public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNodeProxy childNodeProxy) { super(new RPChromosomeRegion(startChromID, startBase, endChromID, endBase)); this.childNodeProxy = childNodeProxy; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNode childNode) { super(new RPChromosomeRegion(startChromID, startBase, endChromID, endBase)); this.childNode = childNode; }
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; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNode childNode) { chromosomeBounds = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); this.childNode = childNode; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, RPTreeNode childNode) { chromosomeBounds = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); this.childNode = childNode; }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, long childDataOffset) { chromosomeBounds = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); }
public RPTreeChildNodeItem(int startChromID, int startBase, int endChromID, int endBase, long childDataOffset) { chromosomeBounds = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); }
public RPChromosomeRegion getExtremes(RPChromosomeRegion testRegion) { RPChromosomeRegion newRegion = new RPChromosomeRegion(this); // update node bounds if (testRegion.startChromID < newRegion.startChromID || (testRegion.startChromID == newRegion.startChromID && testRegion.startBase < newRegion.startBase)) { newRegion.startChromID = testRegion.startChromID; newRegion.startBase = testRegion.startBase; } if (testRegion.endChromID > newRegion.endChromID || (testRegion.endChromID == newRegion.endChromID && testRegion.endBase > newRegion.endBase)) { newRegion.endChromID = testRegion.endChromID; newRegion.endBase = testRegion.endBase; } return newRegion; }
public RPChromosomeRegion getExtremes(RPChromosomeRegion testRegion) { RPChromosomeRegion newRegion = new RPChromosomeRegion(this); // update node bounds if (testRegion.startChromID < newRegion.startChromID || (testRegion.startChromID == newRegion.startChromID && testRegion.startBase < newRegion.startBase)) { newRegion.startChromID = testRegion.startChromID; newRegion.startBase = testRegion.startBase; } if (testRegion.endChromID > newRegion.endChromID || (testRegion.endChromID == newRegion.endChromID && testRegion.endBase > newRegion.endBase)) { newRegion.endChromID = testRegion.endChromID; newRegion.endBase = testRegion.endBase; } return newRegion; }
public RPTreeLeafNode(){ leafItems = new ArrayList<RPTreeLeafNodeItem>(); // init with null bounds chromosomeBounds = new RPChromosomeRegion(); }
public RPTreeLeafNode(){ leafItems = new ArrayList<RPTreeLeafNodeItem>(); // init with null bounds chromosomeBounds = new RPChromosomeRegion(); }
public void insertItem(RPTreeNodeItem item) { RPTreeNodeItem newItem = item; // Quick implementation: assumes all keys are inserted in rank order // todo: or compare key and insert at rank location items.add(newItem); // Update node bounds or start node chromosome bounds with first entry if (chromosomeBounds == null) { chromosomeBounds = new RPChromosomeRegion(newItem.getChromosomeBounds()); } else { chromosomeBounds = chromosomeBounds.getExtremes(newItem.getChromosomeBounds()); } }
public boolean insertItem(RPTreeNodeItem item) { RPTreeChildNodeItem newItem = (RPTreeChildNodeItem) item; // Quick implementation: assumes all keys are inserted in rank order // todo: or compare key and insert at rank location childItems.add(newItem); // Update node bounds or start node chromosome bounds with first entry if (chromosomeBounds == null) chromosomeBounds = new RPChromosomeRegion(newItem.getChromosomeBounds()); else chromosomeBounds = chromosomeBounds.getExtremes(newItem.getChromosomeBounds()); // success return true; }
public boolean insertItem(RPTreeNodeItem item) { RPTreeChildNodeItem newItem = (RPTreeChildNodeItem) item; // Quick implementation: assumes all keys are inserted in rank order // todo: or compare key and insert at rank location childItems.add(newItem); // Update node bounds or start node chromosome bounds with first entry if (chromosomeBounds == null) chromosomeBounds = new RPChromosomeRegion(newItem.getChromosomeBounds()); else chromosomeBounds = chromosomeBounds.getExtremes(newItem.getChromosomeBounds()); // success return true; }
