public class StringAlignment extends Object implements Comparable<StringAlignment>, Storable
String
s. It
contains the String
s that were aligned and expanded by
gap-symbols, and the edit-costs according to the employed
Costs
instance.Constructor and Description |
---|
StringAlignment(double cost,
String... strings)
This constructor creates an instance storing the aligned Strings and the costs of the alignment.
|
StringAlignment(double cost,
String[] strings,
Result res)
This constructor creates an instance storing the aligned Strings and the costs of the alignment.
|
StringAlignment(StringBuffer xml)
Restores
StringAlignment object from its XML representation. |
Modifier and Type | Method and Description |
---|---|
int |
compareTo(StringAlignment o) |
protected void |
fromXML(StringBuffer xml)
Parses the XML representation.
|
String |
getAlignedString(int index)
Returns the aligned
String with index index . |
Result |
getAnnotationResult()
Returns the annotation result.
|
double |
getCost()
Returns the costs.
|
int |
getLength()
This method return the length of the alignment.
|
int |
getNumberOfAlignedSequences()
Returns the number of sequences in this alignment.
|
String |
toString() |
String |
toString(int chunkSize,
int simplifyIdx,
List<String> annot)
This method returns a String representation of the alignment with a given chunk size.
|
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
public StringAlignment(StringBuffer xml) throws NonParsableException
StringAlignment
object from its XML representation.xml
- the XML representationNonParsableException
- if the XML could not be parsedpublic StringAlignment(double cost, String... strings)
cost
- the cost of the alignmentstrings
- the aligned and expanded Stringspublic StringAlignment(double cost, String[] strings, Result res)
cost
- the cost of the alignmentstrings
- the aligned and expanded Stringsres
- a result describing the alignmentpublic Result getAnnotationResult()
public double getCost()
public int getNumberOfAlignedSequences()
public String getAlignedString(int index)
String
with index index
.public String toString(int chunkSize, int simplifyIdx, List<String> annot)
chunkSize
symbols.chunkSize
- the size of the chunkssimplifyIdx
- if non-negative the alignment is given relative to the sequence with the corresponding index; i.e. match is represented by "." and mismatch by the corresponding symbolannot
- a list of annotations for the aligned Strings, can be null
public int getLength()
public int compareTo(StringAlignment o)
compareTo
in interface Comparable<StringAlignment>
protected void fromXML(StringBuffer xml) throws NonParsableException
xml
- the XML representationNonParsableException
- if XML could not be parsedpublic StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.