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

Example 16 with BEASTObject

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

the class BeautiBase method assertPriorsEqual.

void assertPriorsEqual(String... ids) {
    System.err.println("assertPriorsEqual");
    CompoundDistribution prior = (CompoundDistribution) doc.pluginmap.get("prior");
    List<Distribution> priors = prior.pDistributions.get();
    for (String id : ids) {
        boolean found = false;
        for (BEASTObject node : priors) {
            if (node.getID().equals(id)) {
                found = true;
            }
        }
        assertThat(found).as("Could not find beastObject with ID " + id).isEqualTo(true);
    }
    List<String> extras = new ArrayList<>();
    for (BEASTObject node : priors) {
        boolean found = false;
        for (String id : ids) {
            if (node.getID().equals(id)) {
                found = true;
            }
        }
        if (!found) {
            extras.add(node.getID());
        }
    }
    if (extras.size() != 0) {
        System.err.println("Extra ids found: " + Arrays.toString(extras.toArray(new String[] {})));
    }
    assertThat(ids.length).as("list of beastObjects do not match").isEqualTo(priors.size());
    ;
}

Example 17 with BEASTObject

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

the class BeautiBase method pluginListAsString.

private String pluginListAsString(List<?> list) {
    if (list.size() == 0) {
        return "";
    }
    StringBuffer bf = new StringBuffer();
    for (Object o : list) {
        BEASTObject beastObject = (BEASTObject) o;
        bf.append('"');
        bf.append(beastObject.getID());
        bf.append("\", ");
    }
    String str = bf.toString();
    return "(" + str.substring(0, str.length() - 2) + ");";
}

Example 18 with BEASTObject

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

the class BeautiBase method asserListsEqual.

private void asserListsEqual(List<?> list, String[] ids) {
    // check all ids are in list
    for (String id : ids) {
        boolean found = false;
        for (Object o : list) {
            BEASTObject node = (BEASTObject) o;
            if (node.getID().equals(id)) {
                found = true;
                break;
            }
        }
        assertThat(found).as("Could not find beastObject with ID " + id).isEqualTo(true);
    }
    // check all items in list have a unique ie
    Set<String> idsInList = new HashSet<String>();
    Set<String> duplicates = new HashSet<String>();
    for (Object o : list) {
        String id = ((BEASTObject) o).getID();
        if (idsInList.contains(id)) {
            duplicates.add(id);
        } else {
            idsInList.add(id);
        }
    }
    assertThat(duplicates.size()).as("Duplicate ids found: " + Arrays.toString(duplicates.toArray())).isEqualTo(0);
    if (list.size() != ids.length) {
        // list.size > ids.length, otherwise it would have been picked up above
        List<String> extraIDs = new ArrayList<String>();
        for (Object o : list) {
            String id = ((BEASTObject) o).getID();
            boolean found = false;
            for (String id2 : ids) {
                if (id2.equals(id)) {
                    found = true;
                    break;
                }
            }
            if (!found) {
                extraIDs.add(id);
            }
        }
        assertThat(ids.length).as("list of beastObjects do not match: found extra items " + Arrays.toString(extraIDs.toArray())).isEqualTo(list.size());
    }
}

Example 19 with BEASTObject

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

the class BeautiPanelConfig method sync.

@SuppressWarnings("unchecked")
public void sync(int partitionIndex) {
    if (parentInputs.size() > 0 && _input.get() != null) {
        final Input<?> input = parentInputs.get(partitionIndex);
        if (isList) {
            List<Object> list = (List<Object>) _input.get();
            List<Object> targetList = ((List<Object>) input.get());
            // only clear former members
            for (BEASTInterface beastObject : startInputs) {
                targetList.remove(beastObject);
            }
            targetList.addAll(list);
            // sync outputs of items in list
            for (Object o : list) {
                if (o instanceof BEASTInterface) {
                    ((BEASTInterface) o).getOutputs().add(parentBEASTObjects.get(partitionIndex));
                }
            }
        } else {
            try {
                // System.err.println("sync " + parentBEASTObjects.get(partitionIndex) + "[" + input.getName() + "] = " + _input.get());
                input.setValue(_input.get(), parentBEASTObjects.get(partitionIndex));
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 20 with BEASTObject

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

the class BeautiPanelConfig method resolveInput.

