Alignments
Class DuplicationAlignment
java.lang.Object
Alignments.Alignment
Alignments.DuplicationAlignment
- All Implemented Interfaces:
- java.lang.Iterable<Site>
public class DuplicationAlignment
- extends Alignment
Represents a duplication "alignment" - a set of gene families with their
associated size in each species
- Version:
- 1.0
Method Summary |
static void |
writeFile(Alignment a,
java.io.File f)
Writes a alignment to a file in the duplication alignment format described
above. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DuplicationAlignment
public DuplicationAlignment(java.io.File f)
throws InputException,
AlignmentException
- Creates a duplication alignment from a file. File is tab seperated.
First row is a header file. First field is ignored while subsequent fields
are the name of the species. Each additional row represents a family.
The first field is an ID for the family while subsequent fields are the
size of the family in the appropiate species.
- Parameters:
f
- The input file
- Throws:
InputException
- Thrown if there is a problem with the input file
AlignmentException
- Thrown if any family contains the wrong number
of species
DuplicationAlignment
public DuplicationAlignment(java.io.File f,
Ambiguous ambig)
throws InputException,
AlignmentException
- Creates a duplication alignment which contains ambiguous data. File format
is described
DuplicationAlignment(java.io.File)
.
- Parameters:
f
- The input fileambig
- Desription o the ambiguous data
- Throws:
InputException
- Thrown if there is a problem with the input file
AlignmentException
- Thrown if any family contains the wrong number
of species
writeFile
public static void writeFile(Alignment a,
java.io.File f)
throws OutputException
- Writes a alignment to a file in the duplication alignment format described
above.
- Parameters:
a
- The alignment to write to the file. Need not be a duplication alignmentf
- The file to write to
- Throws:
OutputException
- Thrown if there is a problem creating the file