contextFold.rna
Class RNA

java.lang.Object
  extended by contextFold.rna.RNA

public class RNA
extends java.lang.Object


Field Summary
static byte A
           
static char[] ALL_RNA_CHARS
           
static char annotationLineStart
           
static java.util.regex.Pattern annotationPattern
           
static java.lang.String annotationRegexp
           
 java.lang.String annotations
           
 java.util.Map<java.lang.String,java.lang.String> annotationsMap
           
static java.lang.String annotationSplit
           
static byte C
           
static int CLOSE
           
static java.util.Map<java.lang.Character,java.lang.Character> close2open
           
 java.util.List<int[]> foldings
           
static byte G
           
 int length
           
static java.util.regex.Pattern nonRNACharPattern
           
static int OPEN
           
static java.util.Map<java.lang.Character,char[]> possibleReplacements
           
 int[] predicted
           
static int PS_CLOSE
           
static int PS_OPEN
           
static java.lang.String pseudoClose
           
static java.util.regex.Pattern pseudoClosePattern
           
static java.util.regex.Pattern pseudoFoldPattern
           
static java.lang.String pseudoOpen
           
static java.util.regex.Pattern pseudoOpenPattern
           
static java.util.regex.Pattern RNAStrPattern
           
static int ROUND
           
 byte[] seq
           
 java.lang.String seqString
           
static int SHARP
           
static java.lang.String STANDARD_RNA_CHARS
           
static java.lang.String standardClose
           
static java.util.regex.Pattern standardClosePattern
           
static java.util.Map<java.lang.Character,java.lang.Character> standardComplementary
           
static java.util.regex.Pattern standardFoldPattern
           
static java.lang.String standardOpen
           
static java.util.regex.Pattern standardOpenPattern
           
static char[][] structFormat
           
static byte T
           
static byte U
           
static int UN_PAIRED
           
 
Constructor Summary
RNA(byte[] seq, java.lang.String annotations)
           
RNA(java.lang.String input)
           
RNA(java.lang.String seq, java.lang.String annotations)
           
 
Method Summary
 void addFold(int[] fold)
           
 void addFold(java.lang.String foldSeq)
           
 void addFold(java.lang.String foldStr, int format)
           
static java.lang.String byteToStr(byte[] seq)
           
static byte[] charToByte(char[] charSeq)
           
 boolean equals(java.lang.Object obj)
           
static void filter(java.util.List<RNA> rnas, int maxLength)
           
static void filter(java.util.List<RNA> rnas, java.lang.String annotationFilter)
           
static java.lang.String foldToBracets(int[] fold)
           
static java.lang.String foldToBracets(int[] fold, int format)
           
 byte get(int i)
           
 java.lang.String getAnnotationVal(java.lang.String annotation)
           
static int[] getFold(java.lang.String string)
           
static int[] getFold(java.lang.String foldStr, int format)
          Returns the index paring described by a dot-bracket string.
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.
 int[] getFoldNo(int i)
           
static int[] getNonCrossingFold(java.lang.String struct)
           
static char getPossibleRplacement(char ch)
           
static int[] getPseudoFold(java.lang.String struct)
           
 java.lang.String getStringFold()
           
 java.lang.String getStringFold(int foldIx)
           
 java.lang.String getStringSequence()
           
 int[] goldFold()
           
 int hashCode()
           
static boolean isPseudoFold(java.lang.String foldStr)
           
static boolean isStandardRNAChar(char charAt)
           
static boolean isStandardRNAString(java.lang.String str)
           
 int[] lastPrediction()
           
static RNA randomRNA(int length)
           
static java.lang.String randomRNAString(int length)
           
static java.lang.String RNAListStatistics(java.util.List<RNA> rnas)
           
 byte[] sequence()
           
static void setRandomSeed()
           
static void setRandomSeed(long seed)
           
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.
static byte[] stringToByte(java.lang.String seq)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

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
Constructor Detail

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)
Method Detail

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)