Examples with Conversion bacter.Conversion used on opensource projects

Example 21 with Conversion

use of bacter.Conversion in project bacter by tgvaughan.

the class ConvertedEdgeSlide method proposal.

@Override
public double proposal() {
    double logHR = 0.0;
    if (acg.getTotalConvCount() == 0)
        return Double.NEGATIVE_INFINITY;
    // Select edge at random:
    Conversion conv = chooseConversion();
    // Decide whether to move departure or arrival point
    boolean moveDeparture = Randomizer.nextBoolean();
    // Get current (old) attachment height
    double oldHeight;
    if (moveDeparture) {
        oldHeight = conv.getHeight1();
    } else {
        oldHeight = conv.getHeight2();
    }
    // Choose window:
    double w = apertureSizeInput.get() * acg.getRoot().getHeight();
    // Set new height
    double newHeight = oldHeight + (Randomizer.nextDouble() - 0.5) * w;
    // Check for boundary violation
    if (moveDeparture) {
        if (newHeight > conv.getHeight2() || newHeight > acg.getRoot().getHeight())
            return Double.NEGATIVE_INFINITY;
    } else {
        if (newHeight < conv.getHeight1())
            return Double.NEGATIVE_INFINITY;
    }
    // Get node below current (old) attachment point
    Node nodeBelow;
    if (moveDeparture)
        nodeBelow = conv.getNode1();
    else
        nodeBelow = conv.getNode2();
    // Choose node below new attachment point
    if (newHeight < oldHeight) {
        while (newHeight < nodeBelow.getHeight()) {
            if (nodeBelow.isLeaf())
                return Double.NEGATIVE_INFINITY;
            if (Randomizer.nextBoolean())
                nodeBelow = nodeBelow.getLeft();
            else
                nodeBelow = nodeBelow.getRight();
            logHR += -Math.log(0.5);
        }
    } else {
        while (!nodeBelow.isRoot() && newHeight > nodeBelow.getParent().getHeight()) {
            nodeBelow = nodeBelow.getParent();
            logHR += Math.log(0.5);
        }
    }
    // Write changes back to recombination object
    if (moveDeparture) {
        conv.setHeight1(newHeight);
        conv.setNode1(nodeBelow);
    } else {
        conv.setHeight2(newHeight);
        conv.setNode2(nodeBelow);
    }
    return logHR;
}

Example 22 with Conversion

use of bacter.Conversion in project bacter by tgvaughan.

the class ACGCladeSystem method mergeOverlappingConvs.

private List<Conversion> mergeOverlappingConvs(List<Conversion> conversions) {
    List<Conversion> mergedList = new ArrayList<>();
    List<Conversion> convOrderedByStart = new ArrayList<>(conversions);
    convOrderedByStart.sort((o1, o2) -> o1.getStartSite() - o2.getStartSite());
    List<Conversion> convOrderedByEnd = new ArrayList<>(conversions);
    convOrderedByEnd.sort((o1, o2) -> o1.getEndSite() - o2.getEndSite());
    int nActive = 0;
    Conversion currentMergedConv = null;
    int mergedConvCount = 0;
    double mergedConvHeight1 = 0.0;
    double mergedConvHeight2 = 0.0;
    while (!convOrderedByStart.isEmpty() || !convOrderedByEnd.isEmpty()) {
        int nextStart = convOrderedByStart.isEmpty() ? Integer.MAX_VALUE : convOrderedByStart.get(0).getStartSite();
        int nextEnd = convOrderedByEnd.isEmpty() ? Integer.MAX_VALUE : convOrderedByEnd.get(0).getEndSite();
        if (nextStart < nextEnd) {
            nActive += 1;
            if (nActive == 1) {
                currentMergedConv = convOrderedByStart.get(0).getCopy();
                currentMergedConv.acgIndex = convOrderedByStart.get(0).acgIndex;
                mergedConvCount = 1;
                mergedConvHeight1 = currentMergedConv.getHeight1();
                mergedConvHeight2 = currentMergedConv.getHeight2();
            } else {
                mergedConvCount += 1;
                mergedConvHeight1 += convOrderedByStart.get(0).getHeight1();
                mergedConvHeight2 += convOrderedByStart.get(0).getHeight2();
            }
            convOrderedByStart.remove(0);
        } else {
            nActive -= 1;
            if (nActive == 0) {
                assert currentMergedConv != null;
                currentMergedConv.setEndSite(nextEnd);
                currentMergedConv.setHeight1(mergedConvHeight1 / mergedConvCount);
                currentMergedConv.setHeight2(mergedConvHeight2 / mergedConvCount);
                mergedList.add(currentMergedConv);
            }
            convOrderedByEnd.remove(0);
        }
    }
    return mergedList;
}

Example 23 with Conversion

use of bacter.Conversion in project bacter by tgvaughan.

the class ACGCladeSystem method getConversionSummaries.

