Examples of org.broad.igv.feature.RegionOfInterest

org.broad.igv.feature.RegionOfInterest
@author eflakes

    }




    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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    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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            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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        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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            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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                int[] selectedRows = regionTable.getSelectedRows();
                if (selectedRows != null && selectedRows.length > 0
                        && regions.size() >= selectedRows.length)  //dhmay: this is hacky. Bad things can happen with clear regions
                {
                    RegionOfInterest firstStartRegion = null;
                    RegionOfInterest lastEndRegion = null;


                    Set<String> selectedChrs = new HashSet<String>();


                    //Figure out which region has the first start and which has the last end
                    for (int selectedRowIndex : selectedRows) {
                        int selectedModelRow = regionTableRowSorter.convertRowIndexToModel(selectedRowIndex);
                        RegionOfInterest region = regions.get(selectedModelRow);
                        selectedChrs.add(region.getChr());
                        if (firstStartRegion == null || region.getStart() < firstStartRegion.getStart())
                            firstStartRegion = region;
                        if (lastEndRegion == null || region.getEnd() > lastEndRegion.getEnd())
                            lastEndRegion = region;
                    }


                    //If there are multiple chromosomes represented in the selection, do nothing.
                    //Because what would we do? Maybe a status message should be displayed somehow, but a

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                JOptionPane.showMessageDialog(IGV.getMainFrame(),
                        "Regions cannot be created in the All Chromosomes view.",
                        "Error", JOptionPane.INFORMATION_MESSAGE);
            } else {
                Range r = FrameManager.getDefaultFrame().getCurrentRange();
                RegionOfInterest newRegion = new RegionOfInterest(r.getChr(), r.getStart(), r.getEnd(), "");
                IGV.getInstance().getSession().addRegionOfInterestWithNoListeners(newRegion);
            }
            updateButtonsEnabled();
        }

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                    for (RegionOfInterest roi : selectedRegions) {
                        loci.add(roi.getLocusString());
                    }
                } else {
                    //Need to preserve current zoom, iff checkbox not selected and only choosing 1
                    RegionOfInterest roi = selectedRegions.get(0);
                    Range range = FrameManager.getDefaultFrame().getCurrentRange();
                    int length = range.getLength();
                    int start = roi.getCenter() - length / 2;
                    int end = start + length;
                    //Shift so we don't go below 0
                    if(start < 0){
                        end += Math.abs(start);
                        start = 0;
                    }
                    loci.add(new RegionOfInterest(roi.getChr(), start, end, roi.getDescription()).getLocusString());
                }
                GeneList geneList = new GeneList("Regions of Interest", loci, false);
                IGV.getInstance().getSession().setCurrentGeneList(geneList);
                IGV.getInstance().resetFrames();

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