## org.biojavax.bio.phylo.io.phylip
Class PHYLIPFileBuilder

    java.lang.Object
      org.biojavax.bio.phylo.io.phylip.PHYLIPFileBuilder

All Implemented Interfaces:
  PHYLIPFileListener

    public class PHYLIPFileBuilder

extends Object
implements PHYLIPFileListener

Builds a PHYLIP file by listening to events.

Since:
  1.6
Author:
  Richard Holland, Tobias Thierer, Jim Balhoff

Constructor Summary
`PHYLIPFileBuilder()`

Method Summary
`void` `endFile()` Finished reading a file.
`Alignment` `getAlignment()`
`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
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### PHYLIPFileBuilder

    public PHYLIPFileBuilder()

Method Detail

### startFile

    public void startFile()

  Description copied from interface: `PHYLIPFileListener`
  About to start a new file.

  Specified by:
    `startFile` in interface `PHYLIPFileListener`

### endFile

    public void endFile()
                 throws ParseException

  Description copied from interface: `PHYLIPFileListener`
  Finished reading a file.

  Specified by:
    `endFile` in interface `PHYLIPFileListener`
  Throws:
    `ParseException`

### setSequenceCount

    public void setSequenceCount(int count)

  Description copied from interface: `PHYLIPFileListener`
  Set the number of sequences in the alignment.

  Specified by:
    `setSequenceCount` in interface `PHYLIPFileListener`
  Parameters:
    `count` - the expected number of sequences

### setSitesCount

    public void setSitesCount(int count)

  Description copied from interface: `PHYLIPFileListener`
  Set the number of sites in the alignment

  Specified by:
    `setSitesCount` in interface `PHYLIPFileListener`
  Parameters:
    `count` - the expected number of sites

### setCurrentSequenceName

    public void setCurrentSequenceName(String name)

  Description copied from interface: `PHYLIPFileListener`
  Set the name of the sequence which is about to be received. If the name has already been seen, the sequence should be appended.

  Specified by:
    `setCurrentSequenceName` in interface `PHYLIPFileListener`
  Parameters:
    `name` - the label for the current sequence

### receiveSequence

    public void receiveSequence(String sequence)

  Description copied from interface: `PHYLIPFileListener`
  Receive sequence data for the current sequence.

  Specified by:
    `receiveSequence` in interface `PHYLIPFileListener`
  Parameters:
    `sequence` - sequence text for the current sequence

### getAlignment

    public Alignment getAlignment()