public final class AlignmentHelper extends Object implements Serializable
| Modifier and Type | Field and Description |
|---|---|
protected String |
markup |
protected BitArray |
match |
protected int |
offset |
protected int[] |
seq1Position |
protected String |
seq1String |
protected int[] |
seq2Position |
protected String |
seq2String |
| Constructor and Description |
|---|
AlignmentHelper(String seq1String,
String seq2String,
int[] seq1Position,
int[] seq2Position,
BitArray match) |
AlignmentHelper(String seq1String,
String seq2String,
int[] seq1Position,
int[] seq2Position,
BitArray match,
int offset) |
| Modifier and Type | Method and Description |
|---|---|
String |
getLine1()
Gets the first line of formatted alignment (query sequence)
|
String |
getLine1Compact() |
String |
getLine2()
Gets the second line of formatted alignment (alignment markup)
|
String |
getLine3()
Gets the third line of formatted alignment (subject sequence)
|
String |
getLine3Compact() |
String |
getMarkup()
Get the alignment markup line
|
AlignmentHelper |
getRange(int from,
int to) |
AlignmentHelper |
getRange(int from,
int to,
int offset) |
String |
getSeq1String()
Get the aligned query sequence
|
String |
getSeq2String()
Get the aligned subject sequence
|
int |
getSequence1PositionAt(int i) |
int |
getSequence2PositionAt(int i) |
double |
identity()
Gets the identity of alignment, i.e.
|
int |
size()
Gets the size of aligned region
|
AlignmentHelper[] |
split(int length) |
AlignmentHelper[] |
split(int length,
int offset) |
String |
toCompactString()
Gets the alignment string in contact format (no markup line, mismatches shown by lower-case characters)
|
String |
toString() |
String |
toStringWithSeq2Quality(SequenceQuality quality) |
protected final String seq1String
protected final String seq2String
protected final String markup
protected final int[] seq1Position
protected final int[] seq2Position
protected final BitArray match
protected final int offset
public AlignmentHelper(String seq1String, String seq2String, int[] seq1Position, int[] seq2Position, BitArray match)
public AlignmentHelper getRange(int from, int to)
public AlignmentHelper getRange(int from, int to, int offset)
public AlignmentHelper[] split(int length)
public AlignmentHelper[] split(int length, int offset)
public double identity()
public int size()
public int getSequence1PositionAt(int i)
public int getSequence2PositionAt(int i)
public String getSeq1String()
public String getSeq2String()
public String getMarkup()
public String getLine1()
public String getLine1Compact()
public String getLine2()
public String getLine3()
public String toStringWithSeq2Quality(SequenceQuality quality)
public String getLine3Compact()
public String toCompactString()
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