Examples with PartitionTreeModel dr.app.beauti.options.PartitionTreeModel used on opensource projects

Example 1 with PartitionTreeModel

use of dr.app.beauti.options.PartitionTreeModel in project beast-mcmc by beast-dev.

the class TaxonSetPanel method setCurrentTaxonSet.

protected void setCurrentTaxonSet(Taxa taxonSet) {
    this.currentTaxonSet = taxonSet;
    includedTaxa.clear();
    excludedTaxa.clear();
    if (currentTaxonSet != null) {
        for (int i = 0; i < taxonSet.getTaxonCount(); i++) {
            includedTaxa.add(taxonSet.getTaxon(i));
        }
        Collections.sort(includedTaxa);
        // get taxa associated to each tree
        PartitionTreeModel treeModel = options.taxonSetsTreeModel.get(currentTaxonSet);
        TaxonList alignment = options.getDataPartitions(treeModel).get(0).getTaxonList();
        Taxa taxa = new Taxa(alignment);
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            excludedTaxa.add(taxa.getTaxon(i));
        }
        excludedTaxa.removeAll(includedTaxa);
        Collections.sort(excludedTaxa);
    }
    setTaxonSetTitle();
    setupTaxonSetsComboBoxes();
    includedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTableModel.fireTableDataChanged();
}

Example 2 with PartitionTreeModel

use of dr.app.beauti.options.PartitionTreeModel in project beast-mcmc by beast-dev.

the class TMRCAStatisticsGenerator method writeTMRCAStatistics.

/**
     * Generate tmrca statistics
     *
     * @param writer       the writer
     */
public void writeTMRCAStatistics(XMLWriter writer) {
    List<Taxa> taxonSets;
    Map<Taxa, Boolean> taxonSetsMono;
    if (options.useStarBEAST) {
        taxonSets = options.speciesSets;
        taxonSetsMono = options.speciesSetsMono;
        writer.writeComment("Species Sets");
        writer.writeText("");
        for (Taxa taxa : taxonSets) {
            writer.writeOpenTag(TMRCAStatisticParser.TMRCA_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "tmrca(" + taxa.getId() + ")") });
            // make tmrca(tree.name) eay to read in log for Tracer
            writer.writeOpenTag(TMRCAStatisticParser.MRCA);
            writer.writeIDref(TaxaParser.TAXA, taxa.getId());
            writer.writeCloseTag(TMRCAStatisticParser.MRCA);
            writer.writeIDref(SpeciesTreeModelParser.SPECIES_TREE, SP_TREE);
            writer.writeCloseTag(TMRCAStatisticParser.TMRCA_STATISTIC);
            if (taxonSetsMono.get(taxa)) {
                //                    && treeModel.getPartitionTreePrior().getNodeHeightPrior() != TreePriorType.YULE
                //                    && options.getKeysFromValue(options.taxonSetsTreeModel, treeModel).size() > 1) {
                writer.writeOpenTag(MonophylyStatisticParser.MONOPHYLY_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "monophyly(" + taxa.getId() + ")") });
                writer.writeOpenTag(MonophylyStatisticParser.MRCA);
                writer.writeIDref(TaxaParser.TAXA, taxa.getId());
                writer.writeCloseTag(MonophylyStatisticParser.MRCA);
                writer.writeIDref(SpeciesTreeModelParser.SPECIES_TREE, SP_TREE);
                writer.writeCloseTag(MonophylyStatisticParser.MONOPHYLY_STATISTIC);
            }
        }
    } else {
        taxonSets = options.taxonSets;
        taxonSetsMono = options.taxonSetsMono;
        writer.writeComment("Taxon Sets");
        writer.writeText("");
        for (Taxa taxa : taxonSets) {
            PartitionTreeModel treeModel = options.taxonSetsTreeModel.get(taxa);
            writer.writeOpenTag(TMRCAStatisticParser.TMRCA_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "tmrca(" + treeModel.getPrefix() + taxa.getId() + ")"), new Attribute.Default<Boolean>(TMRCAStatisticParser.STEM, options.taxonSetsIncludeStem.get(taxa)) });
            // make tmrca(tree.name) eay to read in log for Tracer
            writer.writeOpenTag(TMRCAStatisticParser.MRCA);
            writer.writeIDref(TaxaParser.TAXA, taxa.getId());
            writer.writeCloseTag(TMRCAStatisticParser.MRCA);
            writer.writeIDref(TreeModel.TREE_MODEL, treeModel.getPrefix() + TreeModel.TREE_MODEL);
            writer.writeCloseTag(TMRCAStatisticParser.TMRCA_STATISTIC);
            if (taxonSetsMono.get(taxa)) {
                //                    && treeModel.getPartitionTreePrior().getNodeHeightPrior() != TreePriorType.YULE
                //                    && options.getKeysFromValue(options.taxonSetsTreeModel, treeModel).size() > 1) {
                writer.writeOpenTag(MonophylyStatisticParser.MONOPHYLY_STATISTIC, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, "monophyly(" + taxa.getId() + ")") });
                writer.writeOpenTag(MonophylyStatisticParser.MRCA);
                writer.writeIDref(TaxaParser.TAXA, taxa.getId());
                writer.writeCloseTag(MonophylyStatisticParser.MRCA);
                writer.writeIDref(TreeModel.TREE_MODEL, treeModel.getPrefix() + TreeModel.TREE_MODEL);
                writer.writeCloseTag(MonophylyStatisticParser.MONOPHYLY_STATISTIC);
            }
        }
    }
}

