Source code

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 * Created on Sep 3, 2007
021 *
022 */
023package org.biojava.nbio.structure;
024
025import org.slf4j.Logger;
026import org.slf4j.LoggerFactory;
027
028import java.lang.reflect.Method;
029import java.util.Formatter;
030import java.util.Locale;
031
032
033/** A class to represent database cross references. This is just a simple bean that contains the infor from one
034 * DBREF line
035 *
036 * @author Andreas Prlic
037 * @since 4:56:14 PM
038 * @version %I% %G%
039 */
040public class DBRef implements PDBRecord {
041
042        private final static Logger logger = LoggerFactory.getLogger(DBRef.class);
043
044        private static final long serialVersionUID = -1050178577542224379L;
045
046        private Structure parent;
047        private String idCode;
048        private String chainName;
049        private int seqbegin;
050        private char insertBegin;
051        private int seqEnd;
052        private char insertEnd;
053
054        private String database;
055        private String dbAccession;
056        private String dbIdCode;
057
058        private int dbSeqBegin;
059        private char idbnsBegin;
060        private int dbSeqEnd;
061        private char idbnsEnd;
062
063        private Long id;
064
065        public DBRef() {
066                insertBegin = ' ';
067                insertEnd   = ' ';
068                idbnsBegin  = ' ';
069                idbnsEnd    = ' ';
070        }
071
072        /** Get the ID used by Hibernate.
073         *
074         * @return the ID used by Hibernate
075         * @see #setId(Long)
076         */
077        public Long getId() {
078                return id;
079        }
080
081        /** Set the ID used by Hibernate.
082         *
083         * @param id the id assigned by Hibernate
084         * @see #getId()
085         */
086        public void setId(Long id) {
087                this.id = id;
088        }
089
090        /** Set the structure object that this DBRef relates to.
091         *
092         * @param s a structure object
093         * @see #getParent()
094         */
095        public void setParent(Structure s){
096                parent = s;
097
098        }
099
100        /** Get the structure object that this DBRef relates to.
101         *
102         * @return s a structure object
103         * @see #setParent(Structure)
104         */
105        public Structure getParent(){
106                return parent;
107        }
108
109        /** Convert the DBRef object to a DBREF record as it is used in PDB files
110         *
111         * @return a PDB - DBREF formatted line
112         */
113        @Override
114        public String toPDB(){
115
116                 StringBuffer buf = new StringBuffer();
117                 toPDB(buf);
118                 return buf.toString();
119
120        }
121
122        /** Append the PDB representation of this DBRef to the provided StringBuffer
123         *
124         * @param buf the StringBuffer to write to.
125         */
126        @Override
127        public void toPDB(StringBuffer buf){
128                 Formatter formatter = new Formatter(new StringBuilder(),Locale.UK);
129//        DBREF  3ETA A  990  1295  UNP    P06213   INSR_HUMAN    1017   1322
130//        DBREF  3EH2 A    2   767  UNP    P53992   SC24C_HUMAN    329   1094
131//        DBREF 3EH2 A    2   767     UNP   P53992  SC24C_HUMAN   329   1094
132//        DBREF  3ETA A  990  1295  UNP    P06213   INSR_HUMAN    1017   1322
133                formatter.format("DBREF  %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c            ",
134                                idCode, chainName,seqbegin,insertBegin,seqEnd,insertEnd,
135                                database,dbAccession,dbIdCode,
136                                dbSeqBegin,idbnsBegin,dbSeqEnd,idbnsEnd
137                                );
138
139                buf.append(formatter.toString());
140                formatter.close();
141
142        }
143        /** String representation of a DBRef.
144         * @return a String
145         */
146        @Override
147        public String toString(){
148                StringBuilder buf = new StringBuilder();
149
150                try {
151
152                        @SuppressWarnings("rawtypes")
153                        Class c = Class.forName(DBRef.class.getName());
154                        Method[] methods  = c.getMethods();
155
156                        for (Method m : methods) {
157                                String name = m.getName();
158
159                                if (name.substring(0, 3).equals("get")) {
160                                        if (name.equals("getClass")) {
161                                                continue;
162                                        }
163                                        Object o = m.invoke(this);
164                                        if (o != null) {
165                                                buf.append(name.substring(3, name.length()));
166                                                buf.append(": ").append(o).append(" ");
167                                        }
168                                }
169                        }
170                } catch (Exception e){
171                        logger.error("Exception: ", e);
172                }
173
174                return buf.toString();
175        }
176
177
178        /** get the idCode for this entry
179         *
180         * @return the idCode
181         * @see #setIdCode(String)
182         */
183        public String getIdCode() {
184                return idCode;
185        }
186
187        /** Set the idCode for this entry.
188         *
189         * @param idCode the idCode for this entry
190         * @see #getIdCode()
191         */
192        public void setIdCode(String idCode) {
193                this.idCode = idCode;
194        }
195
196        /** The name of the corresponding chain.
197         *
198         * @return chainName the name of the corresponding chain.
199         */
200        public String getChainName() {
201                return chainName;
202        }
203
204
205        /** The name of the corresponding chain.
206         *
207         * @param chainName the name of the corresponding chain
208         * @see #getChainName()
209         */
210        public void setChainName(String chainName) {
211                this.chainName = chainName;
212        }
213
214
215        /** The database of the db-ref.
