+ // check we have just one contact matrix mapping
+ Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
+
+ // and can be found for the annotation on the sequence
+ ContactMatrixI newviewMat = newviewSeq
+ .getContactMatrixFor(newviewSeq.getAnnotation()[0]);
+ Assert.assertNotNull(newviewMat);
+
+ Assert.assertTrue(newviewMat == restoredMat);
+
+ // save the two views and restore. Now look at visible annotation to check all views have shared refs.
+
+ tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
+ ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ newAl = af.getAlignPanels().get(0).getAlignment();
+ AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
+
+ newviewAl = af.getAlignPanels().get(1).getAlignment();
+ AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+
+ // annotations are shared across alignment views - so should still have an identical pair of annotations.
+ Assert.assertTrue(view1aa==view2aa);
+ // identical annotations means identical contact matrix mappings
+ Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+
+ // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+ // Assert.assertTrue(view1aa!=view2aa);
+ // restoredMat = newAl.getContactMatrixFor(view1aa);
+ // newviewMat = newviewAl.getContactMatrixFor(view2aa);
+ // Assert.assertTrue(restoredMat!=newviewMat);
+
+ }
+
+ @Test(groups = "Functional")
+ public void testStoreAndRestoreIDwidthAndAnnotationHeight() throws IOException
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ final String SECONDVIEW = "With Diffferent IDwidth";
+ // create a new tempfile
+ File tempfile = File.createTempFile("jvIdWidthStoreRestore", "jvp");
+
+
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("examples/exampleFile.jvp",
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read in the example file correctly.");
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 144,
+ "Legacy project import should have fixed ID width");
+ assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertTrue(af.alignPanel.getIdPanel().getIdCanvas()
+ .isManuallyAdjusted());
+ assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
+ "New project exported and import should have adjusted ID width");
+
+ af.alignPanel.getAlignViewport().setIdWidth(100);
+ af.alignPanel.updateLayout();
+ assertTrue(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+ // now make it autoadjusted
+ af.alignPanel.getAlignViewport().setIdWidth(-1);
+ af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
+ af.alignPanel.updateLayout();
+ assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
+ "New project exported and import should have adjusted ID width");
+
+ jv2xml = new jalview.project.Jalview2XML(false);
+ tempfile.delete();
+ jv2xml.saveState(tempfile);
+ assertTrue(jv2xml.errorMessage == null,
+ "Failed to save dummy project with PCA: test broken");
+ af = null;
+ // load again.
+ Desktop.instance.closeAll_actionPerformed(null);
+ af = new FileLoader().LoadFileWaitTillLoaded(
+ tempfile.getCanonicalPath(), DataSourceType.FILE);
+ assertFalse(af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+ assertTrue(af.alignPanel.getAlignViewport().getIdWidth()>-1,
+ "New project exported and import should have adjusted ID width");
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff