Examples with JTabbedPaneFixture org.fest.swing.fixture.JTabbedPaneFixture used on opensource projects

Example 1 with JTabbedPaneFixture

use of org.fest.swing.fixture.JTabbedPaneFixture in project beast2 by CompEvol.

the class FixedMeanRateTest method testFixedMeanRate.

@Test
public void testFixedMeanRate() throws Exception {
    importAlignment("examples/nexus", new File("26.nex"), new File("29.nex"));
    beautiFrame.menuItemWithPath("Mode", "Automatic set fix mean substitution rate flag").click();
    warning("Setting fixed mean rates");
    JTabbedPaneFixture f = beautiFrame.tabbedPane();
    f = f.selectTab("Site Model");
    beautiFrame.checkBox("mutationRate.isEstimated").check();
    beautiFrame.checkBox("FixMeanMutationRate").check();
    warning("link/unlink site models");
    f.selectTab("Partitions");
    beautiFrame.table().selectCells(TableCell.row(0).column(0), TableCell.row(1).column(0));
    beautiFrame.button("Link Site Models").click();
    beautiFrame.button("Unlink Site Models").click();
    // saveFile("/Users/remcobouckaert/tmp", "x.xml");
    makeSureXMLParses();
    DeltaExchangeOperator operator = (DeltaExchangeOperator) beauti.doc.pluginmap.get("FixMeanMutationRatesOperator");
    int nrOfParameters = operator.parameterInput.get().size();
    if (nrOfParameters != 2) {
        throw new IllegalArgumentException("Expected 2 parameters for deltaExchangeOperator, not " + nrOfParameters);
    }
}

Example 2 with JTabbedPaneFixture

use of org.fest.swing.fixture.JTabbedPaneFixture in project beast2 by CompEvol.

the class FixedMeanRateTest method testFixedMeanRateSharedSiteModel.

@Test
public void testFixedMeanRateSharedSiteModel() throws Exception {
    importAlignment("examples/nexus", new File("26.nex"), new File("29.nex"), new File("47.nex"));
    warning("Setting fixed mean rates");
    JTabbedPaneFixture f = beautiFrame.tabbedPane();
    f = f.selectTab("Site Model");
    beautiFrame.checkBox("mutationRate.isEstimated").check();
    // beautiFrame.checkBox("FixMeanMutationRate").check();
    warning("link/unlink site models");
    f.selectTab("Partitions");
    beautiFrame.table().selectCells(TableCell.row(0).column(1), TableCell.row(1).column(1), TableCell.row(2).column(1));
    beautiFrame.button("Link Site Models").click();
    beautiFrame.button("Unlink Site Models").click();
    DeltaExchangeOperator operator = (DeltaExchangeOperator) beauti.doc.pluginmap.get("FixMeanMutationRatesOperator");
    int nrOfParameters = operator.parameterInput.get().size();
    if (nrOfParameters != 3) {
        throw new IllegalArgumentException("Expected 3 parameters for deltaExchangeOperator, not " + nrOfParameters);
    }
    List<Integer> weights = operator.parameterWeightsInput.get().valuesInput.get();
    Assert.assertEquals(weights.size(), 3);
    Assert.assertEquals(weights.get(0), (Integer) 614);
    Assert.assertEquals(weights.get(1), (Integer) 601);
    Assert.assertEquals(weights.get(2), (Integer) 819);
    beautiFrame.table().selectCells(TableCell.row(0).column(1), TableCell.row(2).column(1));
    beautiFrame.button("Link Site Models").click();
    operator = (DeltaExchangeOperator) beauti.doc.pluginmap.get("FixMeanMutationRatesOperator");
    nrOfParameters = operator.parameterInput.get().size();
    if (nrOfParameters != 2) {
        throw new IllegalArgumentException("Expected 2 parameters for deltaExchangeOperator, not " + nrOfParameters);
    }
    weights = operator.parameterWeightsInput.get().valuesInput.get();
    Assert.assertEquals(weights.size(), 2);
    Assert.assertEquals(weights.get(0), (Integer) (614 + 819));
    Assert.assertEquals(weights.get(1), (Integer) 601);
    makeSureXMLParses();
}

Example 3 with JTabbedPaneFixture

use of org.fest.swing.fixture.JTabbedPaneFixture in project beast2 by CompEvol.

the class BeautiSimpleTest method simpleTest.