/**
 * Find the input associated with this panel
 * based on the path Input.
 */
@SuppressWarnings("unchecked")
public final Input<?> resolveInput(BeautiDoc doc, int partitionIndex) {
    try {
        // if (parentBEASTObjects != null && parentBEASTObjects.size() > 0 && _input != null)
        // System.err.println("sync " + parentBEASTObjects.get(partitionIndex) + "[?] = " + _input.get());
        List<BEASTInterface> beastObjects;
        if (hasPartitionsInput.get() == Partition.none) {
            beastObjects = new ArrayList<>();
            beastObjects.add(doc.mcmc.get());
        } else {
            beastObjects = doc.getPartitions(hasPartitionsInput.get().toString());
        }
        parentBEASTObjects = new ArrayList<>();
        parentInputs = new ArrayList<>();
        parentBEASTObjects.add(doc);
        parentInputs.add(doc.mcmc);
        type = doc.mcmc.getType();
        isList = false;
        for (int i = 0; i < pathComponents.length; i++) {
            List<BEASTInterface> oldPlugins = beastObjects;
            beastObjects = new ArrayList<>();
            parentBEASTObjects = new ArrayList<>();
            parentInputs = new ArrayList<>();
            for (BEASTInterface beastObject : oldPlugins) {
                final Input<?> namedInput = beastObject.getInput(pathComponents[i]);
                type = namedInput.getType();
                if (namedInput.get() instanceof List<?>) {
                    isList = true;
                    List<?> list = (List<?>) namedInput.get();
                    if (conditionalAttribute[i] == null) {
                        for (Object o : list) {
                            BEASTInterface beastObject2 = (BEASTInterface) o;
                            beastObjects.add(beastObject2);
                            parentBEASTObjects.add(beastObject);
                            parentInputs.add(namedInput);
                        }
                    // throw new Exception ("Don't know which element to pick from the list. List component should come with a condition. " + m_sPathComponents[i]);
                    } else {
                        int matches = 0;
                        for (int j = 0; j < list.size(); j++) {
                            BEASTInterface beastObject2 = (BEASTInterface) list.get(j);
                            if (matches(beastObject2, conditionalAttribute[i], conditionalValue[i])) {
                                beastObjects.add(beastObject2);
                                parentBEASTObjects.add(beastObject);
                                parentInputs.add(namedInput);
                                matches++;
                                break;
                            }
                        }
                        if (matches == 0) {
                            parentInputs.add(namedInput);
                            parentBEASTObjects.add(beastObject);
                        }
                    }
                } else if (namedInput.get() instanceof BEASTInterface) {
                    isList = false;
                    if (conditionalAttribute[i] == null) {
                        beastObjects.add((BEASTInterface) namedInput.get());
                        parentBEASTObjects.add(beastObject);
                        parentInputs.add(namedInput);
                    } else {
                        if (matches(beastObject, conditionalAttribute[i], conditionalValue[i])) {
                            // if ((m_sConditionalAttribute[i].equals("id") && beastObject.getID().equals(m_sConditionalValue[i])) ||
                            // (m_sConditionalAttribute[i].equals("type") && beastObject.getClass().getName().equals(m_sConditionalValue[i]))) {
                            beastObjects.add(beastObject);
                            parentBEASTObjects.add(beastObject);
                            parentInputs.add(namedInput);
                        }
                    }
                } else {
                    throw new IllegalArgumentException("input " + pathComponents[i] + "  is not a beastObject or list");
                }
            }
        }
        if (typeInput.get() != null) {
            type = Class.forName(typeInput.get());
        }
        // sanity check
        if (!isList && (hasPartitionsInput.get() == Partition.none) && beastObjects.size() > 1) {
            Log.warning.println("WARNING: multiple beastObjects match, but hasPartitions=none");
            // this makes sure that all mathing beastObjects are available in one go
            isList = true;
            // this suppresses syncing
            parentInputs.clear();
        }
        inputs.clear();
        startInputs.clear();
        for (BEASTInterface beastObject : beastObjects) {
            inputs.add(beastObject);
            startInputs.add(beastObject);
        }
        if (!isList) {
            _input = new FlexibleInput<>();
        } else {
            _input = new FlexibleInput<>(new ArrayList<>());
        }
        _input.setRule(Validate.REQUIRED);
        syncTo(partitionIndex);
        if (isList) {
            checkForDups((List<Object>) _input.get());
        }
        return _input;
    } catch (Exception e) {
        Log.err.println("Warning: could not find objects in path " + Arrays.toString(pathComponents));
    }
    return null;
}