Examples with TaxonSet beast.evolution.alignment.TaxonSet used on opensource projects

Example 11 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class TaxonSetInputEditor method newTaxonSet.

private TaxonSet newTaxonSet(String match) {
    if (getDoc().taxaset.containsKey(match)) {
        Taxon t = doc.taxaset.get(match);
        if (t instanceof TaxonSet) {
            TaxonSet set = (TaxonSet) t;
            set.taxonsetInput.get().clear();
            return set;
        } else {
        // TODO handle situation where taxon and set have same name (issue #135)
        }
    }
    TaxonSet set = new TaxonSet();
    set.setID(match);
    return set;
}

Example 12 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class TaxonSetInputEditor method parseTrait.

void parseTrait(String trait) {
    Map<String, String> traitmap = new HashMap<>();
    for (String line : trait.split(",")) {
        String[] strs = line.split("=");
        if (strs.length == 2) {
            traitmap.put(strs[0].trim(), strs[1].trim());
        }
    }
    m_taxonset.clear();
    Set<Taxon> taxa = new HashSet<>();
    Set<String> taxonIDs = new HashSet<>();
    for (Alignment alignment : getDoc().alignments) {
        if (alignment instanceof FilteredAlignment) {
            alignment = ((FilteredAlignment) alignment).alignmentInput.get();
        }
        for (String id : alignment.getTaxaNames()) {
            if (!taxonIDs.contains(id)) {
                Taxon taxon = getDoc().getTaxon(id);
                taxa.add(taxon);
                taxonIDs.add(id);
            }
        }
    }
    HashMap<String, TaxonSet> map = new HashMap<>();
    List<String> unknowns = new ArrayList<>();
    for (Taxon taxon : taxa) {
        if (!(taxon instanceof TaxonSet)) {
            String match = traitmap.get(taxon.getID());
            if (match == null) {
                match = "UNKNOWN";
                unknowns.add(taxon.getID());
            }
            try {
                if (map.containsKey(match)) {
                    TaxonSet set = map.get(match);
                    set.taxonsetInput.setValue(taxon, set);
                } else {
                    TaxonSet set = newTaxonSet(match);
                    set.taxonsetInput.setValue(taxon, set);
                    map.put(match, set);
                }
            } catch (Exception ex) {
                ex.printStackTrace();
            }
        }
    }
    // add taxon sets
    for (TaxonSet set : map.values()) {
        m_taxonset.add(set);
    }
    if (unknowns.size() > 0) {
        showMisMatchMessage(unknowns);
    }
}

Example 13 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class TaxonSetInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, int itemNr, ExpandOption isExpandOption, boolean addButtons) {
    m_input = input;
    m_beastObject = beastObject;
    this.itemNr = itemNr;
    TaxonSet taxonset = (TaxonSet) m_input.get();
    if (taxonset == null) {
        return;
    }
    List<Taxon> taxonsets = new ArrayList<>();
    List<Taxon> taxa = taxonset.taxonsetInput.get();
    for (Taxon taxon : taxa) {
        taxonsets.add(taxon);
    }
    add(getContent(taxonsets));
    if (taxa.size() == 1 && taxa.get(0).getID().equals("Beauti2DummyTaxonSet") || taxa.size() == 0) {
        taxa.clear();
        try {
            // species is first character of taxon
            guessTaxonSets("(.).*", 0);
            for (Taxon taxonset2 : m_taxonset) {
                for (Taxon taxon : ((TaxonSet) taxonset2).taxonsetInput.get()) {
                    m_lineageset.add(taxon);
                    m_taxonMap.put(taxon.getID(), taxonset2.getID());
                }
            }
        } catch (Exception e) {
            e.printStackTrace();
        }
        taxonSetToModel();
        modelToTaxonset();
    }
}

Example 14 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class MRCAPriorInputEditor method disableTipSampling.

// remove TipDatesRandomWalker from list of operators
private static void disableTipSampling(BEASTInterface m_beastObject, BeautiDoc doc) {
    // First, find the operator
    TipDatesRandomWalker operator = null;
    MRCAPrior prior = (MRCAPrior) m_beastObject;
    TaxonSet taxonset = prior.taxonsetInput.get();
    // However, if there is an TipDatesRandomWalker with taxonset as input, we want to remove it.
    for (BEASTInterface o : taxonset.getOutputs()) {
        if (o instanceof TipDatesRandomWalker) {
            operator = (TipDatesRandomWalker) o;
        }
    }
    if (operator == null) {
        // should never happen
        return;
    }
    // remove from list of operators
    Object o = doc.mcmc.get().getInput("operator");
    if (o instanceof Input<?>) {
        Input<List<Operator>> operatorInput = (Input<List<Operator>>) o;
        List<Operator> operators = operatorInput.get();
        operators.remove(operator);
    }
}

Example 15 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class MRCAPriorInputEditor method init.

