genomicsnpanalyzer
Class Worker

java.lang.Object
  genomicsnpanalyzer.Worker

public class Worker
extends java.lang.Object

Field Summary

static byte	A
static byte	C
static byte	CANNOT_ANNOTATE
static java.awt.Color	CANNOT_ANNOTATE_COLOR
static java.lang.String[]	chromosomes
static byte	CNV_3PRIME_UTR
static java.awt.Color	CNV_3PRIME_UTR_COLOR
static byte	CNV_5PRIME_UTR
static java.awt.Color	CNV_5PRIME_UTR_COLOR
static byte	CNV_CANNOT_ANNOTATE
static java.awt.Color	CNV_CANNOT_ANNOTATE_COLOR
static byte	CNV_CODING_DISRUPTED_FRAMESHIFT
static java.awt.Color	CNV_CODING_DISRUPTED_FRAMESHIFT_COLOR
static byte	CNV_CODING_DISRUPTED_OTHER
static java.awt.Color	CNV_CODING_DISRUPTED_OTHER_COLOR
static byte	CNV_DOWNSTREAM
static java.awt.Color	CNV_DOWNSTREAM_COLOR
static byte	CNV_INTERGENIC
static java.awt.Color	CNV_INTERGENIC_COLOR
static byte	CNV_INTRONIC
static java.awt.Color	CNV_INTRONIC_COLOR
static byte	CNV_INTRONIC_EXON_BOUNDARY
static java.awt.Color	CNV_INTRONIC_EXON_BOUNDARY_COLOR
static byte	CNV_SPLICE_SITE
static java.awt.Color	CNV_SPLICE_SITE_COLOR
static byte	CNV_TRANSCRIPT_INCLUDED
static java.awt.Color	CNV_TRANSCRIPT_INCLUDED_COLOR
static byte	CNV_UPSTREAM
static java.awt.Color	CNV_UPSTREAM_COLOR
static java.lang.String[]	CNVFunctionsList
static byte	DOWNSTREAM
static java.awt.Color	DOWNSTREAM_COLOR
static java.lang.String[]	ensemblIndelTypeList
static byte	ESSENTIAL_SPLICE_SITE
static java.awt.Color	ESSENTIAL_SPLICE_SITE_COLOR
static byte	EXONIC_NON_CODING_RNA
static java.awt.Color	EXONIC_NON_CODING_RNA_COLOR
static int	ExonSplice3
static int	ExonSplice3_E
static int	ExonSplice3_I
static int	ExonSplice5
static int	ExonSplice5_E
static int	ExonSplice5_I
static byte	FRAMESHIFT_CODING
static java.awt.Color	FRAMESHIFT_CODING_COLOR
static java.lang.String[]	FunctionsList
static byte	G
static java.lang.String	IMMUNEKEYWORDS
static byte	INTERGENIC
static java.awt.Color	INTERGENIC_COLOR
static byte	INTRONIC
static java.awt.Color	INTRONIC_COLOR
static byte	INTRONIC_EXON_BOUNDARY
static java.awt.Color	INTRONIC_EXON_BOUNDARY_COLOR
static byte	NON_SYNONYMOUS_CODING
static java.awt.Color	NON_SYNONYMOUS_CODING_COLOR
static byte	PRIME_UTR3
static java.awt.Color	PRIME_UTR3_COLOR
static byte	PRIME_UTR5
static java.awt.Color	PRIME_UTR5_COLOR
static byte	REFERENCE
static java.awt.Color	REFERENCE_COLOR
static byte	REGULATION_REGION
static java.awt.Color	REGULATION_REGION_COLOR
static byte	SPLICE_SITE
static java.awt.Color	SPLICE_SITE_COLOR
static byte	STOP_GAINED
static java.awt.Color	STOP_GAINED_COLOR
static byte	STOP_LOST
static java.awt.Color	STOP_LOST_COLOR
static byte	SV_3PRIME_UTR
static byte	SV_5PRIME_UTR
static byte	SV_CANNOT_ANNOTATE
static byte	SV_CODING_DISRUPTED
static byte	SV_CODING_DISRUPTED_POSSIBLE
static byte	SV_DOWNSTREAM
static byte	SV_INTERGENIC
static byte	SV_INTRONIC
static byte	SV_INTRONIC_EXON_BOUNDARY
static byte	SV_TRANSCRIPT_INCLUDED
static byte	SV_UPSTREAM
static java.lang.String[]	SVFunctionsList
static java.lang.String[]	SVTypeList
static byte	SYNONYMOUS_CODING
static java.awt.Color	SYNONYMOUS_CODING_COLOR
static byte	T
static byte	UPSTREAM
static java.awt.Color	UPSTREAM_COLOR

