public void print() { log.debug("Child node item :\n"); log.debug(" StartChromID = " + chromosomeBounds.getStartChromID() + "\n"); log.debug(" StartBase = " + chromosomeBounds.getStartBase() + "\n"); log.debug(" EndChromID = " + chromosomeBounds.getEndChromID() + "\n"); log.debug(" EndBase = " + chromosomeBounds.getEndBase() + "\n"); } }
public void print() { log.debug("Child node item :\n"); log.debug(" StartChromID = " + chromosomeBounds.getStartChromID() + "\n"); log.debug(" StartBase = " + chromosomeBounds.getStartBase() + "\n"); log.debug(" EndChromID = " + chromosomeBounds.getEndChromID() + "\n"); log.debug(" EndBase = " + chromosomeBounds.getEndBase() + "\n"); // child node specific entries childNode.printItems(); }
public void print() { log.debug("Child node item :\n"); log.debug(" StartChromID = " + chromosomeBounds.getStartChromID() + "\n"); log.debug(" StartBase = " + chromosomeBounds.getStartBase() + "\n"); log.debug(" EndChromID = " + chromosomeBounds.getEndChromID() + "\n"); log.debug(" EndBase = " + chromosomeBounds.getEndBase() + "\n"); // child node specific entries childNode.printItems(); }
/** * Method returns the current Wig item and advances to the next Wig record. * <p/> * Returns: * Wig item for current BigWig data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an NoSuchElementException will be thrown. */ public WigItem next() { // return next Wig item in list if (wigItemIndex < wigItemList.size()) return (wigItemList.get(wigItemIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (wigItemList.get(wigItemIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for wig region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current bed feature and advances to the next bed record. * <p/> * Returns: * Bed feature for current BigBed data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an UnsupportedOperationException will be thrown. */ public ZoomDataRecord next() { // Is there a need to fetch next data block? if (zoomRecordIndex < zoomRecordList.size()) return (zoomRecordList.get(zoomRecordIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (zoomRecordList.get(zoomRecordIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for zoom region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current Wig item and advances to the next Wig record. * <p/> * Returns: * Wig item for current BigWig data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an NoSuchElementException will be thrown. */ public WigItem next() { // return next Wig item in list if (wigItemIndex < wigItemList.size()) return (wigItemList.get(wigItemIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (wigItemList.get(wigItemIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for wig region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current bed feature and advances to the next bed record. * <p/> * Returns: * Bed feature for current BigBed data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an UnsupportedOperationException will be thrown. */ public ZoomDataRecord next() { // Is there a need to fetch next data block? if (zoomRecordIndex < zoomRecordList.size()) return (zoomRecordList.get(zoomRecordIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (zoomRecordList.get(zoomRecordIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for zoom region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current Wig item and advances to the next Wig record. * <p/> * Returns: * Wig item for current BigWig data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an NoSuchElementException will be thrown. */ public WigItem next() { // return next Wig item in list if (wigItemIndex < wigItemList.size()) return (wigItemList.get(wigItemIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (wigItemList.get(wigItemIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for wig region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current bed feature and advances to the next bed record. * <p/> * Returns: * Bed feature for current BigBed data record. * <p/> * Note: If "next" method is called when a "next item" does not exist, * an UnsupportedOperationException will be thrown. */ public ZoomDataRecord next() { // Is there a need to fetch next data block? if (zoomRecordIndex < zoomRecordList.size()) return (zoomRecordList.get(zoomRecordIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, isContained); if (nHits > 0) { // Note: getDataBlock initializes bed feature index to 0 return (zoomRecordList.get(zoomRecordIndex++)); // return 1st Data Block item } else { String result = String.format("Failed to find data for zoom region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.info(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current bed feature and advances to the next bed record. * * Returns: * Bed feature for current BigBed data record. * * Note: If "next" method is called when a "next item" does not exist, * an UnsupportedOperationException will be thrown. */ public BedFeature next() { // Is there a need to fetch next data block? if(bedFeatureIndex < bedFeatureList.size()) return(bedFeatureList.get(bedFeatureIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, contained); if(nHits > 0){ // Note: getDataBlock initializes bed feature index to 0 return(bedFeatureList.get(bedFeatureIndex++)); // return 1st Data Block item } else{ String result = String.format("Failed to find data for bed region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
/** * Method returns the current bed feature and advances to the next bed record. * * Returns: * Bed feature for current BigBed data record. * * Note: If "next" method is called when a "next item" does not exist, * an UnsupportedOperationException will be thrown. */ public BedFeature next() { // Is there a need to fetch next data block? if(bedFeatureIndex < bedFeatureList.size()) return(bedFeatureList.get(bedFeatureIndex++)); // attempt to get next leaf item data block else { int nHits = getHitRegion(selectionRegion, contained); if(nHits > 0){ // Note: getDataBlock initializes bed feature index to 0 return(bedFeatureList.get(bedFeatureIndex++)); // return 1st Data Block item } else{ String result = String.format("Failed to find data for bed region (%d,%d,%d,%d)\n", hitRegion.getStartChromID(), hitRegion.getStartBase(), hitRegion.getEndChromID(), hitRegion.getEndBase()); log.error(result); return null; //throw new NoSuchElementException(result); } } }
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; // 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 = 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 = 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 = 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; // 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; }