/**
 * Determine contiguous regions on specified locus where the fraction of
 * ACGs having a conversion active is greater than the given threshold.
 *
 * @param from BitSet representing source clade
 * @param to BitSet representing destination clade
 * @param locus locus to consider
 * @param threshold minimum fraction of sampled conversions included
 * @return List of regions
 */
public List<ConversionSummary> getConversionSummaries(BitSet from, BitSet to, Locus locus, int nACGs, double threshold) {
    BitSetPair bsPair = new BitSetPair(from, to);
    List<ConversionSummary> convSummaryList = new ArrayList<>();
    // Return empty list if on conversions meet the criteria.
    if (!conversionLists.containsKey(bsPair) || !conversionLists.get(bsPair).containsKey(locus))
        return convSummaryList;
    int thresholdCount = (int) Math.ceil(nACGs * threshold);
    List<Conversion> convOrderedByStart = new ArrayList<>();
    convOrderedByStart.addAll(conversionLists.get(bsPair).get(locus));
    convOrderedByStart.sort((Conversion o1, Conversion o2) -> o1.getStartSite() - o2.getStartSite());
    List<Conversion> convOrderedByEnd = new ArrayList<>();
    convOrderedByEnd.addAll(conversionLists.get(bsPair).get(locus));
    convOrderedByEnd.sort((Conversion o1, Conversion o2) -> o1.getEndSite() - o2.getEndSite());
    List<Conversion> activeConversions = new ArrayList<>();
    ConversionSummary conversionSummary = null;
    BitSet includedACGindices = new BitSet();
    while (!convOrderedByStart.isEmpty() || !convOrderedByEnd.isEmpty()) {
        int nextStart = convOrderedByStart.isEmpty() ? Integer.MAX_VALUE : convOrderedByStart.get(0).getStartSite();
        int nextEnd = convOrderedByEnd.isEmpty() ? Integer.MAX_VALUE : convOrderedByEnd.get(0).getEndSite();
        if (nextStart < nextEnd) {
            activeConversions.add(convOrderedByStart.get(0));
            if (activeConversions.size() >= thresholdCount) {
                if (conversionSummary == null) {
                    conversionSummary = new ConversionSummary();
                    convSummaryList.add(conversionSummary);
                    conversionSummary.addConvs(activeConversions);
                    includedACGindices.clear();
                    for (Conversion conv : activeConversions) includedACGindices.set(conv.acgIndex);
                } else {
                    conversionSummary.addConv(convOrderedByStart.get(0));
                    includedACGindices.set(convOrderedByStart.get(0).acgIndex);
                }
            }
            convOrderedByStart.remove(0);
        } else {
            activeConversions.remove(convOrderedByEnd.get(0));
            if (activeConversions.size() == thresholdCount - 1) {
                assert conversionSummary != null;
                conversionSummary.nIncludedACGs = includedACGindices.cardinality();
                conversionSummary = null;
            }
            convOrderedByEnd.remove(0);
        }
    }
    return convSummaryList;
}

Example 24 with Conversion

use of bacter.Conversion in project bacter by tgvaughan.

the class CFConvSwapExperiment method connectEdge.

public static void connectEdge(ConversionGraph acg, Node node, Node destEdgeBase, double destTime) {
    if (node.isRoot())
        throw new IllegalArgumentException("Programmer error: " + "root argument passed to connectEdge().");
    Node parent = node.getParent();
    if (destEdgeBase.isRoot()) {
        parent.addChild(destEdgeBase);
    } else {
        Node grandParent = destEdgeBase.getParent();
        grandParent.removeChild(destEdgeBase);
        grandParent.addChild(parent);
        parent.addChild(destEdgeBase);
    }
    parent.setHeight(destTime);
    for (Locus locus : acg.getLoci()) {
        for (Conversion conv : acg.getConversions(locus)) {
            if (conv.getNode1() == destEdgeBase && conv.getHeight1() > destTime)
                conv.setNode1(parent);
            if (conv.getNode2() == destEdgeBase && conv.getHeight2() > destTime)
                conv.setNode2(parent);
        }
    }
}

Example 25 with Conversion

use of bacter.Conversion in project bacter by tgvaughan.

the class ConversionGraphStatsLogger method getMeanTractLength.

/**
 * Obtain mean length of converted regions described by ACG.
 *
 * @param acg
 * @param locus
 * @return mean length, or NaN if ACG has no converted edges.
 */
public static double getMeanTractLength(ConversionGraph acg, Locus locus) {
    if (acg.getConvCount(locus) < 1)
        return Double.NaN;
    double mean = 0;
    for (Conversion conv : acg.getConversions(locus)) mean += conv.getEndSite() - conv.getStartSite() + 1;
    mean /= acg.getConvCount(locus);
    return mean;
}