Package org.biojavax.bio.phylo.io.phylip
Interface PHYLIPFileListener
-
- All Known Implementing Classes:
PHYLIPFileBuilder
public interface PHYLIPFileListener
Listens to events fired by the PHYLIP parser. Use these events to handle data directly or construct objects.- Since:
- 1.6
- Author:
- Richard Holland, Tobias Thierer, Jim Balhoff
-
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
endFile()
Finished reading a file.void
receiveSequence(String sequence)
Receive sequence data for the current sequence.void
setCurrentSequenceName(String name)
Set the name of the sequence which is about to be received.void
setSequenceCount(int count)
Set the number of sequences in the alignment.void
setSitesCount(int count)
Set the number of sites in the alignmentvoid
startFile()
About to start a new file.
-
-
-
Method Detail
-
startFile
void startFile()
About to start a new file.
-
endFile
void endFile() throws ParseException
Finished reading a file.- Throws:
ParseException
-
setSequenceCount
void setSequenceCount(int count)
Set the number of sequences in the alignment.- Parameters:
count
- the expected number of sequences
-
setSitesCount
void setSitesCount(int count)
Set the number of sites in the alignment- Parameters:
count
- the expected number of sites
-
setCurrentSequenceName
void setCurrentSequenceName(String name)
Set the name of the sequence which is about to be received. If the name has already been seen, the sequence should be appended.- Parameters:
name
- the label for the current sequence
-
receiveSequence
void receiveSequence(String sequence)
Receive sequence data for the current sequence.- Parameters:
sequence
- sequence text for the current sequence
-
-