Package jebl.evolution.align
Class ProfileCharacter
java.lang.Object
jebl.evolution.align.ProfileCharacter
- Version:
- $Id: ProfileCharacter.java 1025 2009-10-23 01:29:48Z matt_kearse $ Represents a single residue in a multiple alignment profile It can represent character frequencies inside an alignment column as a fraction of the total number of characters in that column.
- Author:
- Matt Kearse
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addCharacter
(char character, int increment) void
addGaps
(int count) void
addProfileCharacter
(ProfileCharacter character) void
clear()
float
static ProfileCharacter
getImmutableProfileCharacter
(char character) An immutable ProfileCharacter that uses less memory than a mutable profile character.boolean
int
print()
void
removeProfileCharacter
(ProfileCharacter character) static float
score
(ProfileCharacter character1, ProfileCharacter character2, Scores scores) static float
scoreSelf
(ProfileCharacter character, Scores scores) toString()
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Constructor Details
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ProfileCharacter
public ProfileCharacter(int alphabetSize)
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Method Details
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getImmutableProfileCharacter
An immutable ProfileCharacter that uses less memory than a mutable profile character. The same immtuable ProfileCharacter may also be returned from other calls to this method.- Parameters:
character
- the single character to wrap in a profile.- Returns:
- an immutable ProfileCharacter
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addCharacter
public void addCharacter(char character, int increment) -
addProfileCharacter
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removeProfileCharacter
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addGaps
public void addGaps(int count) -
score
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scoreSelf
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print
public int print() -
toString
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isAllGaps
public boolean isAllGaps() -
clear
public void clear() -
gapFraction
public float gapFraction()- Returns:
- the fraction of characters that are gap Characters in this profile
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