Constructor Summary

Worker()
Creates a new instance of Worker

Method Summary

static java.lang.String[]	AmbiguousBase(java.lang.String str)
static java.lang.String	AmbiguousByteBaseToStr(byte b)
static byte	AmbiguousStrBaseToByte(java.lang.String str)
static int	BP2Byte(java.lang.String b)
static int	BP2ByteLastBP(java.lang.String b)
static java.lang.String	Byte2BP(int i)
static byte[]	Byte2ByteBP(int i)
static java.lang.String	byteBaseArrayToStrSlash(byte[] b)
static char	byteBP2char(byte b)
static char[]	byteBP2CharArray(byte[] b)
static java.lang.String	ByteChrToStr(byte byteChr)
static java.lang.String	byteCodon2StrCodon(byte[] c)
static java.lang.String	ByteIlluminaStrandToStr(byte b)
static java.lang.String	ByteStrandToStr(byte b)
static byte	charBP2byte(char b)
static java.lang.String	codon2aa(java.lang.String codon, int mode)
static byte	DetermineIlluminaStrandType1(char b1, char b2)
static byte	DetermineIlluminaStrandType2(char b5, char b3)
static int	GetAAIndex(char AAChar)
static byte[]	getBytes(java.lang.Object obj)
static java.lang.String	getCommaNumber(int n)
static java.lang.String	GetINDELID_FULL(CNVLociFunction thisloci)
static java.lang.String	GetINDELID(CNVLociFunction thisloci)
static byte	getReverseByteBP(byte b)
static byte[]	getReverseByteBPArray(byte[] b)
static char	getReverseCharBP(char b)
static java.lang.String	getRsStr(boolean isRsOrENS, int rsn)
static Numreads4	getSNPNumreads4(java.lang.String s, byte allele)
static java.lang.String	GetSNVID(LociFunction thisloci)
static java.lang.String	GetSVID(SVLociFunction thisloci)
static double	isDouble(java.lang.String str)
static boolean	IsExonSplice3(byte[] b)
static boolean	IsExonSplice5(byte[] b)
static int	isInt(java.lang.String str)
static byte[]	ReadSequence(java.io.RandomAccessFile rf, int readstart, int readend)
static java.lang.String	RemoveComma(java.lang.String s)
static java.lang.String	RemoveDoubleTab(java.lang.String str)
static byte[]	StrBasesToBytes(java.lang.String str)
static byte	StrBaseToByte(java.lang.String str)
static byte	StrChrToByte(java.lang.String strChr)
static int	StrChrToInt(java.lang.String strChr)
static int	StrLocToInt(java.lang.String str)
static byte[]	StrSlashBasesToBytes(java.lang.String str)
static byte	StrStrandToByte(java.lang.String str)
static void	TestFileExist(java.lang.String path)
static java.lang.Object	toObject(byte[] bytearray)

