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 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.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;
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(),
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(
assertNotNull(af);
AlignmentI ds = null;
- for (AlignFrame alignFrame : Desktop.getAlignFrames())
+ for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
{
if (ds == null)
{
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));
+
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(ov1);
+ // int width = scaling == 1.0 ? 225 : 200;
+ // int width = scaling == 1.0 ? 225 : 200;
+ Rectangle ov1Rectangle = ov1.getFrameBounds();
+ assertEquals(ov1Rectangle,
+ new Rectangle(20, 30, ov1Rectangle.width, 400));
+ int width = ov1Rectangle.width;
+ assertTrue(width >= 200 && width <= 225,
+ "Rectangle width was not in the range expected (200<=width<=225; width="
+ + width + ")");
assertTrue(ov1.isShowHiddenRegions());
}
}
@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);
{
paevals[i][j] = ((i - j < 2)
|| ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
- paevals[j][i] = paevals[i][j];
+ paevals[j][i] = -paevals[i][j];
}
}
PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
sq.getLength(), sq.getLength());
assertEquals(vals[3][4], paevals[3][4]);
- dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
+ 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);
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.");
+ // FIXME JAL-4281 test made platform dependent to pass, but probably
+ // shouldn't be platform dependent
+ int idWidth = af.alignPanel.getAlignViewport().getIdWidth();
+ double scaling = jalview.gui.JvSwingUtilsTest.getScaling(af.alignPanel);
+ // int expectedWidth = Platform.isMac() ? 144 : Platform.isLinux() ? scaling
+ // == 1.0 ? 131 : 128 : 138;
+ int minExpectedWidth = 128;
+ int maxExpectedWidth = 144;
+ assertTrue(minExpectedWidth <= idWidth && maxExpectedWidth >= idWidth,
+ "Legacy project import should have fixed ID width. Not within the expected range ("
+ + minExpectedWidth + "-" + maxExpectedWidth + ")");
+ 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