private List<BedFeature> readBedDataBlock(RPTreeLeafNodeItem leafHitItem) { // get the chromosome names associated with the hit region ID's int startChromID = leafHitItem.getChromosomeBounds().getStartChromID(); int endChromID = leafHitItem.getChromosomeBounds().getEndChromID(); chromosomeMap = chromIDTree.getChromosomeIDMap(startChromID, endChromID); boolean isLowToHigh = chromDataTree.isIsLowToHigh(); int uncompressBufSize = chromDataTree.getUncompressBuffSize(); // decompress leaf item data block for feature extraction BigBedDataBlock bedDataBlock = new BigBedDataBlock(fis, leafHitItem, chromosomeMap, isLowToHigh, uncompressBufSize); // get data block Bed feature list and set next index to first item return bedDataBlock.getBedData(selectionRegion, contained); }
public void print() { super.print(); // child node specific entries childNode.printItems(); }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel, int startChromID, int endChromID) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeRegion(startChromID, endChromID); return chromosomeBounds; }
public MethylScore next() { BedFeature feat = null; while (feat == null && bedIterator.hasNext()) { feat = bedIterator.next(); String[] restOfFields = feat.getRestOfFields(); MethylScore score = type == Type.ZILLER ? createZillerScore(feat, restOfFields) : createUSCScore(feat, restOfFields); return score; } return null; }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeBounds(); return chromosomeBounds; }
public ArrayList<RPChromosomeRegion> getZoomLevelRegions(int zoomLevel) { ArrayList<RPChromosomeRegion> regionList = zoomLevels.getZoomLevelRPTree(zoomLevel).getAllChromosomeRegions(); return regionList; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNodeProxy childNodeProxy) { super(new RPChromosomeRegion(startChromID, startBase, endChromID, endBase)); this.childNodeProxy = childNodeProxy; }
public BBZoomLevelHeader(SeekableStream fis, long fileOffset, int zoomLevel, boolean isLowToHigh){ this.fis = fis; zoomLevelHeaderOffset = fileOffset; this.zoomLevel = zoomLevel; readZoomLevelHeader(zoomLevelHeaderOffset, this.zoomLevel, isLowToHigh); }
public RPTreeHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh) { long itemsCount; rpTreeOffset = fileOffset; // Note: a bad R+ Tree header will result in false returned headerOK = readHeader(fis, rpTreeOffset, isLowToHigh); }
public BBFileHeader(String path, SeekableStream fis, long fileOffset) { // save the path and seekable file handle this.path = path; this.fis = fis; fileHeaderOffset = fileOffset; // read in BBFile header isHeaderOK = readBBFileHeader(fileHeaderOffset); }
public BPTreeHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh) { long itemsCount; // save the seekable file handle and B+ Tree file offset headerOffset = fileOffset; // Note: a bad B+ Tree header will result in false returned headerOK = readHeader(fis, headerOffset, isLowToHigh); }
public RPChromosomeRegion getChromosomeRegion(int startChromID, int endChromID) { RPChromosomeRegion region; // Search the R+ tree to extract the chromosome region. RPTreeNode thisNode = rootNode; RPChromosomeRegion seedRegion = null; // null until a chromosome match region = findChromosomeRegion(thisNode, startChromID, endChromID, seedRegion); return region; }
public RPTreeNode getChildNode() { if (childNode == null) { RPTreeNodeProxy proxy = childNodeProxy; childNode = RPTree.readRPTreeNode(proxy.fis, proxy.fileOffset, proxy.isLowToHigh, true); } return childNode; }
public int getChromosomeID(String chromKey) { int chromosomeID; // Search the B+ tree to extract the Chromosome ID. BPTreeNode thisNode = rootNode; chromosomeID = findChromosomeID(thisNode, chromKey); return chromosomeID; }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeBounds(); return chromosomeBounds; }
public RPChromosomeRegion getZoomLevelBounds(int zoomLevel, int startChromID, int endChromID) { RPChromosomeRegion chromosomeBounds = zoomLevels.getZoomLevelRPTree(zoomLevel).getChromosomeRegion(startChromID, endChromID); return chromosomeBounds; }
public ArrayList<RPChromosomeRegion> getZoomLevelRegions(int zoomLevel) { ArrayList<RPChromosomeRegion> regionList = zoomLevels.getZoomLevelRPTree(zoomLevel).getAllChromosomeRegions(); return regionList; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNode childNode) { super(new RPChromosomeRegion(startChromID, startBase, endChromID, endBase)); this.childNode = childNode; }
public BBZoomLevelHeader(SeekableStream fis, long fileOffset, int zoomLevel, boolean isLowToHigh){ this.fis = fis; zoomLevelHeaderOffset = fileOffset; this.zoomLevel = zoomLevel; readZoomLevelHeader(zoomLevelHeaderOffset, this.zoomLevel, isLowToHigh); } /*
public RPTreeLeafNodeItem(int startChromID, int startBase, int endChromID, int endBase, long dataOffset, long dataSize) { super(new RPChromosomeRegion(startChromID, startBase, endChromID, endBase)); this.dataOffset = dataOffset; this.dataSize = dataSize; }