Methods inherited from class java.lang.Object

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

Field Detail

chromosomes

public static java.lang.String[] chromosomes

A

public static byte A

T

public static byte T

G

public static byte G

C

public static byte C

IMMUNEKEYWORDS

public static java.lang.String IMMUNEKEYWORDS

ExonSplice3

public static int ExonSplice3

ExonSplice3_E

public static int ExonSplice3_E

ExonSplice3_I

public static int ExonSplice3_I

ExonSplice5

public static int ExonSplice5

ExonSplice5_I

public static int ExonSplice5_I

ExonSplice5_E

public static int ExonSplice5_E

FunctionsList

public static java.lang.String[] FunctionsList

STOP_GAINED

public static byte STOP_GAINED

STOP_LOST

public static byte STOP_LOST

FRAMESHIFT_CODING

public static byte FRAMESHIFT_CODING

NON_SYNONYMOUS_CODING

public static byte NON_SYNONYMOUS_CODING

ESSENTIAL_SPLICE_SITE

public static byte ESSENTIAL_SPLICE_SITE

SPLICE_SITE

public static byte SPLICE_SITE

REGULATION_REGION

public static byte REGULATION_REGION

INTRONIC_EXON_BOUNDARY

public static byte INTRONIC_EXON_BOUNDARY

PRIME_UTR5

public static byte PRIME_UTR5

PRIME_UTR3

public static byte PRIME_UTR3

EXONIC_NON_CODING_RNA

public static byte EXONIC_NON_CODING_RNA

UPSTREAM

public static byte UPSTREAM

DOWNSTREAM

public static byte DOWNSTREAM

INTRONIC

public static byte INTRONIC

SYNONYMOUS_CODING

public static byte SYNONYMOUS_CODING

INTERGENIC

public static byte INTERGENIC

REFERENCE

public static byte REFERENCE

CANNOT_ANNOTATE

public static byte CANNOT_ANNOTATE

STOP_GAINED_COLOR

public static java.awt.Color STOP_GAINED_COLOR

STOP_LOST_COLOR

public static java.awt.Color STOP_LOST_COLOR

FRAMESHIFT_CODING_COLOR

public static java.awt.Color FRAMESHIFT_CODING_COLOR

NON_SYNONYMOUS_CODING_COLOR

public static java.awt.Color NON_SYNONYMOUS_CODING_COLOR

ESSENTIAL_SPLICE_SITE_COLOR

public static java.awt.Color ESSENTIAL_SPLICE_SITE_COLOR

SPLICE_SITE_COLOR

public static java.awt.Color SPLICE_SITE_COLOR

REGULATION_REGION_COLOR

public static java.awt.Color REGULATION_REGION_COLOR

INTRONIC_EXON_BOUNDARY_COLOR

public static java.awt.Color INTRONIC_EXON_BOUNDARY_COLOR

PRIME_UTR5_COLOR

public static java.awt.Color PRIME_UTR5_COLOR

PRIME_UTR3_COLOR

public static java.awt.Color PRIME_UTR3_COLOR

EXONIC_NON_CODING_RNA_COLOR

public static java.awt.Color EXONIC_NON_CODING_RNA_COLOR

UPSTREAM_COLOR

public static java.awt.Color UPSTREAM_COLOR

DOWNSTREAM_COLOR

public static java.awt.Color DOWNSTREAM_COLOR

INTRONIC_COLOR

public static java.awt.Color INTRONIC_COLOR

SYNONYMOUS_CODING_COLOR

public static java.awt.Color SYNONYMOUS_CODING_COLOR

INTERGENIC_COLOR

public static java.awt.Color INTERGENIC_COLOR

REFERENCE_COLOR

