org.utgenome.format.wig
Class WIGDatabaseReader

java.lang.Object
  org.utgenome.format.wig.WIGDatabaseReader

public class WIGDatabaseReader
extends Object

Wig database (sqlite) reader

Author:

yoshimura, leo

Nested Class Summary

static class	WIGDatabaseReader.AvgSelector
static class	WIGDatabaseReader.MAXSelector
static class	WIGDatabaseReader.MedianSelector
static class	WIGDatabaseReader.MINSelector

Constructor Summary

WIGDatabaseReader(File file, GraphWindow windowFunc)

WIGDatabaseReader(String inputFileURL, GraphWindow windowFunc)

Method Summary

void	close()
static CompactWIGData	convertResolution(WigGraphData w, ChrLoc location, int windowWidth)
CompactWIGData	fillPixelsWithMedian(CompactWIGData cwig, int pixelWidth, int trackId, int start, int end)
ArrayList<String>	getBrowser()
ArrayList<String>	getChromList()
CompactWIGData	getCompactWigData(int trackId, int start, int end, int pixelWidth)
static List<CompactWIGData>	getCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
HashMap<Integer,Float>	getData(int trackId)
HashMap<Integer,Float>	getData(int trackId, int start, int end)
HashMap<Integer,Float>	getData(int windowWidth, int trackId, int start, int end)
static List<CompactWIGData>	getRoughCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
HashMap<String,String>	getTrack(int trackId)
ArrayList<Integer>	getTrackIdList()
ArrayList<Integer>	getTrackIdList(String chrom)
WigGraphData	getWigData(int trackId)
WigGraphData	getWigData(int trackId, int start, int end)
WigGraphData	getWigData(int windowWidth, int trackId, int start, int end)
static List<WigGraphData>	getWigDataList(File fileName, int windowWidth, ChrLoc location, GraphWindow windowFunc)
ArrayList<WigGraphData>	getWigDataList(int windowWidth, String chrom, int start, int end)
ArrayList<WigGraphData>	getWigDataList(String chrom, int start, int end)
static CompactWIGData	prepareCompactWigData(WigGraphData w, ChrLoc location)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WIGDatabaseReader

public WIGDatabaseReader(File file,
                         GraphWindow windowFunc)
                  throws UTGBException

Throws:

UTGBException

WIGDatabaseReader

public WIGDatabaseReader(String inputFileURL,
                         GraphWindow windowFunc)
                  throws UTGBException

Throws:

UTGBException

Method Detail

close

public void close()
           throws SQLException

Throws:

SQLException

getBrowser

public ArrayList<String> getBrowser()
                             throws SQLException

Throws:

SQLException

getTrackIdList

public ArrayList<Integer> getTrackIdList(String chrom)
                                  throws SQLException

Throws:

SQLException

getTrackIdList

public ArrayList<Integer> getTrackIdList()
                                  throws SQLException

Throws:

SQLException

getChromList

public ArrayList<String> getChromList()
                               throws SQLException

Throws:

SQLException

getTrack

public HashMap<String,String> getTrack(int trackId)
                                throws SQLException

Throws:

SQLException

getData

public HashMap<Integer,Float> getData(int trackId,
                                      int start,
                                      int end)
                               throws SQLException,
                                      IOException,
                                      DataFormatException,
                                      NumberFormatException,
                                      ClassNotFoundException,
                                      UTGBException

Throws:

SQLException

IOException

DataFormatException

NumberFormatException

ClassNotFoundException

UTGBException

fillPixelsWithMedian

public CompactWIGData fillPixelsWithMedian(CompactWIGData cwig,
                                           int pixelWidth,
                                           int trackId,
                                           int start,
                                           int end)
                                    throws SQLException,
                                           UTGBException

Throws:

SQLException

UTGBException

getData

public HashMap<Integer,Float> getData(int windowWidth,
                                      int trackId,
                                      int start,
                                      int end)
                               throws SQLException,
                                      IOException,
                                      DataFormatException,
                                      NumberFormatException,
                                      ClassNotFoundException,
                                      UTGBException

Throws:

SQLException

IOException

DataFormatException

NumberFormatException

ClassNotFoundException

UTGBException

getData

public HashMap<Integer,Float> getData(int trackId)
                               throws NumberFormatException,
                                      SQLException,
                                      IOException,
                                      DataFormatException,
                                      ClassNotFoundException,
                                      UTGBException

Throws:

NumberFormatException

SQLException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getWigData

public WigGraphData getWigData(int windowWidth,
                               int trackId,
                               int start,
                               int end)
                        throws SQLException,
                               NumberFormatException,
                               IOException,
                               DataFormatException,
                               ClassNotFoundException,
                               UTGBException

Throws:

SQLException

NumberFormatException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getWigData

public WigGraphData getWigData(int trackId,
                               int start,
                               int end)
                        throws SQLException,
                               NumberFormatException,
                               IOException,
                               DataFormatException,
                               ClassNotFoundException,
                               UTGBException

Throws:

SQLException

NumberFormatException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getCompactWigData

public CompactWIGData getCompactWigData(int trackId,
                                        int start,
                                        int end,
                                        int pixelWidth)
                                 throws SQLException,
                                        UTGBException

Throws:

SQLException

UTGBException

getWigData

public WigGraphData getWigData(int trackId)
                        throws SQLException,
                               NumberFormatException,
                               IOException,
                               DataFormatException,
                               ClassNotFoundException,
                               UTGBException

Throws:

SQLException

NumberFormatException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getWigDataList

public ArrayList<WigGraphData> getWigDataList(int windowWidth,
                                              String chrom,
                                              int start,
                                              int end)
                                       throws SQLException,
                                              NumberFormatException,
                                              IOException,
                                              DataFormatException,
                                              ClassNotFoundException,
                                              UTGBException

Throws:

SQLException

NumberFormatException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getWigDataList

public ArrayList<WigGraphData> getWigDataList(String chrom,
                                              int start,
                                              int end)
                                       throws SQLException,
                                              NumberFormatException,
                                              IOException,
                                              DataFormatException,
                                              ClassNotFoundException,
                                              UTGBException

Throws:

SQLException

NumberFormatException

IOException

DataFormatException

ClassNotFoundException

UTGBException

getWigDataList

public static List<WigGraphData> getWigDataList(File fileName,
                                                int windowWidth,
                                                ChrLoc location,
                                                GraphWindow windowFunc)
                                         throws UTGBException,
                                                SQLException

Throws:

UTGBException

SQLException

getRoughCompactWigDataList

public static List<CompactWIGData> getRoughCompactWigDataList(File path,
                                                              int pixelWidth,
                                                              ChrLoc location,
                                                              GraphWindow windowFunc)
                                                       throws UTGBException,
                                                              SQLException

Throws:

UTGBException

SQLException

getCompactWigDataList

public static List<CompactWIGData> getCompactWigDataList(File path,
                                                         int pixelWidth,
                                                         ChrLoc location,
                                                         GraphWindow windowFunc)
                                                  throws UTGBException,
                                                         SQLException

Throws:

UTGBException

SQLException

prepareCompactWigData

public static CompactWIGData prepareCompactWigData(WigGraphData w,
                                                   ChrLoc location)

convertResolution

public static CompactWIGData convertResolution(WigGraphData w,
                                               ChrLoc location,
                                               int windowWidth)