@Test
public void simpleTest() throws Exception {
    importAlignment("examples/nexus", new File("anolis.nex"));
    // load anolis.nex
    JTabbedPaneFixture f = beautiFrame.tabbedPane();
    f.requireVisible();
    f.requireTitle("Partitions", Index.atIndex(0));
    String[] titles = f.tabTitles();
    assertArrayEquals(titles, "[Partitions, Tip Dates, Site Model, Clock Model, Priors, MCMC]");
    System.err.println(Arrays.toString(titles));
    f = f.selectTab("Partitions");
    JTableFixture t = beautiFrame.table();
    String[][] tc = t.contents();
    System.err.println(Arrays.toString(tc[0]));
    assertArrayEquals(tc[0], "[anolis, anolis, 29, 1456, nucleotide, anolis, anolis, anolis, false]");
    assertThat(f).isNotNull();
    assertStateEquals("Tree.t:anolis", "birthRate.t:anolis");
    assertOperatorsEqual("YuleBirthRateScaler.t:anolis", "YuleModelTreeScaler.t:anolis", "YuleModelTreeRootScaler.t:anolis", "YuleModelUniformOperator.t:anolis", "YuleModelSubtreeSlide.t:anolis", "YuleModelNarrow.t:anolis", "YuleModelWide.t:anolis", "YuleModelWilsonBalding.t:anolis");
    assertPriorsEqual("YuleModel.t:anolis", "YuleBirthRatePrior.t:anolis");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.anolis", "TreeHeight.t:anolis", "YuleModel.t:anolis", "birthRate.t:anolis");
    ScreenshotTaker screenshotTaker = new ScreenshotTaker();
    (new File("/tmp/simpleTest1.png")).delete();
    (new File("/tmp/simpleTest2.png")).delete();
    (new File("/tmp/simpleTest3.png")).delete();
    (new File("/tmp/simpleTest4.png")).delete();
    screenshotTaker.saveComponentAsPng(beauti.frame, "/tmp/simpleTest1.png");
    // Set the site model to HKY (estimated)
    f.selectTab("Site Model");
    JComboBoxFixture substModel = beautiFrame.comboBox("substModel");
    substModel.selectItem("HKY");
    printBeautiState(f);
    assertStateEquals("Tree.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "freqParameter.s:anolis");
    assertOperatorsEqual("YuleBirthRateScaler.t:anolis", "YuleModelTreeScaler.t:anolis", "YuleModelTreeRootScaler.t:anolis", "YuleModelUniformOperator.t:anolis", "YuleModelSubtreeSlide.t:anolis", "YuleModelNarrow.t:anolis", "YuleModelWide.t:anolis", "YuleModelWilsonBalding.t:anolis", "KappaScaler.s:anolis", "FrequenciesExchanger.s:anolis");
    assertPriorsEqual("YuleModel.t:anolis", "YuleBirthRatePrior.t:anolis", "KappaPrior.s:anolis");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.anolis", "TreeHeight.t:anolis", "YuleModel.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "freqParameter.s:anolis");
    // Set the site model to HKY (G4) (estimated)
    f.selectTab("Site Model");
    JTextComponentFixture categoryCount = beautiFrame.textBox("gammaCategoryCount");
    categoryCount.setText("4");
    printBeautiState(f);
    // assertStateEquals("Tree.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "freqParameter.s:anolis");
    // assertOperatorsEqual("YuleBirthRateScaler.t:anolis", "YuleModelTreeScaler.t:anolis", "YuleModelTreeRootScaler.t:anolis", "YuleModelUniformOperator.t:anolis", "YuleModelSubtreeSlide.t:anolis", "YuleModelNarrow.t:anolis", "YuleModelWide.t:anolis", "YuleModelWilsonBalding.t:anolis", "KappaScaler.s:anolis", "FrequenciesExchanger.s:anolis");