public boolean insertItem(RPTreeNodeItem item){ RPTreeLeafNodeItem newItem = (RPTreeLeafNodeItem)item; // Note: assumes all keys are inserted in rank order leafItems.add(newItem); // todo: compare region and insert at appropriate indexed rank location // leafHitItem.add( index, (RPTreeLeafNodeItem)item ); // update leaf node chromosome bounds - use extremes // Update node bounds or start node chromosome bounds with first entry if(chromosomeBounds == null) chromosomeBounds = new RPChromosomeRegion(newItem.getChromosomeBounds()); else chromosomeBounds = chromosomeBounds.getExtremes(newItem.getChromosomeBounds()); // successful insert return true; }
public boolean insertItem(RPTreeNodeItem item){ RPTreeLeafNodeItem newItem = (RPTreeLeafNodeItem)item; // Note: assumes all keys are inserted in rank order leafItems.add(newItem); // todo: compare region and insert at appropriate indexed rank location // leafHitItem.add( index, (RPTreeLeafNodeItem)item ); // update leaf node chromosome bounds - use extremes // Update node bounds or start node chromosome bounds with first entry if(chromosomeBounds == null) chromosomeBounds = new RPChromosomeRegion(newItem.getChromosomeBounds()); else chromosomeBounds = chromosomeBounds.getExtremes(newItem.getChromosomeBounds()); // successful insert return true; }
private int getHitList(RPChromosomeRegion hitRegion, boolean contained) { // hit list for hit region; subject to mMaxLeafHits limitation leafHitList = zoomDataTree.getChromosomeDataHits(hitRegion, contained); // check if any leaf items were selected int nHits = leafHitList.size(); if (nHits == 0) return 0; // no data hits found else leafItemIndex = 0; // reset hit item index to start of list // find hit bounds int startChromID = leafHitList.get(0).getChromosomeBounds().getStartChromID(); int startBase = leafHitList.get(0).getChromosomeBounds().getStartBase(); int endChromID = leafHitList.get(nHits - 1).getChromosomeBounds().getEndChromID(); int endBase = leafHitList.get(nHits - 1).getChromosomeBounds().getEndBase(); // save hit region definition; not currently used but useful for debug this.hitRegion = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); return nHits; }
private int getHitList(RPChromosomeRegion hitRegion, boolean contained) { // hit list for hit region; subject to mMaxLeafHits limitation leafHitList = chromDataTree.getChromosomeDataHits(hitRegion, contained); // check if any leaf items were selected int nHits = leafHitList.size(); if (nHits == 0) return 0; else leafItemIndex = 0; // reset hit item index to start of list // find hit bounds from first and last hit items int startChromID = leafHitList.get(0).getChromosomeBounds().getStartChromID(); int startBase = leafHitList.get(0).getChromosomeBounds().getStartBase(); int endChromID = leafHitList.get(nHits - 1).getChromosomeBounds().getEndChromID(); int endBase = leafHitList.get(nHits - 1).getChromosomeBounds().getEndBase(); // save hit region; not currently used but useful for debug this.hitRegion = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); return nHits; }
private int getHitList(RPChromosomeRegion hitRegion, boolean contained) { // hit list for hit region; subject to mMaxLeafHits limitation leafHitList = chromDataTree.getChromosomeDataHits(hitRegion, contained); // check if any leaf items were selected int nHits = leafHitList.size(); if (nHits == 0) return 0; else leafItemIndex = 0; // reset hit item index to start of list // find hit bounds from first and last hit items int startChromID = leafHitList.get(0).getChromosomeBounds().getStartChromID(); int startBase = leafHitList.get(0).getChromosomeBounds().getStartBase(); int endChromID = leafHitList.get(nHits - 1).getChromosomeBounds().getEndChromID(); int endBase = leafHitList.get(nHits - 1).getChromosomeBounds().getEndBase(); // save hit region; not currently used but useful for debug this.hitRegion = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); return nHits; }
private int getHitList(RPChromosomeRegion hitRegion, boolean contained) { // hit list for hit region; subject to mMaxLeafHits limitation leafHitList = zoomDataTree.getChromosomeDataHits(hitRegion, contained); // check if any leaf items were selected int nHits = leafHitList.size(); if (nHits == 0) return 0; // no data hits found else leafItemIndex = 0; // reset hit item index to start of list // find hit bounds int startChromID = leafHitList.get(0).getChromosomeBounds().getStartChromID(); int startBase = leafHitList.get(0).getChromosomeBounds().getStartBase(); int endChromID = leafHitList.get(nHits - 1).getChromosomeBounds().getEndChromID(); int endBase = leafHitList.get(nHits - 1).getChromosomeBounds().getEndBase(); // save hit region definition; not currently used but useful for debug this.hitRegion = new RPChromosomeRegion(startChromID, startBase, endChromID, endBase); return nHits; }