Example 3 with PartitionTreeModel

use of dr.app.beauti.options.PartitionTreeModel in project beast-mcmc by beast-dev.

the class PartitionTreePriorPanel method setupPanel.

private void setupPanel() {
    removeAll();
    JTextArea citationText = new JTextArea(1, 40);
    citationText.setLineWrap(true);
    citationText.setWrapStyleWord(true);
    citationText.setEditable(false);
    citationText.setFont(this.getFont());
    citationText.setOpaque(false);
    //        citationText.setBackground(this.getBackground());
    //        JScrollPane scrollPane = new JScrollPane(citation, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
    //                    JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
    //        scrollPane.setOpaque(true);
    String calYule = "Heled J, Drummond AJ (2011), Syst Biol, doi: 10.1093/sysbio/syr087 [Calibrated Yule]";
    String citation;
    if (treePriorCombo.getSelectedItem() == TreePriorType.SPECIES_YULE || treePriorCombo.getSelectedItem() == TreePriorType.SPECIES_YULE_CALIBRATION || treePriorCombo.getSelectedItem() == TreePriorType.SPECIES_BIRTH_DEATH) {
        //*BEAST
        addComponentWithLabel("Species Tree Prior:", treePriorCombo);
        addComponentWithLabel("Population Size Model:", populationSizeCombo);
        addLabel("Note: *BEAST only needs to select the prior for species tree.");
        if (treePriorCombo.getSelectedItem() == TreePriorType.SPECIES_YULE_CALIBRATION) {
            //                addComponentWithLabel("Calibration Correction Type:", calibrationCorrectionCombo);
            citation = calYule;
            addComponentWithLabel("Citation:", citationText);
            citationText.setText(citation);
        }
    } else {
        // non *BEAST
        String citationCoalescent = "Kingman JFC (1982) Stoch Proc Appl 13, 235-248 [Constant Coalescent].";
        addComponentWithLabel("Tree Prior:", treePriorCombo);
        if (!treesPanel.linkTreePriorCheck.isEnabled()) {
            treesPanel.updateLinkTreePriorEnablility();
        }
        switch((TreePriorType) treePriorCombo.getSelectedItem()) {
            case CONSTANT:
                citation = citationCoalescent;
                break;
            case EXPONENTIAL:
            case LOGISTIC:
            case EXPANSION:
                addComponentWithLabel("Parameterization for growth:", parameterizationCombo);
                partitionTreePrior.setParameterization((TreePriorParameterizationType) parameterizationCombo.getSelectedItem());
                //citationCoalescent +  "\n" +
                citation = "Griffiths RC, Tavare S (1994) Phil Trans R Soc Lond B Biol Sci 344, 403-410 [Parametric Coalescent].";
                //                        + "\nDrummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Mol Biol Evol 22, 1185-1192.";
                break;
            case SKYLINE:
                groupCountField.setColumns(6);
                addComponentWithLabel("Number of groups:", groupCountField);
                addComponentWithLabel("Skyline Model:", bayesianSkylineCombo);
                //citationCoalescent + "\n" +
                citation = "Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Mol Biol Evol 22, 1185-1192 [Skyline Coalescent].";
                break;
            case EXTENDED_SKYLINE:
                addComponentWithLabel("Model Type:", extendedBayesianSkylineCombo);
                treesPanel.linkTreePriorCheck.setSelected(true);
                treesPanel.linkTreePriorCheck.setEnabled(false);
                treesPanel.updateShareSameTreePriorChanged();
                //citationCoalescent + "\n" +
                citation = "Heled J, Drummond AJ (2008) BMC Evol Biol 8, 289 [Extended Skyline Coalescent].";
