Examples with BEASTInterface beast.core.BEASTInterface used on opensource projects

Example 61 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BeautiAlignmentProvider method getXMLData.

public static BEASTInterface getXMLData(File file) {
    String xml = "";
    try {
        // parse as BEAST 2 xml fragment
        XMLParser parser = new XMLParser();
        BufferedReader fin = new BufferedReader(new FileReader(file));
        while (fin.ready()) {
            xml += fin.readLine() + "\n";
        }
        fin.close();
        BEASTInterface runnable = parser.parseBareFragment(xml, false);
        BEASTInterface alignment = getAlignment(runnable);
        alignment.initAndValidate();
        return alignment;
    } catch (Exception ex) {
        // attempt to parse as BEAST 1 xml
        try {
            String ID = file.getName();
            ID = ID.substring(0, ID.lastIndexOf('.')).replaceAll("\\..*", "");
            BEASTInterface alignment = parseBeast1XML(ID, xml);
            if (alignment != null) {
                alignment.setID(file.getName().substring(0, file.getName().length() - 4).replaceAll("\\..*", ""));
            }
            return alignment;
        } catch (Exception ex2) {
            ex.printStackTrace();
            JOptionPane.showMessageDialog(null, "Loading of " + file.getName() + " failed: " + ex.getMessage() + "\n" + ex2.getMessage());
        }
        return null;
    }
}

Example 62 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BeautiAlignmentProvider method replaceItem.

@SuppressWarnings({ "rawtypes", "unchecked" })
private void replaceItem(BeautiDoc doc, BEASTInterface oldData, BEASTInterface newData) {
    doc.pluginmap.remove(newData.getID());
    Set<BEASTInterface> outputs = new LinkedHashSet<>();
    outputs.addAll(oldData.getOutputs());
    for (BEASTInterface o : outputs) {
        for (Input i : o.listInputs()) {
            if (i.get() == oldData) {
                i.setValue(newData, o);
            } else if (i.get() != null && i.get() instanceof List) {
                List list = (List) i.get();
                int index = list.indexOf(oldData);
                if (index >= 0) {
                    list.set(index, newData);
                    newData.getOutputs().add(o);
                }
            }
        }
    }
}

Example 63 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class AlignmentListInputEditor method getPartition.

private String getPartition(Input<?> input) {
    BEASTInterface beastObject = (BEASTInterface) input.get();
    String id = beastObject.getID();
    String partition = BeautiDoc.parsePartition(id);
    return partition;
}

Example 64 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class BeautiConnector method isActivated.

