Constructor and Description |
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BasicMsa() |
Modifier and Type | Method and Description |
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void |
addSequence(Sequence sequence,
boolean check_for_equal_length) |
Msa |
copy() |
Msa |
createSubAlignment(int[] sequences,
int[] positions) |
int[] |
findSequence(java.lang.String name,
boolean case_sensitive,
boolean partial_match) |
int |
getLength() |
int |
getNumberOfSequences() |
char |
getResidueAt(int col,
int row) |
Sequence |
getSequence(int i) |
boolean |
isAppearsAligned() |
boolean |
isEmpty() |
void |
removeSequence(int i) |
public void addSequence(Sequence sequence, boolean check_for_equal_length)
public Msa copy()
public Msa createSubAlignment(int[] sequences, int[] positions)
public int[] findSequence(java.lang.String name, boolean case_sensitive, boolean partial_match)
public int getNumberOfSequences()
getNumberOfSequences
in interface Msa
public char getResidueAt(int col, int row)
getResidueAt
in interface Msa
public Sequence getSequence(int i)
getSequence
in interface Msa
public boolean isAppearsAligned()
public boolean isEmpty()
public void removeSequence(int i)