                break;
            case GMRF_SKYRIDE:
                addComponentWithLabel("Smoothing:", gmrfBayesianSkyrideCombo);
                treesPanel.linkTreePriorCheck.setSelected(true);
                treesPanel.linkTreePriorCheck.setEnabled(false);
                //For GMRF, one tree prior has to be associated to one tree model. The validation is in BeastGenerator.checkOptions()
                addLabel("<html>For the Skyride, tree model/tree prior combination not implemented by BEAST. " + "The Skyride is only available for a single tree<br>model partition in this release. " + "Please try the Skygrid or link all tree models." + "</html>");
                //citationCoalescent + "\n" +
                citation = "Minin VN, Bloomquist EW, Suchard MA (2008) Mol Biol Evol 25, 1459-1471 [Skyride Coalescent].";
                break;
            case SKYGRID:
                skyGridInterval.setColumns(6);
                addComponentWithLabel("# parameters ( = # grid-points + 1):", skyGridPointsCombo);
                addComponentWithLabel("Time at last point:", skyGridInterval);
                addLabel("It is advisable to set this cut-off time commensurate with the expected root height for optimal model interpretability.");
                treesPanel.linkTreePriorCheck.setSelected(true);
                treesPanel.linkTreePriorCheck.setEnabled(false);
                treesPanel.updateShareSameTreePriorChanged();
                //citationCoalescent + "\n" +
                citation = "Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA (2013) Mol Biol Evol 30, 713-724 [SkyGrid Coalescent].";
                break;
            case YULE:
                citation = "Gernhard T (2008) J Theor Biol 253, 769-778 [Yule Process]." + "\nYule GU (1925) Phil Trans R Soc Lond B Biol Sci 213, 21-87 [Yule Process].";
                break;
            case YULE_CALIBRATION:
                //                    addComponentWithLabel("Calibration Correction Type:", calibrationCorrectionCombo);
                citation = calYule;
                break;
            case BIRTH_DEATH:
                citation = BirthDeathModelParser.getCitation();
                break;
            case BIRTH_DEATH_INCOMPLETE_SAMPLING:
                citation = BirthDeathModelParser.getCitationRHO();
                break;
            case BIRTH_DEATH_SERIAL_SAMPLING:
                citation = BirthDeathSerialSamplingModelParser.getCitationPsiOrg();
                break;
            case BIRTH_DEATH_BASIC_REPRODUCTIVE_NUMBER:
                citation = BirthDeathSerialSamplingModelParser.getCitationRT();
                break;
            default:
                throw new RuntimeException("No such tree prior has been specified so cannot refer to it");
        }
        if (treesPanel.options.maximumTipHeight > 0)
            citation = citation + //                    "Rodrigo AG, Felsenstein J (1999) in Molecular Evolution of HIV (Crandall K), pp. 233-272 [Serially Sampled Data]."
            "\n" + "Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Genetics 161, 1307-1320 [Serially Sampled Data].";
        addComponentWithLabel("Citation:", citationText);
        citationText.setText(citation);
    }
    //        treesPanel.treeModelPanels.get(treesPanel.currentTreeModel).setOptions();
    for (PartitionTreeModel model : treesPanel.treeModelPanels.keySet()) {
        if (model != null) {
            treesPanel.treeModelPanels.get(model).setOptions();
            treesPanel.treeModelPanels.get(model).setupPanel();
        }
    }
    //        createTreeAction.setEnabled(options != null && options.dataPartitions.size() > 0);
    //        fireTableDataChanged();
    validate();
    repaint();
}

