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java.lang.Objectorg.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder
public class PHYLIPFileBuilder
Builds a PHYLIP file by listening to events.
Constructor Summary | |
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PHYLIPFileBuilder()
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Method Summary | |
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void |
endFile()
Finished reading a file. |
Alignment |
getAlignment()
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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 alignment |
void |
startFile()
About to start a new file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PHYLIPFileBuilder()
Method Detail |
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public void startFile()
PHYLIPFileListener
startFile
in interface PHYLIPFileListener
public void endFile() throws ParseException
PHYLIPFileListener
endFile
in interface PHYLIPFileListener
ParseException
public void setSequenceCount(int count)
PHYLIPFileListener
setSequenceCount
in interface PHYLIPFileListener
count
- the expected number of sequencespublic void setSitesCount(int count)
PHYLIPFileListener
setSitesCount
in interface PHYLIPFileListener
count
- the expected number of sitespublic void setCurrentSequenceName(String name)
PHYLIPFileListener
setCurrentSequenceName
in interface PHYLIPFileListener
name
- the label for the current sequencepublic void receiveSequence(String sequence)
PHYLIPFileListener
receiveSequence
in interface PHYLIPFileListener
sequence
- sequence text for the current sequencepublic Alignment getAlignment()
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