    // assertPriorsEqual("YuleModel.t:anolis", "YuleBirthRatePrior.t:anolis", "KappaPrior.s:anolis");
    // assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.anolis", "TreeHeight.t:anolis", "YuleModel.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "freqParameter.s:anolis");
    // 
    // f.selectTab("Site Model");
    // JCheckBoxFixture shapeIsEstimated = beautiFrame.checkBox("shape.isEstimated");
    // shapeIsEstimated.check();
    // printBeautiState(f);
    assertStateEquals("Tree.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "gammaShape.s:anolis", "freqParameter.s:anolis");
    assertOperatorsEqual("YuleBirthRateScaler.t:anolis", "YuleModelTreeScaler.t:anolis", "YuleModelTreeRootScaler.t:anolis", "YuleModelUniformOperator.t:anolis", "YuleModelSubtreeSlide.t:anolis", "YuleModelNarrow.t:anolis", "YuleModelWide.t:anolis", "YuleModelWilsonBalding.t:anolis", "KappaScaler.s:anolis", "gammaShapeScaler.s:anolis", "FrequenciesExchanger.s:anolis");
    assertPriorsEqual("YuleModel.t:anolis", "YuleBirthRatePrior.t:anolis", "KappaPrior.s:anolis", "GammaShapePrior.s:anolis");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.anolis", "TreeHeight.t:anolis", "YuleModel.t:anolis", "birthRate.t:anolis", "kappa.s:anolis", "gammaShape.s:anolis", "freqParameter.s:anolis");
    screenshotTaker.saveComponentAsPng(beauti.frame, "/tmp/simpleTest2.png");
    // rename tree from 'anolis' to 'tree'
    f.selectTab("Partitions");
    JTableCellFixture cell = beautiFrame.table().cell(TableCell.row(0).column(7));
    Component editor = cell.editor();
    JComboBoxFixture comboBox = new JComboBoxFixture(robot(), (JComboBox<?>) editor);
    cell.startEditing();
    comboBox.selectAllText();
    comboBox.enterText("tree");
    comboBox.pressAndReleaseKeys(KeyEvent.VK_ENTER);
    cell.stopEditing();
    printBeautiState(f);
    assertStateEquals("Tree.t:tree", "birthRate.t:tree", "kappa.s:anolis", "gammaShape.s:anolis", "freqParameter.s:anolis");
    assertOperatorsEqual("YuleBirthRateScaler.t:tree", "YuleModelTreeScaler.t:tree", "YuleModelTreeRootScaler.t:tree", "YuleModelUniformOperator.t:tree", "YuleModelSubtreeSlide.t:tree", "YuleModelNarrow.t:tree", "YuleModelWide.t:tree", "YuleModelWilsonBalding.t:tree", "KappaScaler.s:anolis", "gammaShapeScaler.s:anolis", "FrequenciesExchanger.s:anolis");
    assertPriorsEqual("YuleModel.t:tree", "YuleBirthRatePrior.t:tree", "GammaShapePrior.s:anolis", "KappaPrior.s:anolis");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.anolis", "TreeHeight.t:tree", "YuleModel.t:tree", "birthRate.t:tree", "kappa.s:anolis", "gammaShape.s:anolis", "freqParameter.s:anolis");
    screenshotTaker.saveComponentAsPng(beauti.frame, "/tmp/simpleTest3.png");
    // Create a Normal calibration prior and monophyletic constraint on Human-Chimp split of 6 +/- 0.5.
    f.selectTab("Priors");
    screenshotTaker.saveComponentAsPng(beauti.frame, "/tmp/simpleTest4.png");
    makeSureXMLParses();
}

