|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.algorithms.alignment.StringAlignment
public class StringAlignment
Class for the representation of an alignment of 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 Summary | |
---|---|
StringAlignment(double cost,
String... strings)
This constructor creates an instance storing the aligned Strings and the costs of the alignment. |
Method Summary | |
---|---|
String |
getAlignedString(int index)
Returns the aligned String with index index . |
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. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public StringAlignment(double cost, String... strings)
cost
- the cost of the alignmentstrings
- the aligned and expanded StringsMethod Detail |
---|
public double getCost()
public int getNumberOfAlignedSequences()
public String getAlignedString(int index)
String
with index index
.
index
- the index of the String
String
with index index
public String toString()
toString
in class Object
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()
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |