info.bioinfweb.libralign.model.utils

Class AlignmentModelUtils

java.lang.Object

info.bioinfweb.libralign.model.utils.AlignmentModelUtils

public class AlignmentModelUtils
extends java.lang.Object

Provider general tool methods to be used with instances of AlignmentModel.

Since:

0.4.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	THYMINE
static java.lang.String	URACILE

Constructor Summary

Constructors

Constructor and Description
AlignmentModelUtils()

Method Summary

Modifier and Type	Method and Description
static <T> java.util.List<T>	charSequenceToTokenList(java.lang.CharSequence sequence, TokenSet<T> tokenSet) Converts a character sequence to a sequence of tokens.
static <T> java.util.List<T>	charSequenceToTokenList(java.lang.CharSequence sequence, TokenSet<T> tokenSet, boolean allowWhitespace, T defaultToken) Convenience method that uses CharSequenceTokenScanner to parse all tokens contained in the specified string and returns these as a list.
static void	reverseComplement(AlignmentModel<?> model, java.lang.String sequenceID) Reverse complements a whole nucleotide sequence.
static <T> void	reverseComplement(AlignmentModel<T> model, java.lang.String sequenceID, int start, int end) Reverse complements a part of a nucleotide sequence.
static java.lang.String	selectionAsString(AlignmentArea area, boolean separateBySpace) Converts the current selection to a String.

Methods inherited from class java.lang.Object

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

Field Detail

THYMINE

public static final java.lang.String THYMINE

See Also:

Constant Field Values

URACILE

public static final java.lang.String URACILE

See Also:

Constant Field Values

Constructor Detail

AlignmentModelUtils

public AlignmentModelUtils()

Method Detail

charSequenceToTokenList

public static <T> java.util.List<T> charSequenceToTokenList(java.lang.CharSequence sequence,
                                                            TokenSet<T> tokenSet)

Converts a character sequence to a sequence of tokens. Each character in sequence is considered to be a valid token representation in the specified set.

Note that CharSequenceTokenScanner or charSequenceToTokenList(CharSequence, TokenSet, boolean, Object) are more powerful alternatives to this method that allow longer token representations and handled invalid representations.

Parameters:

sequence - the character sequence to be converted

tokenSet - the token set used to create token objects

Returns:

the sequence of tokens created from sequence

Throws:

java.lang.IllegalArgumentException - if a character in sequence is not a valid token representation in tokenSet

See Also:

CharSequenceTokenScanner, charSequenceToTokenList(CharSequence, TokenSet, boolean, Object)

charSequenceToTokenList

public static <T> java.util.List<T> charSequenceToTokenList(java.lang.CharSequence sequence,
                                                            TokenSet<T> tokenSet,
                                                            boolean allowWhitespace,
                                                            T defaultToken)

Convenience method that uses CharSequenceTokenScanner to parse all tokens contained in the specified string and returns these as a list.

Parameters:

sequence - the sequence to parse tokens from

tokenSet - the token set containing the tokens to be parsed

allowWhitespace - Specify true here to allow whitespace between token representations or false if not. Note that specifying false will lead to a IllegalArgumentException if the specified token set contains representations longer than one character.

defaultToken - a default token to be returned if invalid token representations are found (If null is specified here, #next() will throw an exception if an invalid representation is found.)

Throws:

java.lang.IllegalArgumentException - if allowWhitespace was set to false although tokenSet contains token representations that are longer than one character

InvalidTokenRepresentationException - if no according token can be found for a string representation and no default token was defined

reverseComplement

public static <T> void reverseComplement(AlignmentModel<T> model,
                                         java.lang.String sequenceID,
                                         int start,
                                         int end)

Reverse complements a part of a nucleotide sequence. Nucleotide tokens need to have a one-character string representation, in order to be recognized by this method. Non-nucleotide tokens and all tokens with a string representation with a length different from 1 are left unchanged in the reverted sequence.

Parameters:

model - the alignment model containing the sequence

sequenceID - the ID of the sequence to be reverse complemented

start - the first position of the subsequence to be reverse complemented

end - the first position behind the subsequence to be reverse complemented

See Also:

PherogramArea#reverseComplement()

reverseComplement

public static void reverseComplement(AlignmentModel<?> model,
                                     java.lang.String sequenceID)

Reverse complements a whole nucleotide sequence.

Parameters:

model - the alignment model containing the sequence

sequenceID - the ID of the sequence to be reverse complemented

selectionAsString

public static java.lang.String selectionAsString(AlignmentArea area,
                                                 boolean separateBySpace)

Converts the current selection to a String.

Parameters:

area - the alignment area containing the according alignment and selection model

separateBySpace - Specify true here, if single token representations shall be separated by a space character, or false otherwise. (true should usually be specified, if token representations can be longer than one character.)

Returns:

the string representation of the current selection or an empty string if nothing is selected