contextFold.rna
Class RNA
java.lang.Object
contextFold.rna.RNA
public class RNA
- extends java.lang.Object
Constructor Summary |
RNA(byte[] seq,
java.lang.String annotations)
|
RNA(java.lang.String input)
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RNA(java.lang.String seq,
java.lang.String annotations)
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Methods inherited from class java.lang.Object |
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
annotationLineStart
public static char annotationLineStart
annotationSplit
public static java.lang.String annotationSplit
A
public static final byte A
- See Also:
- Constant Field Values
C
public static final byte C
- See Also:
- Constant Field Values
G
public static final byte G
- See Also:
- Constant Field Values
U
public static final byte U
- See Also:
- Constant Field Values
T
public static final byte T
- See Also:
- Constant Field Values
ROUND
public static final int ROUND
- See Also:
- Constant Field Values
SHARP
public static final int SHARP
- See Also:
- Constant Field Values
OPEN
public static final int OPEN
- See Also:
- Constant Field Values
CLOSE
public static final int CLOSE
- See Also:
- Constant Field Values
UN_PAIRED
public static final int UN_PAIRED
- See Also:
- Constant Field Values
PS_OPEN
public static final int PS_OPEN
- See Also:
- Constant Field Values
PS_CLOSE
public static final int PS_CLOSE
- See Also:
- Constant Field Values
structFormat
public static final char[][] structFormat
ALL_RNA_CHARS
public static final char[] ALL_RNA_CHARS
standardOpen
public static final java.lang.String standardOpen
- See Also:
- Constant Field Values
standardClose
public static final java.lang.String standardClose
- See Also:
- Constant Field Values
pseudoOpen
public static final java.lang.String pseudoOpen
- See Also:
- Constant Field Values
pseudoClose
public static final java.lang.String pseudoClose
- See Also:
- Constant Field Values
standardOpenPattern
public static final java.util.regex.Pattern standardOpenPattern
standardClosePattern
public static final java.util.regex.Pattern standardClosePattern
standardFoldPattern
public static final java.util.regex.Pattern standardFoldPattern
pseudoOpenPattern
public static final java.util.regex.Pattern pseudoOpenPattern
pseudoClosePattern
public static final java.util.regex.Pattern pseudoClosePattern
pseudoFoldPattern
public static final java.util.regex.Pattern pseudoFoldPattern
standardComplementary
public static final java.util.Map<java.lang.Character,java.lang.Character> standardComplementary
close2open
public static final java.util.Map<java.lang.Character,java.lang.Character> close2open
possibleReplacements
public static final java.util.Map<java.lang.Character,char[]> possibleReplacements
STANDARD_RNA_CHARS
public static final java.lang.String STANDARD_RNA_CHARS
- See Also:
- Constant Field Values
RNAStrPattern
public static final java.util.regex.Pattern RNAStrPattern
nonRNACharPattern
public static final java.util.regex.Pattern nonRNACharPattern
annotationRegexp
public static final java.lang.String annotationRegexp
- See Also:
- Constant Field Values
annotationPattern
public static final java.util.regex.Pattern annotationPattern
seq
public byte[] seq
seqString
public java.lang.String seqString
foldings
public java.util.List<int[]> foldings
predicted
public int[] predicted
length
public final int length
annotations
public java.lang.String annotations
annotationsMap
public java.util.Map<java.lang.String,java.lang.String> annotationsMap
RNA
public RNA(java.lang.String seq,
java.lang.String annotations)
RNA
public RNA(java.lang.String input)
RNA
public RNA(byte[] seq,
java.lang.String annotations)
stringToByte
public static byte[] stringToByte(java.lang.String seq)
charToByte
public static byte[] charToByte(char[] charSeq)
addFold
public void addFold(int[] fold)
addFold
public void addFold(java.lang.String foldSeq)
addFold
public void addFold(java.lang.String foldStr,
int format)
getFold
public static int[] getFold(java.lang.String foldStr,
int format)
- Returns the index paring described by a dot-bracket string.
Note that pseudoknots are currently ignored.
- Parameters:
foldStr
- dot-bracket string.format
- round/sharp.
- Returns:
- an integer array
fold
, s.t. fold[i] = j
implies
that indices i and j are paired.
get
public byte get(int i)
sequence
public byte[] sequence()
toString
public java.lang.String toString()
- Overrides:
toString
in class java.lang.Object
foldToBracets
public static java.lang.String foldToBracets(int[] fold)
foldToBracets
public static java.lang.String foldToBracets(int[] fold,
int format)
byteToStr
public static java.lang.String byteToStr(byte[] seq)
getAnnotationVal
public java.lang.String getAnnotationVal(java.lang.String annotation)
goldFold
public int[] goldFold()
getFoldNo
public int[] getFoldNo(int i)
lastPrediction
public int[] lastPrediction()
filter
public static void filter(java.util.List<RNA> rnas,
java.lang.String annotationFilter)
filter
public static void filter(java.util.List<RNA> rnas,
int maxLength)
getFold
public static int[] getFold(java.lang.String string)
getStringFold
public java.lang.String getStringFold()
getStringFold
public java.lang.String getStringFold(int foldIx)
getStringSequence
public java.lang.String getStringSequence()
setRandomSeed
public static void setRandomSeed(long seed)
setRandomSeed
public static void setRandomSeed()
randomRNA
public static RNA randomRNA(int length)
randomRNAString
public static java.lang.String randomRNAString(int length)
hashCode
public int hashCode()
- Overrides:
hashCode
in class java.lang.Object
equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in class java.lang.Object
isStandardRNAString
public static boolean isStandardRNAString(java.lang.String str)
getFold
public static int[] getFold(java.lang.String foldStr,
java.util.regex.Pattern openPattern,
java.util.regex.Pattern closePattern)
- Returns the index paring described by a dot-bracket string.
- Parameters:
foldStr
- (extended) dot-bracket string.standardOpenPattern
- standardClosePattern
-
- Returns:
- an integer array
fold
, s.t. fold[i] = j
implies
that indices i and j are paired.
getPseudoFold
public static int[] getPseudoFold(java.lang.String struct)
getNonCrossingFold
public static int[] getNonCrossingFold(java.lang.String struct)
standardized
public static java.lang.String standardized(java.lang.String seq,
java.lang.String foldStr)
- Replacing ambiguous characters by RNA nucleotides,
for the sake of efficient learning.
Replacing ambiguous characters which are paired to a nucleotide
with the canonical complementary nucleotide, and replacing
ambiguous base-pairs and unpaired bases with random base-pairs.
- Parameters:
seq
- the original sequence.foldStr
- the folding of the sequence.
- Returns:
- the standardized sequence.
getPossibleRplacement
public static char getPossibleRplacement(char ch)
isPseudoFold
public static boolean isPseudoFold(java.lang.String foldStr)
RNAListStatistics
public static java.lang.String RNAListStatistics(java.util.List<RNA> rnas)
isStandardRNAChar
public static boolean isStandardRNAChar(char charAt)