@Override
public void init(Input<?> input, BEASTInterface beastObject, final int listItemNr, ExpandOption isExpandOption, boolean addButtons) {
    m_bAddButtons = addButtons;
    m_input = input;
    m_beastObject = beastObject;
    this.itemNr = listItemNr;
    Box itemBox = Box.createHorizontalBox();
    MRCAPrior prior = (MRCAPrior) beastObject;
    String text = prior.getID();
    JButton taxonButton = new JButton(text);
    // taxonButton.setMinimumSize(Base.PREFERRED_SIZE);
    // taxonButton.setPreferredSize(Base.PREFERRED_SIZE);
    itemBox.add(taxonButton);
    taxonButton.addActionListener(e -> {
        List<?> list = (List<?>) m_input.get();
        MRCAPrior prior2 = (MRCAPrior) list.get(itemNr);
        try {
            TaxonSet taxonset = prior2.taxonsetInput.get();
            List<Taxon> originalTaxa = new ArrayList<>();
            originalTaxa.addAll(taxonset.taxonsetInput.get());
            Set<Taxon> candidates = getTaxonCandidates(prior2);
            TaxonSetDialog dlg = new TaxonSetDialog(taxonset, candidates, doc);
            if (dlg.showDialog()) {
                if (dlg.taxonSet.taxonsetInput.get().size() == 0) {
                    JOptionPane.showMessageDialog(doc.beauti, "At least one taxon should be included in the taxon set", "Error specifying taxon set", JOptionPane.ERROR_MESSAGE);
                    taxonset.taxonsetInput.get().addAll(originalTaxa);
                    return;
                }
                prior2.taxonsetInput.setValue(dlg.taxonSet, prior2);
                int i = 1;
                String id = dlg.taxonSet.getID();
                while (doc.pluginmap.containsKey(dlg.taxonSet.getID()) && doc.pluginmap.get(dlg.taxonSet.getID()) != dlg.taxonSet) {
                    dlg.taxonSet.setID(id + i);
                    i++;
                }
                BEASTObjectPanel.addPluginToMap(dlg.taxonSet, doc);
                prior2.setID(dlg.taxonSet.getID() + ".prior");
            }
        } catch (Exception e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
        refreshPanel();
    });
    if (prior.distInput.getType() == null) {
        try {
            prior.distInput.setValue(new OneOnX(), prior);
            prior.distInput.setValue(null, prior);
        } catch (Exception e) {
        // TODO: handle exception
        }
    }
    List<BeautiSubTemplate> availableBEASTObjects = doc.getInputEditorFactory().getAvailableTemplates(prior.distInput, prior, null, doc);
    JComboBox<BeautiSubTemplate> comboBox = new JComboBox<>(availableBEASTObjects.toArray(new BeautiSubTemplate[] {}));
    comboBox.setName(text + ".distr");
    if (prior.distInput.get() != null) {
        String id = prior.distInput.get().getID();
        // id = BeautiDoc.parsePartition(id);
        id = id.substring(0, id.indexOf('.'));
        for (BeautiSubTemplate template : availableBEASTObjects) {
            if (template.classInput.get() != null && template.shortClassName.equals(id)) {
                comboBox.setSelectedItem(template);
            }
        }
    } else {
        comboBox.setSelectedItem(BeautiConfig.NULL_TEMPLATE);
    }
    comboBox.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            @SuppressWarnings("unchecked") JComboBox<BeautiSubTemplate> comboBox = (JComboBox<BeautiSubTemplate>) e.getSource();
            BeautiSubTemplate template = (BeautiSubTemplate) comboBox.getSelectedItem();
            List<?> list = (List<?>) m_input.get();
            MRCAPrior prior = (MRCAPrior) list.get(itemNr);
            // }
            try {
                // BEASTObject beastObject2 =
                template.createSubNet(new PartitionContext(""), prior, prior.distInput, true);
            } catch (Exception e1) {
                e1.printStackTrace();
            }
            refreshPanel();
        }
    });
    itemBox.add(comboBox);
    JCheckBox isMonophyleticdBox = new JCheckBox(doc.beautiConfig.getInputLabel(prior, prior.isMonophyleticInput.getName()));
    isMonophyleticdBox.setName(text + ".isMonophyletic");
    isMonophyleticdBox.setSelected(prior.isMonophyleticInput.get());
    isMonophyleticdBox.setToolTipText(prior.isMonophyleticInput.getHTMLTipText());
    isMonophyleticdBox.addActionListener(new MRCAPriorActionListener(prior));
    itemBox.add(isMonophyleticdBox);
    JButton deleteButton = new SmallButton("-", true);
    deleteButton.setToolTipText("Delete this calibration");
    deleteButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            Log.warning.println("Trying to delete a calibration");
            List<?> list = (List<?>) m_input.get();
            MRCAPrior prior = (MRCAPrior) list.get(itemNr);
            doc.disconnect(prior, "prior", "distribution");
            doc.disconnect(prior, "tracelog", "log");
            if (prior.onlyUseTipsInput.get()) {
                disableTipSampling(m_beastObject, doc);
            }
            doc.unregisterPlugin(prior);
            refreshPanel();
        }
    });
    itemBox.add(Box.createGlue());
    itemBox.add(deleteButton);
    add(itemBox);
}