001/*
002
003 *                    BioJava development code
004
005 *
006
007 * This code may be freely distributed and modified under the
008
009 * terms of the GNU Lesser General Public Licence.  This should
010
011 * be distributed with the code.  If you do not have a copy,
012
013 * see:
014
015 *
016
017 *      http://www.gnu.org/copyleft/lesser.html
018
019 *
020
021 * Copyright for this code is held jointly by the individual
022
023 * authors.  These should be listed in @author doc comments.
024
025 *
026
027 * For more information on the BioJava project and its aims,
028
029 * or to join the biojava-l mailing list, visit the home page
030
031 * at:
032
033 *
034
035 *      http://www.biojava.org/
036
037 *
038
039 */
040
041package org.biojava.bio.seq.io.agave;
042
043import java.util.ArrayList;
044import java.util.Iterator;
045import java.util.List;
046
047
048
049/**
050
051 * 
052
053 * @author Hanning Ni    Doubletwist Inc
054  * @author Greg Cox
055
056 */
057
058public class AGAVEMapPosition {
059
060  private String pos  ;
061
062  private List db_ids ;
063
064
065
066  public AGAVEMapPosition() {
067
068  }
069
070  public void  setPos(String pos)
071
072  {
073
074      this.pos = pos ;
075
076  }
077
078  public String getPos()
079
080  {
081
082      return pos ;
083
084  }
085
086  public void addDbId(AGAVEDbId id)
087
088  {
089
090      if( db_ids == null )
091
092          db_ids = new ArrayList(1) ;
093
094      db_ids.add( id );
095
096  }
097
098  public Iterator getDbIds()
099
100  {
101
102      return db_ids.iterator() ;
103
104  }
105
106  public String toString(String indent, String indent_unit)
107
108  {
109
110      StringBuffer tmp = new StringBuffer() ;
111
112      tmp.append(indent + "<map_position pos=\"" + pos + "\">" + "\n" ) ;
113
114      Iterator it  = db_ids.iterator() ;
115
116      while( it.hasNext() )
117
118      {
119
120          tmp.append( ((AGAVEDbId) it.next()).toString(indent + indent_unit, indent_unit) ) ;
121
122      }
123
124      tmp.append(indent + "</map_position>") ;
125
126      return tmp.substring(0) ;
127
128  }
129
130  public String toString()
131
132  {
133
134      StringBuffer tmp = new StringBuffer() ;
135
136      tmp.append("<map_position pos=\"" + pos + "\">" + "\n" ) ;
137
138      Iterator it  = db_ids.iterator() ;
139
140      while( it.hasNext() )
141
142      {
143
144          tmp.append( (AGAVEDbId) it.next() ) ;
145
146      }
147
148      tmp.append("</map_position>") ;
149
150      return tmp.substring(0) ;
151
152  }
153
154}