Examples of RegionOfInterest

com.kurento.kmf.media.RegionOfInterest
Region of interest for some events in a video processing filter
net.imglib2.roi.RegionOfInterest
Maps real values into a 1-d set of bins. Though this class will work with integral data types it is really more appropriate to do so using a {@link Integer1dBinMapper}. @author Barry DeZonia
org.broad.igv.feature.RegionOfInterest
@author eflakes

Examples of org.broad.igv.feature.RegionOfInterest

        ReferenceFrame frame = null;
        final int zoom = 0;
        final String chr = "chr20";
        final int start = Integer.parseInt("14104912") - 1;
        final int end = Integer.parseInt("36031032");
        RegionOfInterest roi = new RegionOfInterest(chr, start, end, "");


        IGV.sortByRegionScore(tracks, roi, type, frame);
        return checkIsSorted(tracks, roi, type, zoom, frame);
    }

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Examples of org.broad.igv.feature.RegionOfInterest


        Collection<RegionOfInterest> regions = IGV.getInstance().getSession().getAllRegionsOfInterest();
        assertEquals(1, regions.size());


        ArrayList<RegionOfInterest> regionsAL = (ArrayList<RegionOfInterest>) regions;
        RegionOfInterest region = regionsAL.get(0);
        assertEquals("chr1", region.getChr());
        assertEquals(49, region.getStart());
        assertEquals(1000, region.getEnd());
        assertEquals(descstr, region.getDescription());


    }

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Examples of org.broad.igv.feature.RegionOfInterest

                            if (start == end) {
                                ++end;
                            }


                            // Create a Region of Interest
                            RegionOfInterest regionOfInterest =
                                    new RegionOfInterest(
                                            chromosomeName,
                                            start,
                                            end,
                                            null);
                            // TODO -- get this ugly reference out of here

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Examples of org.broad.igv.feature.RegionOfInterest

     */
    public void sortByRegionScore(RegionOfInterest region,
                                  final RegionScoreType type,
                                  final ReferenceFrame frame) {


        final RegionOfInterest r = region == null ? new RegionOfInterest(frame.getChrName(), (int) frame.getOrigin(),
                (int) frame.getEnd() + 1, frame.getName()) : region;


        // Create a rank order of samples.  This is done globally so sorting is consistent across groups and panels.
        final List<String> sortedSamples = sortSamplesByRegionScore(r, type, frame);

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Examples of org.broad.igv.feature.RegionOfInterest

        String chromosome = getAttribute(element, SessionAttribute.CHROMOSOME.getText());
        String start = getAttribute(element, SessionAttribute.START_INDEX.getText());
        String end = getAttribute(element, SessionAttribute.END_INDEX.getText());
        String description = getAttribute(element, SessionAttribute.DESCRIPTION.getText());


        RegionOfInterest region = new RegionOfInterest(chromosome, new Integer(start), new Integer(end), description);
        IGV.getInstance().addRegionOfInterest(region);


        NodeList elements = element.getChildNodes();
        process(session, elements, additionalInformation, rootPath);
    }

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Examples of org.broad.igv.feature.RegionOfInterest

    }




    private void defineRegion(String param1, String param2, String param3, String param4) {


        RegionOfInterest roi = null;
        if (param1 != null && param2 != null && param3 != null) {
            int start = Math.max(0, Integer.parseInt(param2) - 1);
            int end = Integer.parseInt(param3);
            String desc = param4 != null ? param4 : "";
            roi = new RegionOfInterest(param1, start, end, desc);
        }
        if (param1 != null) {
            Locus locus = Locus.fromString(param1);
            if (locus != null) {
                int start = Math.max(0, locus.getStart() - 1);
                String desc = param2 != null ? param2 : "";
                roi = new RegionOfInterest(locus.getChr(), start, locus.getEnd(), desc);


            }
        }
        if (roi != null) {
            igv.addRegionOfInterest(roi);

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Examples of org.broad.igv.feature.RegionOfInterest


    private void sort(String sortArg, String locusString, String param3, String param4) {
        RegionScoreType regionSortOption = getRegionSortOption(sortArg);
        String tag = "";
        if (regionSortOption != null) {
            RegionOfInterest roi = null;
            if (locusString != null) {
                Locus locus = Locus.fromString(locusString);
                if (locus != null) {
                    int start = Math.max(0, locus.getStart() - 1);
                    roi = new RegionOfInterest(locus.getChr(), start, locus.getEnd(), "");
                }
            }
            igv.sortByRegionScore(roi, regionSortOption, FrameManager.getDefaultFrame());


        } else {

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Examples of org.broad.igv.feature.RegionOfInterest

            public void actionPerformed(ActionEvent e) {
                if (FrameManager.isGeneListMode()) {
                    return;
                }
                Range currentRange = FrameManager.getDefaultFrame().getCurrentRange();
                RegionOfInterest regionOfInterest =
                        new RegionOfInterest(
                                currentRange.getChr(),
                                currentRange.getStart(),
                                currentRange.getEnd(),
                                null);
                IGV.getInstance().addRegionOfInterest(regionOfInterest);
            }
        });


        final Action regionCenterAction = new EnableWrappedAction(new AbstractAction() {


            public void actionPerformed(ActionEvent e) {
                if (FrameManager.isGeneListMode()) {
                    return;
                }
                int center = (int) FrameManager.getDefaultFrame().getCenter();
                RegionOfInterest regionOfInterest =
                        new RegionOfInterest(
                                FrameManager.getDefaultFrame().getChrName(),
                                center,
                                center + 1,
                                null);
                IGV.getInstance().addRegionOfInterest(regionOfInterest);

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Examples of org.broad.igv.feature.RegionOfInterest

        while (regionTableModel.getRowCount() > 0){
            regionTableModel.removeRow(0);
        }
        regionTableModel.setRowCount(regions.size());
        for (int i = 0; i < regions.size(); i++) {
            RegionOfInterest region = regions.get(i);


            regionTableModel.setValueAt(region.getDescription(), i, TABLE_COLINDEX_DESC);
            regionTableModel.setValueAt(region.getDisplayStart(), i, TABLE_COLINDEX_START);
            regionTableModel.setValueAt(region.getDisplayEnd(), i, TABLE_COLINDEX_END);
            regionTableModel.setValueAt(region.getChr(), i, TABLE_COLINDEX_CHR);
        }
        //Done synching regions, allow ourselves to respond to tableChanged events
        synchingRegions = false;


        regionTableModel.fireTableDataChanged();

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Examples of org.broad.igv.feature.RegionOfInterest

            rowIdx = regionTable.getRowSorter().convertRowIndexToModel(tableRow);
        } catch (ArrayIndexOutOfBoundsException x) {
            return;
        }


        RegionOfInterest region = regions.get(rowIdx);


        //dhmay changing 20110505: just update region values from all columns, instead of checking the event
        //to see which column is affected. This is in response to an intermittent bug.


        Object descObject = regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_DESC);
        if (descObject != null)
            region.setDescription(descObject.toString());


        //stored values are 0-based end-exclusive, viewed values are 1-based end-inclusive.  Check for negative number just in case
        int storeStartValue =
                Math.max(0, (Integer) regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_START) - 1);
        region.setStart(storeStartValue);


        int storeEndValue =
                Math.max(0, (Integer) regionTableModel.getValueAt(rowIdx, TABLE_COLINDEX_END));
        region.setEnd(storeEndValue);
    }

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