Package Files.VCFData
Class Data
- java.lang.Object
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- Files.VCFData.Data
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public class Data extends java.lang.Object
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
add(java.lang.String o, java.lang.String n)
void
addFormat(FormatDefinition fd, Position p, java.lang.String[] d)
void
addPosition(Position position, java.lang.String[] posdata)
void
addPosition(java.lang.String data, java.util.Set<InfoDefinition> infodef, java.util.Set<FormatDefinition> formatdef)
<V> V[][]
asArray(FormatDefinition f, Mapper<V> mapper)
<V> V[][]
asArrayTransposed(FormatDefinition f, Mapper<V> mapper)
byte[][]
asByteArray(FormatDefinition f, ByteMapper mapper)
byte[][]
asByteArrayTransposed(FormatDefinition f, ByteMapper mapper)
double[][]
asDoubleArray(FormatDefinition f, DoubleMapper mapper)
double[][]
asDoubleArrayTransposed(FormatDefinition f, DoubleMapper mapper)
int[][]
asIntArray(FormatDefinition f, IntegerMapper mapper)
int[][]
asIntArrayTransposed(FormatDefinition f, IntegerMapper mapper)
java.lang.String[][]
asStringArray(FormatDefinition f)
java.lang.String[][]
asStringArray(FormatDefinition f, StringMapper mapper)
java.lang.String[][]
asStringArrayTransposed(FormatDefinition f)
java.lang.String[][]
asStringArrayTransposed(FormatDefinition f, StringMapper mapper)
void
changeFormat(FormatDefinition fd, Position p, java.lang.String[] d)
Data
clone()
int
count()
int
countIf(FormatDefinition d, java.lang.String regex)
Position
getPosition(java.lang.String chrom, java.lang.String id)
java.util.List<Position>
getPositions()
java.util.List<java.lang.String>
getSamples()
java.lang.String
getValue(Position p, int s, FormatDefinition f)
java.lang.String
getValue(Position p, java.lang.String s, FormatDefinition f)
static java.lang.String
remove(java.lang.String s, java.util.List<FormatDefinition> defs, FormatDefinition remove)
void
removeFormat(FormatDefinition fd)
void
removeFormat(Position p, FormatDefinition fd)
void
removeInfo(InfoDefinition id)
void
removePosition(Position p)
void
removeSample(java.lang.String s)
static java.lang.String
retrieve(java.lang.String s, java.util.List<FormatDefinition> defs, FormatDefinition wanted)
void
toWriter(java.io.PrintWriter out)
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Method Detail
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addPosition
public void addPosition(java.lang.String data, java.util.Set<InfoDefinition> infodef, java.util.Set<FormatDefinition> formatdef)
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addPosition
public void addPosition(Position position, java.lang.String[] posdata)
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getPosition
public Position getPosition(java.lang.String chrom, java.lang.String id)
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asByteArray
public byte[][] asByteArray(FormatDefinition f, ByteMapper mapper)
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asByteArrayTransposed
public byte[][] asByteArrayTransposed(FormatDefinition f, ByteMapper mapper)
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asIntArray
public int[][] asIntArray(FormatDefinition f, IntegerMapper mapper)
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asIntArrayTransposed
public int[][] asIntArrayTransposed(FormatDefinition f, IntegerMapper mapper)
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asDoubleArray
public double[][] asDoubleArray(FormatDefinition f, DoubleMapper mapper)
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asDoubleArrayTransposed
public double[][] asDoubleArrayTransposed(FormatDefinition f, DoubleMapper mapper)
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asStringArray
public java.lang.String[][] asStringArray(FormatDefinition f)
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asStringArray
public java.lang.String[][] asStringArray(FormatDefinition f, StringMapper mapper)
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asStringArrayTransposed
public java.lang.String[][] asStringArrayTransposed(FormatDefinition f)
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asStringArrayTransposed
public java.lang.String[][] asStringArrayTransposed(FormatDefinition f, StringMapper mapper)
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asArray
public <V> V[][] asArray(FormatDefinition f, Mapper<V> mapper)
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asArrayTransposed
public <V> V[][] asArrayTransposed(FormatDefinition f, Mapper<V> mapper)
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removePosition
public void removePosition(Position p)
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removeInfo
public void removeInfo(InfoDefinition id)
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addFormat
public void addFormat(FormatDefinition fd, Position p, java.lang.String[] d)
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changeFormat
public void changeFormat(FormatDefinition fd, Position p, java.lang.String[] d)
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removeFormat
public void removeFormat(FormatDefinition fd)
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removeFormat
public void removeFormat(Position p, FormatDefinition fd)
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removeSample
public void removeSample(java.lang.String s)
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toWriter
public void toWriter(java.io.PrintWriter out) throws java.io.IOException
- Throws:
java.io.IOException
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count
public int count()
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countIf
public int countIf(FormatDefinition d, java.lang.String regex)
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getPositions
public java.util.List<Position> getPositions()
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getSamples
public java.util.List<java.lang.String> getSamples()
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getValue
public java.lang.String getValue(Position p, int s, FormatDefinition f)
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getValue
public java.lang.String getValue(Position p, java.lang.String s, FormatDefinition f)
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retrieve
public static java.lang.String retrieve(java.lang.String s, java.util.List<FormatDefinition> defs, FormatDefinition wanted)
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remove
public static java.lang.String remove(java.lang.String s, java.util.List<FormatDefinition> defs, FormatDefinition remove)
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add
public java.lang.String add(java.lang.String o, java.lang.String n)
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clone
public Data clone()
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