Class NexusFile

java.lang.Object
org.biojavax.bio.phylo.io.nexus.NexusFile

public class NexusFile extends Object
Represents Nexus files.
Since:
1.6
Author:
Richard Holland, Tobias Thierer, Jim Balhoff
  • Constructor Details

  • Method Details

    • addObject

      public void addObject(NexusObject object)
      Appends an object to the end of the file.
      Parameters:
      object - the NexusObject to append.
    • insertObject

      public void insertObject(NexusObject object, int pos)
      Inserts an object at the given position.
      Parameters:
      object - the NexusObject to insert.
      pos - the position (0-indexed) to add it at.
    • removeObject

      public void removeObject(NexusObject object)
      Removes an object from the file.
      Parameters:
      object - the NexusObject to remove.
    • containsObject

      public boolean containsObject(NexusObject object)
      Checks to see if we contain an object.
      Parameters:
      object - the NexusObject to check.
      Returns:
      true if we contain it.
    • objectIterator

      Iterate over all objects in the file in order.
      Returns:
      an iterator of NexusObjects.
    • commentIterator

      Iterate over all comments in the file in order.
      Returns:
      an iterator of NexusComments.
    • blockIterator

      Iterate over all blocks in the file in order.
      Returns:
      an iterator of NexusBlocks.