public static java.awt.Color REFERENCE_COLOR

CANNOT_ANNOTATE_COLOR

public static java.awt.Color CANNOT_ANNOTATE_COLOR

CNVFunctionsList

public static java.lang.String[] CNVFunctionsList

CNV_CODING_DISRUPTED_FRAMESHIFT

public static byte CNV_CODING_DISRUPTED_FRAMESHIFT

CNV_CODING_DISRUPTED_OTHER

public static byte CNV_CODING_DISRUPTED_OTHER

CNV_TRANSCRIPT_INCLUDED

public static byte CNV_TRANSCRIPT_INCLUDED

CNV_5PRIME_UTR

public static byte CNV_5PRIME_UTR

CNV_3PRIME_UTR

public static byte CNV_3PRIME_UTR

CNV_INTRONIC_EXON_BOUNDARY

public static byte CNV_INTRONIC_EXON_BOUNDARY

CNV_UPSTREAM

public static byte CNV_UPSTREAM

CNV_DOWNSTREAM

public static byte CNV_DOWNSTREAM

CNV_INTRONIC

public static byte CNV_INTRONIC

CNV_INTERGENIC

public static byte CNV_INTERGENIC

CNV_CANNOT_ANNOTATE

public static byte CNV_CANNOT_ANNOTATE

CNV_SPLICE_SITE

public static byte CNV_SPLICE_SITE

CNV_CODING_DISRUPTED_FRAMESHIFT_COLOR

public static java.awt.Color CNV_CODING_DISRUPTED_FRAMESHIFT_COLOR

CNV_CODING_DISRUPTED_OTHER_COLOR

public static java.awt.Color CNV_CODING_DISRUPTED_OTHER_COLOR

CNV_TRANSCRIPT_INCLUDED_COLOR

public static java.awt.Color CNV_TRANSCRIPT_INCLUDED_COLOR

CNV_5PRIME_UTR_COLOR

public static java.awt.Color CNV_5PRIME_UTR_COLOR

CNV_3PRIME_UTR_COLOR

public static java.awt.Color CNV_3PRIME_UTR_COLOR

CNV_INTRONIC_EXON_BOUNDARY_COLOR

public static java.awt.Color CNV_INTRONIC_EXON_BOUNDARY_COLOR

CNV_UPSTREAM_COLOR

public static java.awt.Color CNV_UPSTREAM_COLOR

CNV_DOWNSTREAM_COLOR

public static java.awt.Color CNV_DOWNSTREAM_COLOR

CNV_INTRONIC_COLOR

public static java.awt.Color CNV_INTRONIC_COLOR

CNV_INTERGENIC_COLOR

public static java.awt.Color CNV_INTERGENIC_COLOR

CNV_CANNOT_ANNOTATE_COLOR

public static java.awt.Color CNV_CANNOT_ANNOTATE_COLOR

CNV_SPLICE_SITE_COLOR

public static java.awt.Color CNV_SPLICE_SITE_COLOR

SVFunctionsList

public static java.lang.String[] SVFunctionsList

SV_CODING_DISRUPTED

public static byte SV_CODING_DISRUPTED

SV_CODING_DISRUPTED_POSSIBLE

public static byte SV_CODING_DISRUPTED_POSSIBLE

SV_TRANSCRIPT_INCLUDED

public static byte SV_TRANSCRIPT_INCLUDED

SV_5PRIME_UTR

public static byte SV_5PRIME_UTR

SV_3PRIME_UTR

public static byte SV_3PRIME_UTR

SV_INTRONIC_EXON_BOUNDARY

public static byte SV_INTRONIC_EXON_BOUNDARY

SV_UPSTREAM

public static byte SV_UPSTREAM

SV_DOWNSTREAM

public static byte SV_DOWNSTREAM

SV_INTRONIC

public static byte SV_INTRONIC

SV_INTERGENIC

public static byte SV_INTERGENIC

SV_CANNOT_ANNOTATE

public static byte SV_CANNOT_ANNOTATE

SVTypeList

public static java.lang.String[] SVTypeList

ensemblIndelTypeList

public static java.lang.String[] ensemblIndelTypeList

Constructor Detail

Worker

public Worker()