Example 4 with PartitionTreeModel

use of dr.app.beauti.options.PartitionTreeModel in project beast-mcmc by beast-dev.

the class MCMCPanel method updateTreeFileNameList.

private void updateTreeFileNameList() {
    options.treeFileName.clear();
    options.substTreeFileName.clear();
    String treeFileName;
    for (PartitionTreeModel tree : options.getPartitionTreeModels()) {
        if (options.substTreeLog) {
            treeFileName = getTreeFileName(tree.getPrefix() + "(time).");
        } else {
            treeFileName = getTreeFileName(tree.getPrefix());
        }
        if (addTxt.isSelected())
            treeFileName = treeFileName + ".txt";
        options.treeFileName.add(treeFileName);
        if (options.substTreeLog) {
            treeFileName = getTreeFileName(tree.getPrefix() + "(subst).");
            if (addTxt.isSelected())
                treeFileName = treeFileName + ".txt";
            options.substTreeFileName.add(treeFileName);
        }
    }
    if (options.useStarBEAST) {
        treeFileName = options.fileNameStem + "." + options.starBEASTOptions.SPECIES_TREE_FILE_NAME;
        if (addTxt.isSelected())
            treeFileName = treeFileName + ".txt";
        options.treeFileName.add(treeFileName);
    //TODO: species sub tree
    }
}

Example 5 with PartitionTreeModel

use of dr.app.beauti.options.PartitionTreeModel in project beast-mcmc by beast-dev.

the class STARBEASTGenerator method writeGeneTrees.

private void writeGeneTrees(XMLWriter writer) {
    writer.writeComment("Collection of Gene Trees");
    writer.writeOpenTag(SpeciesBindingsParser.GENE_TREES, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, SpeciesBindingsParser.GENE_TREES) });
    boolean isSameAllPloidyType = true;
    PloidyType checkSamePloidyType = options.getPartitionTreeModels().get(0).getPloidyType();
    for (PartitionTreeModel model : options.getPartitionTreeModels()) {
        if (checkSamePloidyType != model.getPloidyType()) {
            isSameAllPloidyType = false;
            break;
        }
    }
    if (isSameAllPloidyType) {
        // generate gene trees regarding each data partition
        for (PartitionTreeModel model : options.getPartitionTreeModels()) {
            writer.writeIDref(TreeModel.TREE_MODEL, model.getPrefix() + TreeModel.TREE_MODEL);
        }
    } else {
        // give ploidy
        for (PartitionTreeModel model : options.getPartitionTreeModels()) {
            writer.writeOpenTag(SpeciesBindingsParser.GTREE, new Attribute[] { new Attribute.Default<String>(SpeciesBindingsParser.PLOIDY, Double.toString(model.getPloidyType().getValue())) });
            writer.writeIDref(TreeModel.TREE_MODEL, model.getPrefix() + TreeModel.TREE_MODEL);
            writer.writeCloseTag(SpeciesBindingsParser.GTREE);
        }
    }
    writer.writeCloseTag(SpeciesBindingsParser.GENE_TREES);
}