CharSequenceUtilities (Geneious Public API)

java.lang.Object
- com.biomatters.geneious.publicapi.utilities.CharSequenceUtilities

```
public final class CharSequenceUtilities
extends Object
```
Provides static utility methods for creating and manipulating CharSequences (not necessarily Strings). All methods in this class accept arbitrary CharSequences, but are guaranteed to give SequenceCharSequences special treatment where this improves performance. The disadvantage is that changes elsewhere to the concrete class of some CharSequence (e.g. through a wrapper) can have a severe performance impact without any visible warning. It is advisable that any wrappers for CharSequences be aware of SequenceCharSequence and, where applicable, make sure the outermost wrapper stays a SequenceCharSequence for maximum performance. It is guaranteed that when any CharSequence wrapper method in this class encounters a SequenceCharSequence (with potentially long terminal gaps) and the wrapped CharSequence would also have long terminal gaps, then the concrete class of the returned value will be SequenceCharSequence, allowing for efficient handling of the terminal gaps in the result. This class is uninstantiable.

Field Summary

Fields
Modifier and Type Field and Description

static Comparator<CharSequence> CASE_SENSITIVE_ORDER
A Comparator that lexicographically orders CharSequences.

Fields
Modifier and Type	Field and Description
`static Comparator<CharSequence>`	`CASE_SENSITIVE_ORDER` A `Comparator` that lexicographically orders `CharSequence`s.

Method Summary

Methods
Modifier and Type	Method and Description
`static CharSequence`	`asLowerCase(CharSequence charSequence)` A lowercase view of the specified underlying CharSequence, i.e.
`static CharSequence`	`asUpperCase(CharSequence charSequence)` Constructs an uppercase view on the specified underlying CharSequence, i.e.
`static int`	`commonPrefixLength(CharSequence a, CharSequence b)` The length of the longest common (case sensitive) prefix of the two specified CharSequences a and b, i.e.
`static CharSequence`	`concatenate(List<CharSequence> charSequences)` Creates a CharSequence that represents a concatenation of the specified CharSequences in the order in which they appear in the specified list.
`static boolean`	`contains(CharSequence charSequence, char c)` Checks whether a CharSequence contains the specified character.
`static int`	`count(char c, CharSequence charSequence)` Counts the number of occurrences of c in charSequence
`static boolean`	`equals(CharSequence a, CharSequence b)` Checks whether two CharSequences contain the same sequence of characters.
`static boolean`	`equalsIgnoreCase(CharSequence a, CharSequence b)` Checks whether two CharSequences contain the same sequence of characters, ignoring case.
`static CharSequence`	`immutableCopyOf(CharSequence charSequence)` Constructs an immutable CharSequence that consists of the same sequence of characters as the specified CharSequence.
`static boolean`	`isAllGaps(CharSequence charSequence)` Returns true if the given sequence is either empty or contains only gaps.
`static boolean`	`isCharSequenceKnownToBeImmutable(CharSequence charSequence)` Returns true if we know that the specified charSequence will never change.
`static CharSequence`	`repeatedCharSequence(CharSequence internalCharSequence, int numberOfRepeats)` Create a CharSequence that repeats another CharSequence a given number of times.
`static CharSequence`	`reverse(CharSequence charSequence)` Provides a reversed view onto the specified sequence.
`static CharSequence`	`subSequence(CharSequence sequence, int start, int end)` Creates a CharSequence that starts at index `start` and finishes at index `end-1` such that the length of the CharSequence is `start - end`.
`static String`	`toString(CharSequence charSequence)` Constructs a String holding the same sequence of characters as the specified charSequence, without calling `CharSequence.toString()`.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - CASE_SENSITIVE_ORDER
```
public static final Comparator<CharSequence> CASE_SENSITIVE_ORDER
```
    A Comparator that lexicographically orders CharSequences. This Comparator is sensitive to case.
- Method Detail
  - asUpperCase
```
public static CharSequence asUpperCase(CharSequence charSequence)
```
    Constructs an uppercase view on the specified underlying CharSequence, i.e. a CharSequence wrapper cs with cs.length() == charSequence.length() and cs.charAt(i) == Character.toUpperCase(charSequence.charAt(i)). It is guaranteed that if charSequence instanceof SequenceCharSequence, the returned value will also be instanceof SequenceCharSequence (but it may not support log-time modifications).
    