216         * uses the abbreviation as provided in the PDB files:
217         *
218         *<pre>   Database name                         database
219                                                                         (code in columns 27 - 32)
220        ----------------------------------------------------------
221        GenBank                               GB
222        Protein Data Bank                     PDB
223        Protein Identification Resource       PIR
224        SWISS-PROT                            SWS
225        TREMBL                                TREMBL
226        UNIPROT                               UNP
227        </pre>
228         * @return name of database of this DBRef
229         * @see #setDatabase(String)
230         */
231        public String getDatabase() {
232                return database;
233        }
234
235        /** Specifies the database value.
236         *
237         * @param database the database
238         * @see #getDatabase()
239         */
240        public void setDatabase(String database) {
241                this.database = database;
242        }
243
244        /** Sequence database accession code.
245         * @return the dbAccession
246         * @see #setDbAccession(String)
247         * */
248        public String getDbAccession() {
249                return dbAccession;
250        }
251
252        /** Sequence database accession code.
253         * @param dbAccession the dbAccession
254         * @see #getDbAccession()
255         * */
256        public void setDbAccession(String dbAccession) {
257                this.dbAccession = dbAccession;
258        }
259
260
261        /** Sequence database          identification code.
262         *
263         * @return the dbIdCode
264         * @see #setDbIdCode(String)
265         */
266        public String getDbIdCode() {
267                return dbIdCode;
268        }
269
270        /** Sequence database          identification code.
271         *
272         * @param dbIdCode identification code
273         * @see #getDbIdCode()
274         */
275        public void setDbIdCode(String dbIdCode) {
276                this.dbIdCode = dbIdCode;
277        }
278
279        /** Initial sequence number of the
280        database seqment.
281         * @return position
282         * @see #setDbSeqBegin(int)
283         */
284        public int getDbSeqBegin() {
285                return dbSeqBegin;
286        }
287
288
289        /** Initial sequence number of the
290        database seqment.
291         * @param dbSeqBegin a sequence position
292         * @see #getDbSeqBegin()
293         *
294         */
295        public void setDbSeqBegin(int dbSeqBegin) {
296                this.dbSeqBegin = dbSeqBegin;
297        }
298
299
300        /** Ending sequence position  of the database segment.
301         * @return dbSeqEnd
302         * @see #setDbSeqEnd(int)
303         */
304        public int getDbSeqEnd() {
305                return dbSeqEnd;
306        }
307
308
309        /** The begin of the sequence position in the database
310         *
311         * @param dbSeqEnd sequence position
312         * @see #getDbSeqEnd()
313         */
314        public void setDbSeqEnd(int dbSeqEnd) {
315                this.dbSeqEnd = dbSeqEnd;
316        }
317
318        /** Insertion code of initial residue of the segment, if PDB is the
319        reference.
320         * @return idbnsBegin isnertion code
321         * @see #setIdbnsBegin(char)
322         * */
323        public char getIdbnsBegin() {
324                return idbnsBegin;
325        }
326
327        /** Insertion code of initial residue of the segment, if PDB is the
328        reference.
329         * @param idbnsBegin insertion code
330         * @see #getIdbnsBegin()
331         * */
332        public void setIdbnsBegin(char idbnsBegin) {
333                this.idbnsBegin = idbnsBegin;
334        }
335
336        /** Insertion code of the ending
337        residue of the segment, if PDB is
338        the reference.
339         * @return idbnsEnd insertion code
340         * @see #setIdbnsEnd(char)
341         */
342        public char getIdbnsEnd() {
343                return idbnsEnd;
344        }
345
346
347        /** Insertion code of the ending
348        residue of the segment, if PDB is
349        the reference.
350         * @param idbnsEnd the insertion code
351         * @see #setIdbnsEnd(char)
352         */
353        public void setIdbnsEnd(char idbnsEnd) {
354                this.idbnsEnd = idbnsEnd;
355        }
356
357        /** Initial insertion code of the PDB sequence segment.
358         *
359         * @return insertBegin
360         * @see #setInsertBegin(char)
361         */
362
363        public char getInsertBegin() {
364                return insertBegin;
365        }
366
367        /** Initial insertion code of the PDB sequence segment.
368         *
369         * @param insertBegin
370         * @see #getInsertBegin()
371         */
372
373        public void setInsertBegin(char insertBegin) {
374                this.insertBegin = insertBegin;
375        }
376
377        /** Ending insertion code of the PDB sequence segment.
378         *
379         * @return insertEnd insertion code
380         * @see #setInsertEnd(char)
381         */
382        public char getInsertEnd() {
383                return insertEnd;
384        }
385
386        /** Ending insertion code of the PDB sequence segment.
387         *
388         * @param insertEnd insertEnd
389         * @see #getInsertEnd()
390         *
391         */
392        public void setInsertEnd(char insertEnd) {
393                this.insertEnd = insertEnd;
394        }
395
396        /**   Initial sequence number of the PDB sequence segment.
397         *
398         * @return start seq. position
399         * @see #setSeqBegin
400         */
401        public int getSeqBegin() {
402                return seqbegin;
403        }
404
405        /**   Initial sequence number of the PDB sequence segment.
406         *
407         * @param seqbegin start seq. position
408         * @see #getSeqBegin()
409         */
410        public void setSeqBegin(int seqbegin) {
411                this.seqbegin = seqbegin;
412        }
413
414        /**Ending sequence number   of the PDB sequence segment.
415         *
416         * @return sequence end position
417         * @see #getSeqEnd()
418         */
419        public int getSeqEnd() {
420                return seqEnd;
421        }
422
423        /**Ending sequence number   of the PDB sequence segment.
424         *
425         * @param seqEnd sequence end position
426         * @see #setSeqEnd(int)
427         *
428         */
429        public void setSeqEnd(int seqEnd) {
430                this.seqEnd = seqEnd;
431        }
432
433}