Example 4 with JTabbedPaneFixture

use of org.fest.swing.fixture.JTabbedPaneFixture in project beast2 by CompEvol.

the class CloneTest method simpleSiteModelCloneTest.

@Test
public void simpleSiteModelCloneTest() throws Exception {
    warning("0. Load primate-mtDNA.nex");
    importAlignment("examples/nexus", new File("primate-mtDNA.nex"));
    JTabbedPaneFixture f = beautiFrame.tabbedPane();
    // may need to use the following when not running on Hudson
    // JOptionPaneFixture op = beautiFrame.optionPane();
    // if (op.target.isVisible()) {
    // op.okButton().click();
    // }
    // 1. Set the site model to HKY+G4 (estimated)
    warning("1. Set the site model of first partition to HKY+G4 (estimated)");
    f.selectTab("Site Model");
    JComboBoxFixture substModel = beautiFrame.comboBox("substModel");
    substModel.selectItem("HKY");
    JTextComponentFixture categoryCount = beautiFrame.textBox("gammaCategoryCount");
    categoryCount.setText("4");
    JCheckBoxFixture shapeIsEstimated = beautiFrame.checkBox("shape.isEstimated");
    shapeIsEstimated.check();
    printBeautiState(f);
    assertStateEquals("Tree.t:coding", "birthRate.t:coding", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
    assertOperatorsEqual("YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "FrequenciesExchanger.s:coding");
    assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "kappa.s:coding", "gammaShape.s:coding", "freqParameter.s:coding");
    // 2. select all models, clone from first model
    warning("2. select all models, clone from first model");
    JListFixture partitionlist = beautiFrame.list("listOfPartitions");
    partitionlist.selectItems(0, 1, 2, 3, 4);
    JButtonFixture cloneButton = beautiFrame.button("ok");
    cloneButton.click();
    printBeautiState(f);
    assertStateEquals("Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "Tree.t:coding", "birthRate.t:coding", "Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
    assertOperatorsEqual("StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:noncoding", "gammaShapeScaler.s:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:3rdpos", "KappaScaler.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:noncoding", "FrequenciesExchanger.s:coding");
    assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "YuleBirthRatePrior.t:coding", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "KappaPrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:noncoding", "gammaShape.s:1stpos", "kappa.s:1stpos", "gammaShape.s:2ndpos", "kappa.s:2ndpos", "gammaShape.s:3rdpos", "kappa.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:noncoding", "freqParameter.s:coding");
    // 3. set second model back to JC
    warning("3. select all models, clone from first model");
    partitionlist.selectItems(1);
    beautiFrame.comboBox("substModel").selectItem("JC69");
    beautiFrame.textBox("gammaCategoryCount").setText("6");
    printBeautiState(f);
    assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
    assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "gammaShapeScaler.s:noncoding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
    assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:noncoding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "gammaShape.s:noncoding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
    // set category count back to 1
    beautiFrame.checkBox("shape.isEstimated").uncheck();
    beautiFrame.textBox("gammaCategoryCount").setText("1");
    printBeautiState(f);
    assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
    assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:coding", "gammaShapeScaler.s:coding", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos", "FrequenciesExchanger.s:coding");
    assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "KappaPrior.s:coding", "GammaShapePrior.s:coding", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:coding", "gammaShape.s:coding", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos", "freqParameter.s:coding");
