Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

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        if (features.isEmpty()) {
            return blocks;
        }

        Iterator<Feature> iter = features.iterator();
        Feature f = iter.next();
        int blockIndex = 0;
        int exomeStart = 0;
        ExomeBlock block = new ExomeBlock(blockIndex, f.getStart(), exomeStart, f.getEnd() - f.getStart());

        while (iter.hasNext()) {
            f = iter.next();
            if (f.getStart() > block.getGenomeEnd()) {
                blocks.add(block);

                // Start next blocks
                int blockLength = block.getLength();
                exomeStart += blockLength;
                blockIndex++;
                int startingLength = f.getEnd() - f.getStart();
                block = new ExomeBlock(blockIndex, f.getStart(), exomeStart, startingLength);
            } else {
                block.extend(f.getEnd());
            }

        }
        // Add the last block
        blocks.add(block);
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        CloseableTribbleIterator<Feature> iter = null;
        try {
            iter = tribbleFeatureReader.query(chr, start, end);
            List<Feature> featureList = new ArrayList<Feature>();
            while (iter.hasNext()) {
                Feature f = iter.next();
                if (f.getStart() > end) {
                    break;
                } else if (f.getEnd() < start) {
                    continue;
                } else {
                    featureList.add(f);
                }
            }
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        if (packedFeatures == null) {
            return null;
        }

        Feature feature = null;
        List<IGVFeature> features;

        //We search only the specified row if y is a meaningful value.
        //Otherwise we search everything
        int row = ((y - top) / variantBandHeight);
        if (y < 0 || row >= getNumberOfFeatureLevels()) {
            features = packedFeatures.getFeatures();
        } else {
            features = packedFeatures.getRows().get(row).getFeatures();
        }

        if (features != null) {
            feature = FeatureUtils.getFeatureClosest(position, features);
        }
        if (feature == null ||
                ((position < feature.getStart() - maxDistance) || (position > feature.getEnd() + maxDistance))) {
            return null;
        } else {
            return (Variant) feature;
        }
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     */
    @Override
    public Feature nextFeature(String chr, double center, boolean forward, ReferenceFrame frame) throws IOException {

        if (getHideFiltered()) {
            Feature f;
            while ((f = super.nextFeature(chr, center, forward, frame)) != null) {
                if (!(f instanceof Variant) || !((Variant) f).isFiltered()) {
                    return f;
                }
            }
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    }

    @Override
    public boolean handleDataClick(TrackClickEvent te) {
        MouseEvent e = te.getMouseEvent();
        Feature f = getFeatureAtMousePosition(te);

        //We allow any of these modifier keys for multi-select
        if (!e.isShiftDown() && !e.isControlDown() && !e.isMetaDown()) {
            clearSelectedExons();
        }
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            Node parent = walker.getCurrentNode();
            Element n = (Element) walker.firstChild();
            while (n != null) {
                if (n.getTagName().equalsIgnoreCase(tag)) {
                    Feature f = getFeature(walker, chr);
                    if (f != null) {
                        features.add(f);
                    }

                    n = (Element) walker.nextSibling();
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                    else
                        otherBuffer.add(feature);
                }
                if (buffer.isEmpty())
                    return null;
                Feature result = buffer.get(0);
                buffer.remove(0);
                return result;
            }
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        return fullCmd.toArray(new String[0]);
    }

    protected String writeLocus(Argument arg, String chr, int start, int end) throws IOException{
        Feature feat = new SimpleBEDFeature(start, end, chr);
        return createTempFile(Arrays.asList(feat), arg);
    }
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        Locus locus = Locus.fromString(geneOrLocusString);
        if (locus != null && locus.isValid()) {
            return locus;
        } else {
            // Maybe its a gene or feature
            Feature gene = FeatureDB.getFeature(geneOrLocusString);
            if (gene != null) {
                return new Locus(gene.getChr(), gene.getStart(), gene.getEnd());
            }
        }
        return null;
    }
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    public static class GotoFeatureHandler implements IFeatureFound{
        @Override
        public void processResult(Iterator<? extends Feature> searchResult) {
            ReferenceFrame frame = FrameManager.getDefaultFrame();
            Feature f = searchResult.next();

            String chr = GenomeManager.getInstance().getCurrentGenome().getChromosomeAlias(f.getChr());
            double newCenter = f.getStart();
            if (!chr.equals(frame.getChrName())) {
                // Switch chromosomes.  We have to do some tricks to maintain the same resolution scale.
                double range = frame.getEnd() - frame.getOrigin();
                int newOrigin = (int) Math.max(newCenter - range / 2, 0);
                int newEnd = (int) (newOrigin + range);
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Related Classes of htsjdk.tribble.Feature

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  • org.broad.igv.data.expression.GeneToLocusHelper
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