001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojavax.bio.phylo.io.phylip; 022 023import org.biojava.bio.seq.io.ParseException; 024 025/** 026 * Listens to events fired by the PHYLIP parser. Use these events to handle data 027 * directly or construct objects. 028 * 029 * @author Richard Holland 030 * @author Tobias Thierer 031 * @author Jim Balhoff 032 * @since 1.6 033 */ 034 035public interface PHYLIPFileListener { 036 037 /** 038 * About to start a new file. 039 */ 040 public void startFile(); 041 042 /** 043 * Finished reading a file. 044 */ 045 public void endFile() throws ParseException; 046 047 /** 048 * Set the number of sequences in the alignment. 049 * 050 * @param count 051 * the expected number of sequences 052 */ 053 public void setSequenceCount(int count); 054 055 /** 056 * Set the number of sites in the alignment 057 * 058 * @param count 059 * the expected number of sites 060 */ 061 public void setSitesCount(int count); 062 063 /** 064 * Set the name of the sequence which is about to be received. If the name has already 065 * been seen, the sequence should be appended. 066 * 067 * @param name 068 * the label for the current sequence 069 */ 070 public void setCurrentSequenceName(String name); 071 072 /** 073 * Receive sequence data for the current sequence. 074 * 075 * @param sequence 076 * sequence text for the current sequence 077 */ 078 public void receiveSequence(String sequence); 079 080}