    Parameters:
    charSequence - The CharSequence for which to provide an uppercase view.
    
    Returns:
    An uppercased view on charSequence.
    See Also:
    asLowerCase(CharSequence)
  - asLowerCase
```
public static CharSequence asLowerCase(CharSequence charSequence)
```
    A lowercase view of the specified underlying CharSequence, i.e. a CharSequence wrapper cs with cs.length() == charSequence.length() and cs.charAt(i) == Character.toLowerCase(charSequence.charAt(i)). It is guaranteed that if charSequence instanceof SequenceCharSequence, the returned value will also be instanceof SequenceCharSequence (but it may not support log-time modifications).
    
    Parameters:
    charSequence - The CharSequence for which to provide an lowercase view.
    
    Returns:
    An lowercased view on charSequence.
    See Also:
    asUpperCase(CharSequence)
  - commonPrefixLength
```
public static int commonPrefixLength(CharSequence a,
                     CharSequence b)
```
    The length of the longest common (case sensitive) prefix of the two specified CharSequences a and b, i.e. the largest value i >= 0 such that CharSequenceUtilities.equals(a.subSequence(0, i), b.subSequence(0, i)) is true. If the two specified CharSequences represent the same sequence of characters, then their length will be returned. Note: To obtain the length of the longest common suffix of two sequences a and b, you can use getCommonPrefixLength(reverse(a), reverse(b)).
    
    Parameters:
    a - A charSequence
    b - Another charSequence
    
    Returns:
    A non-negative value, the length of the longest common prefix of a and b.
  - reverse
```
public static CharSequence reverse(CharSequence charSequence)
```
    Provides a reversed view onto the specified sequence. It is guaranteed that if charSequence instanceof SequenceCharSequence, the returned value will also be instanceof SequenceCharSequence (but it may not support log-time modifications).
    Warning: There should rarely be a reason to use this method as reversing a nucleotide sequence is usually wrong (use SequenceUtilities.reverseComplement(CharSequence) instead) and reversing a protein sequence isn't meaningful.
    
    Parameters:
    charSequence - The CharSqeuence for which to provide a reversed view
    
    Returns:
    A reversed view of charSequence
  - equals
```
public static boolean equals(CharSequence a,
             CharSequence b)
```
    Checks whether two CharSequences contain the same sequence of characters. This is the same as a.toString().equals(b.toString()), but it avoids construction of the intermediate Strings.
    
    Parameters:
    a - A CharSequence to be compared to b; must not be null.
    b - A CharSequence to be compared to a; must not be null.
    
    Returns:
    true if a and b contain the same sequence of characters
    
    Throws:
    
    NullPointerException - if a or b is null
    See Also:
    equalsIgnoreCase(CharSequence, CharSequence)
  - toString
```
public static String toString(CharSequence charSequence)
```
    Constructs a String holding the same sequence of characters as the specified charSequence, without calling CharSequence.toString(). CharSequence implementations can use this method to implement their toString() method.
    
    Parameters:
    charSequence - CharSequence for which to construct a String; must not be null
    
    Returns:
    A String holding the same sequence of characters as charSequence
  - equalsIgnoreCase
```
public static boolean equalsIgnoreCase(CharSequence a,
                       CharSequence b)
```
    Checks whether two CharSequences contain the same sequence of characters, ignoring case. This is the same as a.toString().equalsIgnoreCase(b.toString()), but it avoids construction of the intermediate Strings.
    
    Parameters:
    a - A CharSequence to be compared to b; must not be null.
    b - A CharSequence to be compared to a; must not be null.
    
    Returns:
    true if a and b contain the same sequence of characters, modulo case.
    
    Throws:
    
    NullPointerException - if a or b is null
    See Also:
    equals(CharSequence, CharSequence)
  - contains
```
public static boolean contains(CharSequence charSequence,
               char c)
```
    Checks whether a CharSequence contains the specified character.
    
    Parameters:
    charSequence - a CharSequence to look for the character in.
    c - the character to look for
    
    Returns:
    true if the CharSequence contains the specified character.
    