Creates a new instance of Worker

Method Detail

RemoveDoubleTab

public static java.lang.String RemoveDoubleTab(java.lang.String str)

isInt

public static int isInt(java.lang.String str)

isDouble

public static double isDouble(java.lang.String str)

getRsStr

public static java.lang.String getRsStr(boolean isRsOrENS,
                                        int rsn)

TestFileExist

public static void TestFileExist(java.lang.String path)

StrChrToByte

public static byte StrChrToByte(java.lang.String strChr)

StrChrToInt

public static int StrChrToInt(java.lang.String strChr)

ByteChrToStr

public static java.lang.String ByteChrToStr(byte byteChr)

StrLocToInt

public static int StrLocToInt(java.lang.String str)

AmbiguousBase

public static java.lang.String[] AmbiguousBase(java.lang.String str)

AmbiguousStrBaseToByte

public static byte AmbiguousStrBaseToByte(java.lang.String str)

AmbiguousByteBaseToStr

public static java.lang.String AmbiguousByteBaseToStr(byte b)

StrBaseToByte

public static byte StrBaseToByte(java.lang.String str)

StrBasesToBytes

public static byte[] StrBasesToBytes(java.lang.String str)

StrSlashBasesToBytes

public static byte[] StrSlashBasesToBytes(java.lang.String str)

byteBaseArrayToStrSlash

public static java.lang.String byteBaseArrayToStrSlash(byte[] b)

StrStrandToByte

public static byte StrStrandToByte(java.lang.String str)

ByteStrandToStr

public static java.lang.String ByteStrandToStr(byte b)

ByteIlluminaStrandToStr

public static java.lang.String ByteIlluminaStrandToStr(byte b)

BP2Byte

public static int BP2Byte(java.lang.String b)

BP2ByteLastBP

public static int BP2ByteLastBP(java.lang.String b)

Byte2BP

public static java.lang.String Byte2BP(int i)

Byte2ByteBP

public static byte[] Byte2ByteBP(int i)

ReadSequence

public static byte[] ReadSequence(java.io.RandomAccessFile rf,
                                  int readstart,
                                  int readend)

byteBP2CharArray

public static char[] byteBP2CharArray(byte[] b)

getReverseByteBP

public static byte getReverseByteBP(byte b)

getReverseCharBP

public static char getReverseCharBP(char b)

getReverseByteBPArray

public static byte[] getReverseByteBPArray(byte[] b)

charBP2byte

public static byte charBP2byte(char b)

byteBP2char

public static char byteBP2char(byte b)

getSNPNumreads4

public static Numreads4 getSNPNumreads4(java.lang.String s,
                                        byte allele)

byteCodon2StrCodon

public static java.lang.String byteCodon2StrCodon(byte[] c)

DetermineIlluminaStrandType1

public static byte DetermineIlluminaStrandType1(char b1,
                                                char b2)

DetermineIlluminaStrandType2

public static byte DetermineIlluminaStrandType2(char b5,
                                                char b3)

IsExonSplice3

public static boolean IsExonSplice3(byte[] b)

IsExonSplice5

public static boolean IsExonSplice5(byte[] b)

GetAAIndex

public static int GetAAIndex(char AAChar)

codon2aa

public static java.lang.String codon2aa(java.lang.String codon,
                                        int mode)

RemoveComma

public static java.lang.String RemoveComma(java.lang.String s)

getCommaNumber

public static java.lang.String getCommaNumber(int n)

GetSNVID

public static java.lang.String GetSNVID(LociFunction thisloci)

GetINDELID

public static java.lang.String GetINDELID(CNVLociFunction thisloci)

GetINDELID_FULL

public static java.lang.String GetINDELID_FULL(CNVLociFunction thisloci)

GetSVID

public static java.lang.String GetSVID(SVLociFunction thisloci)

getBytes

public static byte[] getBytes(java.lang.Object obj)
                       throws java.io.IOException

Throws:

java.io.IOException

toObject

public static java.lang.Object toObject(byte[] bytearray)