Uses of Class
org.utgenome.UTGBException

Packages that use UTGBException

org.utgenome
org.utgenome.format.axt
org.utgenome.format.bed
org.utgenome.format.egt
org.utgenome.format.fasta	FASTA utilities
org.utgenome.format.fastq
org.utgenome.format.illumina
org.utgenome.format.keyword
org.utgenome.format.sam
org.utgenome.format.wig
org.utgenome.gwt.utgb.server	UTGB's server-side libraries for supporting web request handling, managing database connections, initialization of UTGB web applications, etc.
org.utgenome.gwt.utgb.server.app	Contains sample codes of web actions.
org.utgenome.util.kmer
org.utgenome.util.repeat

Uses of UTGBException in org.utgenome

Methods in org.utgenome that return UTGBException

static UTGBException

UTGBException.convert(Exception e)

Uses of UTGBException in org.utgenome.format.axt

Methods in org.utgenome.format.axt that throw UTGBException

static Iterable<AXTAlignment>	AXTLens.lens(BufferedReader in)
static void	AXTLens.lens(BufferedReader in, org.xerial.util.ObjectHandler<AXTAlignment> handler)
static void	AXTLens.lens(File axtFile, org.xerial.util.ObjectHandler<AXTAlignment> handler)
static AXTAlignment	AXTLens.lens(List<String> axtBlock)
static void	AXTLens.parseSummaryLine(AXTAlignment obj, String summaryLine)

Uses of UTGBException in org.utgenome.format.bed

Methods in org.utgenome.format.bed that throw UTGBException

static List<GenomeRange>	BEDDatabase.overlapQuery(File bedPath, ChrLoc location)
static BEDQuery	BED2SilkReader.scan(Reader input, BEDQuery query) Read an input BED data, and retrieves BEDTrack and BEDEntry information through the BEDQuery interface.
String	BED2Silk.toSilk()
void	BED2Silk.toSilk(PrintWriter pout)

Uses of UTGBException in org.utgenome.format.egt

Methods in org.utgenome.format.egt that throw UTGBException

void	EGTXMLReader.load(Reader xmlReader)
static org.xerial.util.Pair<String,String>	EagyGeneLine.parse(String parameter)
static ParameterMap	EagyGeneLine.parseLine(String line) parsing each line then convert its contents into a ParameterMap
static void	EagyGeneLine.setRange(String value, ParameterMap map)

Constructors in org.utgenome.format.egt that throw UTGBException

EagyGeneLine(String line)

Uses of UTGBException in org.utgenome.format.fasta

Methods in org.utgenome.format.fasta that throw UTGBException

static CompactACGT	CompactACGT.createFromString(String seq)
GenomeSequence	CompactFASTA.getSequence(String chr)
GenomeSequence	CompactFASTA.getSequence(String chr, int start)
CompactACGT	CompactFASTA.getSequence(String chr, int start, int end) Retrieves a genome sequence of the specified range [start, end)
CompactACGT	CompactFASTA.getSequence(String chr, int start, int end, boolean isReverse)
FASTASequence	FASTAPullParser.nextSequence() read the next fasta sequence;
static ReferenceSequence	FASTADatabase.querySequence(File fastaFile, ChrLoc location)
static void	FASTADatabase.querySequence(File dbFile, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
static void	FASTADatabase.querySequence(org.xerial.db.sql.sqlite.SQLiteAccess db, ChrLoc location, org.xerial.db.sql.BeanResultHandler<FASTADatabase.NSeq> handler)
CompactACGT	CompactACGT.reverseComplement()
CompactACGT	CompactACGT.subSequence(int start, int length) return a subsequence of this ACGT string.

Constructors in org.utgenome.format.fasta that throw UTGBException

FASTA(File fastaFile)

Uses of UTGBException in org.utgenome.format.fastq

Methods in org.utgenome.format.fastq that throw UTGBException

int	FastqToBAM.convert()
int	FastqToBAM.convert(Reader input1, Reader input2)
FastqRead	FastqReader.next() Read the next FASTQ read entry.
static FastqRead	FastqRead.parse(BufferedReader reader)

Uses of UTGBException in org.utgenome.format.illumina

Methods in org.utgenome.format.illumina that throw UTGBException

FastqRead	QSeqToFASTQ.convertToFastq(String line)
static FastqRead	Seq2Fastq.convertToFastq(String line)

Uses of UTGBException in org.utgenome.format.keyword

Methods in org.utgenome.format.keyword that throw UTGBException

void	KeywordDB.importFromBAM(String ref, InputStream samOrBamInput)
void	KeywordDB.importFromBED(String ref, Reader bed)
void	KeywordDB.importFromFASTAIndex(String ref, Reader fastaIndexFile)
void	KeywordDB.importFromTAB(String ref, Reader tabFileReader)
void	KeywordDB.importKeywordAliasFile(Reader keywordAliasFile)

Constructors in org.utgenome.format.keyword that throw UTGBException

KeywordDB(String dbPath)

