2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import jalview.api.DBRefEntryI;
25 public class DBRefEntry implements DBRefEntryI
27 String source = "", version = "", accessionId = "";
29 private int startRes, endRes;
31 * maps from associated sequence to the database sequence's coordinate system
41 public DBRefEntry(String source, String version, String accessionId)
43 this(source, version, accessionId, null);
49 * canonical source (uppercase only)
51 * (source dependent version string)
53 * (source dependent accession number string)
55 * (mapping from local sequence numbering to source accession
58 public DBRefEntry(String source, String version, String accessionId,
61 this.source = source.toUpperCase();
62 this.version = version;
63 this.accessionId = accessionId;
67 public DBRefEntry(DBRefEntryI entry)
69 this((entry.getSource() == null ? "" : new String(entry.getSource())),
70 (entry.getVersion() == null ? "" : new String(
72 (entry.getAccessionId() == null ? "" : new String(
73 entry.getAccessionId())),
74 (entry.getMap() == null ? null : new Mapping(entry.getMap())));
78 public boolean equals(Object o)
80 // TODO should also override hashCode to ensure equal objects have equal
82 if (o == null || !(o instanceof DBRefEntry))
86 DBRefEntry entry = (DBRefEntry) o;
92 && ((map == null && entry.map == null) || (map != null
93 && entry.map != null && map.equals(entry.map))))
101 * Answers true if this object is either equivalent to, or can be 'improved'
102 * by, the given entry. Specifically, answers true if
104 * <li>source and accession are identical (ignoring case)</li>
105 * <li>version is identical (ignoring case), or this version is of the format
106 * "someSource:0", in which case the version for the other entry replaces it</li>
107 * <li>mappings are not compared but if this entry has no mapping, replace
108 * with that for the other entry</li>
115 public boolean updateFrom(DBRefEntryI other)
127 * source must either match or be both null
129 String otherSource = other.getSource();
130 if ((source == null && otherSource != null)
131 || (source != null && otherSource == null)
132 || (source != null && !source.equalsIgnoreCase(otherSource)))
138 * accession id must either match or be both null
140 String otherAccession = other.getAccessionId();
141 if ((accessionId == null && otherAccession != null)
142 || (accessionId != null && otherAccession == null)
143 || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
149 * if my version is null, "0" or "source:0" then replace with other version,
150 * otherwise the versions have to match
152 String otherVersion = other.getVersion();
153 if ((version == null || version.equals("0") || version.endsWith(":0"))
154 && otherVersion != null)
156 setVersion(otherVersion);
160 if (!version.equalsIgnoreCase(otherVersion))
167 * if I have no mapping, take that of the other dbref
171 setMap(other.getMap());
177 * test for similar DBRef attributes, except for the map object.
180 * @return true if source, accession and version are equal with those of entry
183 public boolean equalRef(DBRefEntryI entry)
185 // TODO is this method and equals() not needed?
195 && (source != null && entry.getSource() != null && source
196 .equalsIgnoreCase(entry.getSource()))
197 && (accessionId != null && entry.getAccessionId() != null && accessionId
198 .equalsIgnoreCase(entry.getAccessionId()))
199 && (version != null && entry.getVersion() != null && version
200 .equalsIgnoreCase(entry.getVersion())))
208 public String getSource()
214 public String getVersion()
220 public String getAccessionId()
227 public void setAccessionId(String accessionId)
229 this.accessionId = accessionId;
234 public void setSource(String source)
236 this.source = source;
241 public void setVersion(String version)
243 this.version = version;
248 public Mapping getMap()
257 public void setMap(Mapping map)
262 public boolean hasMap()
269 * @return source+":"+accessionId
271 public String getSrcAccString()
273 return ((source != null) ? source : "") + ":"
274 + ((accessionId != null) ? accessionId : "");
278 public String toString()
280 return getSrcAccString();
284 public int getStartRes()
290 public void setStartRes(int startRes)
292 this.startRes = startRes;
296 public int getEndRes()
302 public void setEndRes(int endRes)
304 this.endRes = endRes;