    // 4. clone second model to first model
    warning("4. clone second model to first model");
    beautiFrame.list("listOfPartitions").selectItems(0, 1);
    beautiFrame.comboBox().selectItem(1);
    beautiFrame.button("ok").click();
    printBeautiState(f);
    assertStateEquals("Tree.t:3rdpos", "clockRate.c:3rdpos", "birthRate.t:3rdpos", "Tree.t:2ndpos", "clockRate.c:2ndpos", "birthRate.t:2ndpos", "Tree.t:noncoding", "clockRate.c:noncoding", "birthRate.t:noncoding", "Tree.t:coding", "birthRate.t:coding", "Tree.t:1stpos", "clockRate.c:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
    assertOperatorsEqual("StrictClockRateScaler.c:3rdpos", "YuleBirthRateScaler.t:3rdpos", "YuleModelTreeScaler.t:3rdpos", "YuleModelTreeRootScaler.t:3rdpos", "YuleModelUniformOperator.t:3rdpos", "YuleModelSubtreeSlide.t:3rdpos", "YuleModelNarrow.t:3rdpos", "YuleModelWide.t:3rdpos", "YuleModelWilsonBalding.t:3rdpos", "strictClockUpDownOperator.c:3rdpos", "StrictClockRateScaler.c:2ndpos", "YuleBirthRateScaler.t:2ndpos", "YuleModelTreeScaler.t:2ndpos", "YuleModelTreeRootScaler.t:2ndpos", "YuleModelUniformOperator.t:2ndpos", "YuleModelSubtreeSlide.t:2ndpos", "YuleModelNarrow.t:2ndpos", "YuleModelWide.t:2ndpos", "YuleModelWilsonBalding.t:2ndpos", "strictClockUpDownOperator.c:2ndpos", "StrictClockRateScaler.c:noncoding", "YuleBirthRateScaler.t:noncoding", "YuleModelTreeScaler.t:noncoding", "YuleModelTreeRootScaler.t:noncoding", "YuleModelUniformOperator.t:noncoding", "YuleModelSubtreeSlide.t:noncoding", "YuleModelNarrow.t:noncoding", "YuleModelWide.t:noncoding", "YuleModelWilsonBalding.t:noncoding", "strictClockUpDownOperator.c:noncoding", "YuleBirthRateScaler.t:coding", "YuleModelTreeScaler.t:coding", "YuleModelTreeRootScaler.t:coding", "YuleModelUniformOperator.t:coding", "YuleModelSubtreeSlide.t:coding", "YuleModelNarrow.t:coding", "YuleModelWide.t:coding", "YuleModelWilsonBalding.t:coding", "StrictClockRateScaler.c:1stpos", "YuleBirthRateScaler.t:1stpos", "YuleModelTreeScaler.t:1stpos", "YuleModelTreeRootScaler.t:1stpos", "YuleModelUniformOperator.t:1stpos", "YuleModelSubtreeSlide.t:1stpos", "YuleModelNarrow.t:1stpos", "YuleModelWide.t:1stpos", "YuleModelWilsonBalding.t:1stpos", "strictClockUpDownOperator.c:1stpos", "KappaScaler.s:1stpos", "gammaShapeScaler.s:1stpos", "KappaScaler.s:2ndpos", "gammaShapeScaler.s:2ndpos", "KappaScaler.s:3rdpos", "gammaShapeScaler.s:3rdpos", "FrequenciesExchanger.s:2ndpos", "FrequenciesExchanger.s:3rdpos", "FrequenciesExchanger.s:1stpos");
    assertPriorsEqual("YuleModel.t:coding", "YuleModel.t:noncoding", "YuleModel.t:1stpos", "YuleModel.t:2ndpos", "YuleModel.t:3rdpos", "ClockPrior.c:3rdpos", "YuleBirthRatePrior.t:3rdpos", "ClockPrior.c:2ndpos", "YuleBirthRatePrior.t:2ndpos", "ClockPrior.c:noncoding", "YuleBirthRatePrior.t:noncoding", "YuleBirthRatePrior.t:coding", "ClockPrior.c:1stpos", "YuleBirthRatePrior.t:1stpos", "GammaShapePrior.s:1stpos", "KappaPrior.s:1stpos", "GammaShapePrior.s:2ndpos", "KappaPrior.s:2ndpos", "GammaShapePrior.s:3rdpos", "KappaPrior.s:3rdpos");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.3rdpos", "TreeHeight.t:3rdpos", "clockRate.c:3rdpos", "YuleModel.t:3rdpos", "birthRate.t:3rdpos", "treeLikelihood.2ndpos", "TreeHeight.t:2ndpos", "clockRate.c:2ndpos", "YuleModel.t:2ndpos", "birthRate.t:2ndpos", "treeLikelihood.noncoding", "TreeHeight.t:noncoding", "clockRate.c:noncoding", "YuleModel.t:noncoding", "birthRate.t:noncoding", "treeLikelihood.coding", "TreeHeight.t:coding", "YuleModel.t:coding", "birthRate.t:coding", "treeLikelihood.1stpos", "TreeHeight.t:1stpos", "clockRate.c:1stpos", "YuleModel.t:1stpos", "birthRate.t:1stpos", "kappa.s:1stpos", "gammaShape.s:1stpos", "kappa.s:2ndpos", "gammaShape.s:2ndpos", "kappa.s:3rdpos", "gammaShape.s:3rdpos", "freqParameter.s:2ndpos", "freqParameter.s:3rdpos", "freqParameter.s:1stpos");
    makeSureXMLParses();
}