    Throws:
    
    NullPointerException - if charSequence is null
  - count
```
public static int count(char c,
        CharSequence charSequence)
```
    Counts the number of occurrences of c in charSequence
    
    Parameters:
    c - The character to search for
    charSequence - The CharSequence in which to search for c. Must not be null.
    
    Returns:
    The number of times c occurs in charSequence
  - subSequence
```
public static CharSequence subSequence(CharSequence sequence,
                       int start,
                       int end)
```
    Creates a CharSequence that starts at index start and finishes at index end-1 such that the length of the CharSequence is start - end. Useful for implementing CharSequence.subSequence(int, int)
    
    Parameters:
    sequence - a source CharSequence that must not change in length after constructing this SubCharSequence.
    start - the first index (inclusive)
    end - the finish index (exclusive)
    
    Returns:
    A subsequence of the specified charSequence spanning the specified interval.
  - repeatedCharSequence
```
public static CharSequence repeatedCharSequence(CharSequence internalCharSequence,
                                int numberOfRepeats)
```
    Create a CharSequence that repeats another CharSequence a given number of times. It is guaranteed that the returned CharSequence implements XMLSerializable.
    
    Parameters:
    internalCharSequence - the CharSequence to be repeated. The length of internalCharSequence must not change in future.
    numberOfRepeats - the number of times to repeat it
    
    Returns:
    An XMLSerializable CharSequence whose sequence of characters is that of internalCharSequence, repeated numberOfRepeats times.
  - isCharSequenceKnownToBeImmutable
```
public static boolean isCharSequenceKnownToBeImmutable(CharSequence charSequence)
```
    Returns true if we know that the specified charSequence will never change. Returns false if we know that the charSequence is mutable, or if we're not sure.
    This method may be extended in the future to recognise more concrete classes.
    
    Parameters:
    charSequence - A charSequence
    
    Returns:
    true if the specified charSequence is guaranteed to never change.
    
    Throws:
    
    NullPointerException - if charSequence is null
  - immutableCopyOf
```
public static CharSequence immutableCopyOf(CharSequence charSequence)
```
    Constructs an immutable CharSequence that consists of the same sequence of characters as the specified CharSequence. If it is known that the specified charSequence is already immutable, then this may or may not return charSequence itself instead of a copy. The concrete class of the returned value is not specified and shouldn't be relied on.
    
    Parameters:
    charSequence - A CharSequence
    
    Returns:
    An immutable CharSequence that contains the same sequence of characters as charSequence
    
    Throws:
    
    NullPointerException - if charSequence is null
    Since:
    
    Geneious 3.8
  - concatenate
```
public static CharSequence concatenate(List<CharSequence> charSequences)
```
    Creates a CharSequence that represents a concatenation of the specified CharSequences in the order in which they appear in the specified list. In other word concatenate(charSequences).toString().equals(StringUtilities.join("", charSequences)), but the return value may be a wrapper backed by the specified CharSequences, so these CharSequences must not change in length after calling this method. If this is not what you want, then use StringUtilities.join(String, Iterable) instead. As of 2008-05-21, this method's return value isn't guaranteed to be instanceof SequenceCharSequence even if the specified charSequences are. However, such a guarantee may be made in a future version. Therefore, for future safety not only the length but also the character sequence of the specified CharSequences shouldn't change after being passed to this method. Generally, the concrete type of the returned CharSequence is not guaranteed and should not be depended on.
    
    Parameters:
    charSequences - the CharSequences to concatenate. These CharSequences must not change after being passed to this method.
    
    Returns:
    A CharSequence whose sequence of characters is a concatenation of those in charSequences.
  - isAllGaps
```
public static boolean isAllGaps(CharSequence charSequence)
```
    Returns true if the given sequence is either empty or contains only gaps.
    
    Parameters:
    charSequence - the sequence to check within
    
    Returns:
    true if the given sequence is either empty or contains only gaps.

Class CharSequenceUtilities

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CASE_SENSITIVE_ORDER

Method Detail

asUpperCase

asLowerCase

commonPrefixLength

reverse

equals

toString

equalsIgnoreCase

contains

count

subSequence

repeatedCharSequence

isCharSequenceKnownToBeImmutable

immutableCopyOf

concatenate

isAllGaps