Examples with IntervalFeature tracks.IntervalFeature used on opensource projects

Example 11 with IntervalFeature

use of tracks.IntervalFeature in project ASCIIGenome by dariober.

the class Utils method mergeIntervalFeatures.

/**
 * Merge overlapping features. If screenCoords is true, merge is based on the screen coordinates. Otherwise use
 * genomic coordinates.
 * @throws InvalidColourException
 */
public static List<IntervalFeature> mergeIntervalFeatures(List<IntervalFeature> intervalList, boolean screenCoords) throws InvalidGenomicCoordsException, InvalidColourException {
    List<IntervalFeature> mergedList = new ArrayList<IntervalFeature>();
    if (intervalList.size() == 0) {
        return mergedList;
    }
    String mergedChrom = null;
    int mergedFrom = -1;
    int mergedTo = -1;
    int mergedScreenFrom = -1;
    int mergedScreenTo = -1;
    // Number of intervals in the merged one.
    int numMrgIntv = 1;
    // Put here all the different strands found in the merged features.
    Set<Character> strand = new HashSet<Character>();
    for (int i = 0; i < (intervalList.size() + 1); i++) {
        // We do an additional loop to add to the mergedList the last interval.
        // The last loop has interval == null so below you need to account for it
        IntervalFeature interval = null;
        if (i < intervalList.size()) {
            interval = intervalList.get(i);
        }
        if (mergedFrom < 0) {
            // Init interval
            mergedChrom = interval.getChrom();
            mergedFrom = interval.getFrom();
            mergedTo = interval.getTo();
            mergedScreenFrom = interval.getScreenFrom();
            mergedScreenTo = interval.getScreenTo();
            continue;
        }
        // Sanity check: The list to be merged is on the same chrom and sorted by start pos.
        if (i < intervalList.size() && (!mergedChrom.equals(interval.getChrom()) || mergedFrom > interval.getFrom() || mergedFrom > mergedTo)) {
            System.err.println(mergedChrom + " " + mergedFrom + " " + mergedTo);
            throw new RuntimeException();
        }
        boolean overlap = false;
        if (screenCoords && i < intervalList.size() && (mergedScreenFrom <= interval.getScreenTo() && mergedScreenTo >= (interval.getScreenFrom() - 1))) {
            // Overlap: Extend <to> coordinate. See also http://stackoverflow.com/questions/325933/determine-whether-two-date-ranges-overlap
            overlap = true;
        } else if (i < intervalList.size() && (mergedFrom <= interval.getTo() && mergedTo >= (interval.getFrom() - 1))) {
            // Overlap on genomic coordinates
            overlap = true;
        }
        if (overlap) {
            // Overlap found in screen or genomic coords.
            mergedTo = Math.max(interval.getTo(), mergedTo);
            mergedScreenTo = Math.max(interval.getScreenTo(), mergedScreenTo);
            strand.add(interval.getStrand());
            numMrgIntv++;
            overlap = false;
        } else {
            // No overlap add merged interval to list and reset new merged interval
            IntervalFeature x = new IntervalFeature(mergedChrom + "\t" + (mergedFrom - 1) + "\t" + mergedTo, TrackFormat.BED, null);
            x.setScreenFrom(mergedScreenFrom);
            x.setScreenTo(mergedScreenTo);
            if (strand.size() == 1) {
                x.setStrand(strand.iterator().next());
            }
            strand.clear();
            if (x.equals(intervalList.get(i - 1)) && numMrgIntv == 1) {
                mergedList.add(intervalList.get(i - 1));
            } else {
                mergedList.add(x);
            }
            if (i < intervalList.size()) {
                // Do not reset from/to if you are in extra loop.
                mergedFrom = interval.getFrom();
                mergedTo = interval.getTo();
                mergedScreenFrom = interval.getScreenFrom();
                mergedScreenTo = interval.getScreenTo();
                strand.add(interval.getStrand());
                numMrgIntv = 1;
            }
        }
    }
    for (IntervalFeature x : mergedList) {
        x.getIdeogram(true, true);
    }
    return mergedList;
}