Example 5 with JTabbedPaneFixture

use of org.fest.swing.fixture.JTabbedPaneFixture in project beast2 by CompEvol.

the class LinkUnlinkTest method simpleLinkUnlinkTwoAlignmentTest.

@Test
public void simpleLinkUnlinkTwoAlignmentTest() throws Exception {
    warning("Load gopher data 26.nex, 47.nex");
    importAlignment("examples/nexus", new File("26.nex"), new File("47.nex"));
    JTabbedPaneFixture f = beautiFrame.tabbedPane();
    printBeautiState(f);
    selectRows(0, 1);
    warning("Link site models");
    f.selectTab("Partitions");
    beautiFrame.button("Link Site Models").click();
    printBeautiState(f);
    warning("Unlink site models");
    f.selectTab("Partitions");
    beautiFrame.button("Unlink Site Models").click();
    printBeautiState(f);
    assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
    assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
    assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
    warning("Link clock models");
    f.selectTab("Partitions");
    beautiFrame.button("Link Clock Models").click();
    printBeautiState(f);
    warning("Unlink clock models");
    f.selectTab("Partitions");
    beautiFrame.button("Unlink Clock Models").click();
    printBeautiState(f);
    assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
    assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
    assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
    warning("Link trees");
    f.selectTab("Partitions");
    beautiFrame.button("Link Trees").click();
    printBeautiState(f);
    warning("Unlink trees");
    f.selectTab("Partitions");
    beautiFrame.button("Unlink Trees").click();
    printBeautiState(f);
    assertStateEquals("Tree.t:26", "birthRate.t:26", "Tree.t:47", "clockRate.c:47", "birthRate.t:47");
    assertOperatorsEqual("YuleBirthRateScaler.t:26", "YuleModelTreeScaler.t:26", "YuleModelTreeRootScaler.t:26", "YuleModelUniformOperator.t:26", "YuleModelSubtreeSlide.t:26", "YuleModelNarrow.t:26", "YuleModelWide.t:26", "YuleModelWilsonBalding.t:26", "StrictClockRateScaler.c:47", "YuleBirthRateScaler.t:47", "YuleModelTreeScaler.t:47", "YuleModelTreeRootScaler.t:47", "YuleModelUniformOperator.t:47", "YuleModelSubtreeSlide.t:47", "YuleModelNarrow.t:47", "YuleModelWide.t:47", "YuleModelWilsonBalding.t:47", "strictClockUpDownOperator.c:47");
    assertPriorsEqual("YuleModel.t:26", "YuleBirthRatePrior.t:26", "YuleModel.t:47", "ClockPrior.c:47", "YuleBirthRatePrior.t:47");
    assertTraceLogEqual("posterior", "likelihood", "prior", "treeLikelihood.26", "TreeHeight.t:26", "YuleModel.t:26", "birthRate.t:26", "treeLikelihood.47", "TreeHeight.t:47", "clockRate.c:47", "YuleModel.t:47", "birthRate.t:47");
    makeSureXMLParses();
}