Uses of UTGBException in org.utgenome.format.sam

Methods in org.utgenome.format.sam that throw UTGBException

void	Sam2WigConverter.convert(File samOrBam, String chr, int start, int end)
void	Sam2WigConverter.convert(File samOrBam, Writer out) Convert the input SAM file records into WIG format of read depth
static List<GenomeRange>	SAMReader.depthCoverage(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<GenomeRange>	SAMReader.depthCoverageInWIG(File wigFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config)
static List<GenomeRange>	SAMReader.overlapQuery(File bamFile, ChrLoc loc, int pixelWidth, ReadQueryConfig config) Retrieved SAMReads (or SAMReadPair) overlapped with the specified interval

Uses of UTGBException in org.utgenome.format.wig

Methods in org.utgenome.format.wig that throw UTGBException

CompactWIGData	WIGDatabaseReader.fillPixelsWithMedian(CompactWIGData cwig, int pixelWidth, int trackId, int start, int end)
CompactWIGData	WIGDatabaseReader.getCompactWigData(int trackId, int start, int end, int pixelWidth)
static List<CompactWIGData>	WIGDatabaseReader.getCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
HashMap<Integer,Float>	WIGDatabaseReader.getData(int trackId)
HashMap<Integer,Float>	WIGDatabaseReader.getData(int trackId, int start, int end)
HashMap<Integer,Float>	WIGDatabaseReader.getData(int windowWidth, int trackId, int start, int end)
static List<CompactWIGData>	WIGDatabaseReader.getRoughCompactWigDataList(File path, int pixelWidth, ChrLoc location, GraphWindow windowFunc)
WigGraphData	WIGDatabaseReader.getWigData(int trackId)
WigGraphData	WIGDatabaseReader.getWigData(int trackId, int start, int end)
WigGraphData	WIGDatabaseReader.getWigData(int windowWidth, int trackId, int start, int end)
static List<WigGraphData>	WIGDatabaseReader.getWigDataList(File fileName, int windowWidth, ChrLoc location, GraphWindow windowFunc)
ArrayList<WigGraphData>	WIGDatabaseReader.getWigDataList(int windowWidth, String chrom, int start, int end)
ArrayList<WigGraphData>	WIGDatabaseReader.getWigDataList(String chrom, int start, int end)
String	WIG2Silk.toSilk()
void	WIG2Silk.toSilk(PrintWriter out)

Constructors in org.utgenome.format.wig that throw UTGBException

WIGDatabaseReader(File file, GraphWindow windowFunc)

WIGDatabaseReader(String inputFileURL, GraphWindow windowFunc)

Uses of UTGBException in org.utgenome.gwt.utgb.server

Methods in org.utgenome.gwt.utgb.server that throw UTGBException

String	WebTrackBase.createSQL(String sqlTemplate, Object... args) Create an SQL from a given template and variable assignments.
String	WebTrackBase.createSQLFromFile(String sqlFileName, Object... args) Create an SQL from a given file (relative to the caller class) and variable assignments.
static String	WebTrackBase.createSQLStatement(String sqlTemplate, Object... args)
org.xerial.db.sql.DatabaseAccess	WebTrackBase.getDatabaseAccess(String databaseID) Retrieves the database access
static org.xerial.db.sql.DatabaseAccess	UTGBMaster.getDatabaseAccess(String databaseID)
static org.xerial.db.sql.DatabaseAccess	JDBCService.getDatabaseAccess(String projectRootFolder, UTGBConfig.Database db)
static org.xerial.db.sql.DatabaseAccess	JDBCService.getDatabaseAccess(UTGBConfig.Database db)
protected org.xerial.db.sql.DatabaseAccess	UTGBMaster.getDatabaseAccessInternal(String databaseID)
static String	UTGBMaster.getProjectRootFolder()
<T> List<T>	WebTrackBase.loadJSON(Reader jsonStream, Class<T> resultClass) load the json data, and converts them into a list of result class instances
<T> void	WebTrackBase.loadJSON(Reader jsonStream, Class<T> resultClass, org.xerial.util.ObjectHandler<T> resultHandler) Load JSON data from the stream and convert the JSON data into Object of the given resultClass.
protected static UTGBConfig	UTGBMaster.loadUTGBConfig()
<T> void	WebTrackBase.toJSON(String databaseID, String sql, Class<T> resultClass, javax.servlet.http.HttpServletResponse response)
void	RequestHandler.validate(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response) Validate request parameters
void	RequestHandlerBase.validate(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)

Uses of UTGBException in org.utgenome.gwt.utgb.server.app

Methods in org.utgenome.gwt.utgb.server.app that throw UTGBException

static DASResult	DASViewer.queryDAS(String baseURL, String dasType, ChrLoc chrLoc)
void	Sequence.validate(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)

Uses of UTGBException in org.utgenome.util.kmer

Methods in org.utgenome.util.kmer that throw UTGBException

int	KmerIntegerFactory.parseString(String acgt)

Uses of UTGBException in org.utgenome.util.repeat

Methods in org.utgenome.util.repeat that throw UTGBException

void	RepeatChainFinder.IntervalCluster.validate()