Package jebl.evolution.align
Class ProfileCharacter
- java.lang.Object
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- jebl.evolution.align.ProfileCharacter
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public class ProfileCharacter extends java.lang.Object
- 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 Constructor Description ProfileCharacter(int alphabetSize)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCharacter(char character, int increment)
void
addGaps(int count)
void
addProfileCharacter(ProfileCharacter character)
void
clear()
float
gapFraction()
static ProfileCharacter
getImmutableProfileCharacter(char character)
An immutable ProfileCharacter that uses less memory than a mutable profile character.boolean
isAllGaps()
int
print()
void
removeProfileCharacter(ProfileCharacter character)
static float
score(ProfileCharacter character1, ProfileCharacter character2, Scores scores)
static float
scoreSelf(ProfileCharacter character, Scores scores)
java.lang.String
toString()
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Method Detail
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getImmutableProfileCharacter
public static ProfileCharacter getImmutableProfileCharacter(char character)
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)
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addProfileCharacter
public void addProfileCharacter(ProfileCharacter character)
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removeProfileCharacter
public void removeProfileCharacter(ProfileCharacter character)
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addGaps
public void addGaps(int count)
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score
public static float score(ProfileCharacter character1, ProfileCharacter character2, Scores scores)
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scoreSelf
public static float scoreSelf(ProfileCharacter character, Scores scores)
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print
public int print()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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isAllGaps
public boolean isAllGaps()
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clear
public void clear()
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gapFraction
public float gapFraction()
- Returns:
- the fraction of characters that are gap Characters in this profile
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