/**
 * check that conditions in the 'if' input are met *
 */
public boolean isActivated(PartitionContext partitionContext, List<BEASTInterface> posteriorPredecessors, List<BEASTInterface> likelihoodPredecessors, BeautiDoc doc) {
    if (atInitialisationOnly()) {
        return false;
    }
    if (methodnput.get() != null) {
        // if (method != null) {
        try {
            String fullMethod = methodnput.get();
            String className = fullMethod.substring(0, fullMethod.lastIndexOf('.'));
            String methodName = fullMethod.substring(fullMethod.lastIndexOf('.') + 1);
            Class<?> class_ = Class.forName(className);
            method = class_.getMethod(methodName, BeautiDoc.class);
            method.invoke(null, doc);
        } catch (Exception e) {
        // ignore
        }
    }
    boolean isActive = true;
    for (int i = 0; i < conditionIDs.length; i++) {
        // String id = conditionIDs[i].replaceAll("\\$\\(n\\)", partition);
        String id = BeautiDoc.translatePartitionNames(conditionIDs[i], partitionContext);
        BEASTInterface beastObject = doc.pluginmap.get(id);
        if (beastObject == null) {
            if (conditionOperations[i] != Operation.IS_NOT_AN_OPERTOR) {
                return false;
            }
        // System.err.println("isActivated::no beastObject found");
        }
        // System.err.println("isActivated::found " + id);
        try {
            switch(conditionOperations[i]) {
                case IS_IN_POSTERIOR:
                    if (!posteriorPredecessors.contains(beastObject)) {
                        // System.err.println("isActivated::is not in posterior, return false");
                        return false;
                    }
                    break;
                case IS_IN_LIKELIHOOD:
                    if (!likelihoodPredecessors.contains(beastObject)) {
                        // System.err.println("isActivated::is not in posterior, return false");
                        return false;
                    }
                    break;
                // System.err.println("isActivated::is in posterior");
                case IS_NOT_AN_OPERTOR:
                    List<Operator> operators = ((MCMC) doc.mcmc.get()).operatorsInput.get();
                    if (operators.contains(beastObject)) {
                        return false;
                    }
                    break;
                case EQUALS:
                    final Input<?> input = beastObject.getInput(conditionInputs[i]);
                    // System.err.println("isActivated::input " + input.get().toString() + " expected " + conditionValues[i]);
                    if (input.get() == null) {
                        if (!conditionValues[i].equals("null")) {
                            return false;
                        }
                    } else if (!input.get().toString().equals(conditionValues[i])) {
                        // System.err.println("isActivated::return false");
                        return false;
                    }
                    break;
                case NOT_EQUALS:
                    final Input<?> input2 = beastObject.getInput(conditionInputs[i]);
                    // System.err.println("isActivated::input " + input.get().toString() + " expected " + conditionValues[i]);
                    if (input2.get() == null) {
                        if (conditionValues[i].equals("null")) {
                            return false;
                        }
                    } else if (input2.get().toString().equals(conditionValues[i])) {
                        // System.err.println("isActivated::return false");
                        return false;
                    }
                    break;
                default:
                    throw new IllegalArgumentException("Unexpected operation: " + conditionOperations[i]);
            }
        } catch (Exception e) {
            e.printStackTrace();
            return false;
        }
    }
    // }
    return isActive;
}

Example 65 with BEASTInterface

use of beast.core.BEASTInterface in project beast2 by CompEvol.

the class Beauti method addAlignmentProviderMenus.

private void addAlignmentProviderMenus(JMenu fileMenu) {
    List<BeautiAlignmentProvider> providers = doc.beautiConfig.alignmentProvider;
    for (BeautiAlignmentProvider provider : providers) {
        AbstractAction action = new AbstractAction() {

            private static final long serialVersionUID = 1L;

            @Override
            public void actionPerformed(ActionEvent e) {
                try {
                    setCursor(new Cursor(Cursor.WAIT_CURSOR));
                    // get user-specified alignments
                    List<BEASTInterface> beastObjects = provider.getAlignments(doc);
                    if (beastObjects != null) {
                        for (BEASTInterface o : beastObjects) {
                            if (o instanceof Alignment) {
                                try {
                                    BeautiDoc.createTaxonSet((Alignment) o, doc);
                                } catch (Exception ex) {
                                    ex.printStackTrace();
                                }
                            }
                        }
                    }
                    doc.connectModel();
                    doc.fireDocHasChanged();
                    if (beastObjects != null) {
                        for (BEASTInterface o : beastObjects) {
                            if (o instanceof MRCAPrior) {
                                doc.addMRCAPrior((MRCAPrior) o);
                            }
                        }
                    }
                    a_save.setEnabled(true);
                    a_saveas.setEnabled(true);
                } catch (Exception exx) {
                    exx.printStackTrace();
                    String text = "Something went wrong importing the alignment:\n";
                    JTextArea textArea = new JTextArea(text);
                    textArea.setColumns(30);
                    textArea.setLineWrap(true);
                    textArea.setWrapStyleWord(true);
                    textArea.append(exx.getMessage());
                    textArea.setSize(textArea.getPreferredSize().width, 1);
                    textArea.setOpaque(false);
                    JOptionPane.showMessageDialog(null, textArea, "Error importing alignment", JOptionPane.WARNING_MESSAGE);
                }
                setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
            }
        };
        String providerInfo = provider.toString().replaceAll("Add ", "Add partition for ");
        action.putValue(Action.SHORT_DESCRIPTION, providerInfo);
        action.putValue(Action.LONG_DESCRIPTION, providerInfo);
        action.putValue(Action.NAME, provider.toString());
        fileMenu.add(action);
    }
}