Examples of org.broad.igv.feature.Range

org.broad.igv.feature.Range
Basic class to specify a genomic interval. Coordinates are intended to be 0-based half-open Please do not add or remove any fields (want to keep it very simple). Additional methods for calculating overlap are okay @author jacob @author 2013-May-20

    public SpliceJunctionHelper getSpliceJunctionHelper() {
        return this.spliceJunctionHelper;
    }


    public Range getRange() {
        return new Range(getChr(), getStart(), getEnd());
    }

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                ReferenceFrame frame = te.getFrame();
                String locus1 = frame.getFormattedLocusString();


                // Generate a locus string for the read mate.  Keep the window width (in base pairs) == to the current range
                Range range = frame.getCurrentRange();
                int length = range.getLength();
                int s2 = Math.max(0, mateStart - length / 2);
                int e2 = s2 + length;
                String startStr = NumberFormat.getInstance().format(s2);
                String endStr = NumberFormat.getInstance().format(e2);
                String mateLocus = mateChr + ":" + startStr + "-" + endStr;

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        File outFile = new File(outPath);
        try {
            AlignmentDataManager dataManager = alignmentTrack.getDataManager();
            ResourceLocator inlocator = dataManager.getLocator();
            Range range = frame.getCurrentRange();


            //Read directly from file
            //return SAMWriter.writeAlignmentFilePicard(inlocator, outPath, range.getChr(), range.getStart(), range.getEnd());


            //Export those in memory, overlapping current view
            return SAMWriter.writeAlignmentFilePicard(dataManager, outFile, range.getChr(), range.getStart(), range.getEnd());
        } catch (IOException e) {
            log.error(e.getMessage(), e);
            throw new RuntimeException(e);
        }

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        final SAMFileHeader fileHeader = dataManager.getReader().getFileHeader();
        //IGV can only load files sorted in coordinate order, but they aren't always
        //labelled as such.
        fileHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);


        Range range = new Range(sequence, start, end);
        Iterator<Alignment> iter = dataManager.getLoadedInterval(range).getAlignmentIterator();
        Iterator<PicardAlignment> samIter = new SamAlignmentIterable(iter, sequence, start, end);


        SAMWriter writer = new SAMWriter(fileHeader);
        return writer.writeToFile(outFile, samIter, true);

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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);
            }
        });

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        if (zoom == 0) {
            return getChrName();
        } else {


            Range range = getCurrentRange();
            return Locus.getFormattedLocusString(range.getChr(), range.getStart(), range.getEnd());
        }
    }

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    public Range getCurrentRange() {
        int start = 0;
        int end = widthInPixels;
        int startLoc = (int) getChromosomePosition(start) + 1;
        int endLoc = (int) getChromosomePosition(end);
        Range range = new Range(getChrName(), startLoc, endLoc);
        return range;
    }

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            } else if (chr.equalsIgnoreCase("All")) {
                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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                        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);

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org.broad.igv.sam.AlignmentDataManager

org.broad.igv.sam.AlignmentDataManagerTest

org.broad.igv.sam.AlignmentInterval

org.broad.igv.sam.AlignmentPacker

org.broad.igv.sam.AlignmentTrack

org.broad.igv.sam.PositionCache

org.broad.igv.sam.SAMWriter

org.broad.igv.session.Session

org.broad.igv.track.MutationFeatureSource$MutationDataManager

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