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1   package uk.ac.ebi.intenz.tools.sib.sptr_enzyme;
2   
3   import uk.ac.ebi.interfaces.Factory;
4   import uk.ac.ebi.interfaces.uniref.*;
5   import uk.ac.ebi.interfaces.uniparc.UniParcEntry;
6   import uk.ac.ebi.interfaces.uniparc.UniParcException;
7   import uk.ac.ebi.interfaces.uniparc.UniParcCrossReferenceMetaData;
8   import uk.ac.ebi.interfaces.uniparc.UniParcCrossReference;
9   import uk.ac.ebi.interfaces.clustr.CluSTrEntry;
10  import uk.ac.ebi.interfaces.clustr.CluSTrException;
11  import uk.ac.ebi.interfaces.go.*;
12  import uk.ac.ebi.interfaces.interpro.*;
13  import uk.ac.ebi.interfaces.pythia.PythiaEntry;
14  import uk.ac.ebi.interfaces.pythia.PythiaException;
15  import uk.ac.ebi.interfaces.pythia.PredictiveInstance;
16  import uk.ac.ebi.interfaces.integr8.*;
17  import uk.ac.ebi.interfaces.citation.*;
18  import uk.ac.ebi.interfaces.enzyme.EnzymeEntry;
19  import uk.ac.ebi.interfaces.feature.Feature;
20  import uk.ac.ebi.interfaces.feature.FeatureException;
21  import uk.ac.ebi.interfaces.feature.FeatureLocation;
22  import uk.ac.ebi.interfaces.sptr.*;
23  import uk.ac.ebi.interfaces.sptr.Gene;
24  import uk.ac.ebi.interfaces.sptr.SPTREntry;
25  import uk.ac.ebi.interfaces.sptr.spin.SPINSubmission;
26  
27  /**
28   * This class is a simple extension of the abstract {@link uk.ac.ebi.interfaces.Factory Factory},
29   * which allows to create {@link uk.ac.ebi.intenz.tools.sib.sptr_enzyme.EnzymeCrossReference EnzymeCrossReference} instances only.
30   *
31   * @author Michael Darsow
32   * @version preliminary - $Revision: 1.2 $ $Date: 2008/01/28 11:43:22 $
33   */
34  public class EnzymeXrefFactory extends Factory {
35  
36    public SPTREntry newSPTREntryInstance(int entryType) throws SPTRException {
37      return null;
38    }
39  
40    public SPTREntry newSPTREntryInstance() throws SPTRException {
41      return null;
42    }
43  
44    public SPTREntry copySPTREntryInstance(SPTREntry entry) throws SPTRException {
45      return null;
46    }
47  
48    public EnzymeEntry newEnzymeEntryInstance() throws SPTRException {
49      return null;
50    }
51  
52    public EnzymeEntry copyEnzymeEntryInstance(EnzymeEntry entry) throws SPTRException {
53      return null;
54    }
55  
56    public Feature newFeatureInstance(String featureType) throws FeatureException {
57      return null;
58    }
59  
60    public Feature copyFeatureInstance(Feature feature) throws FeatureException {
61      return null;
62    }
63  
64    public FeatureLocation newFeatureLocationInstance() throws FeatureException {
65      return null;
66    }
67  
68    public FeatureLocation copyFeatureLocationInstance(FeatureLocation location) throws FeatureException {
69      return null;
70    }
71  
72    public Author newAuthorInstance() throws CitationException {
73      return null;
74    }
75  
76    public Author copyAuthorInstance(Author author) throws CitationException {
77      return null;
78    }
79  
80    public Book newBookInstance() throws CitationException {
81      return null;
82    }
83  
84    public Book copyBookInstance(Book book) throws CitationException {
85      return null;
86    }
87  
88    public ElectronicArticle newElectronicArticleInstance() throws CitationException {
89      return null;
90    }
91  
92    public ElectronicArticle copyElectronicArticleInstance(ElectronicArticle electronicArticle) throws CitationException {
93      return null;
94    }
95  
96    public JournalArticle newJournalArticleInstance() throws CitationException {
97      return null;
98    }
99  
100   public JournalArticle copyJournalArticleInstance(JournalArticle journalArticle) throws CitationException {
101     return null;
102   }
103 
104   public Patent newPatentInstance() throws CitationException {
105     return null;
106   }
107 
108   public Patent copyPatentInstance(Patent patent) throws CitationException {
109     return null;
110   }
111 
112   public Submission newSubmissionInstance() throws CitationException {
113     return null;
114   }
115 
116   public Submission copySubmissionInstance(Submission submission) throws CitationException {
117     return null;
118   }
119 
120   public Thesis newThesisInstance() throws CitationException {
121     return null;
122   }
123 
124   public Thesis copyThesisInstance(Thesis thesis) throws CitationException {
125     return null;
126   }
127 
128   public UnpublishedObservations newUnpublishedObservationsInstance() throws CitationException {
129     return null;
130   }
131 
132   public UnpublishedObservations copyUnpublishedObservationsInstance(UnpublishedObservations unpublishedObservations) throws CitationException {
133     return null;
134   }
135 
136   public UnpublishedResults newUnpublishedResultsInstance() throws CitationException {
137     return null;
138   }
139 
140   public UnpublishedResults copyUnpublishedResultsInstance(UnpublishedResults unpublishedResults) throws CitationException {
141     return null;
142   }
143 
144   public SPTRComment newSPTRCommentInstance(String type) throws SPTRException {
145     return null;
146   }
147 
148   public SPTRComment copySPTRCommentInstance(SPTRComment sptrComment) throws SPTRException {
149     return null;
150   }
151 
152   public Isoform newIsoformInstance() throws SPTRException {
153     return null;
154   }
155 
156   public Isoform copyIsoformInstance(Isoform isoform) throws SPTRException {
157     return null;
158   }
159 
160   /**
161    * <em class="text">
162    * Returns a new instance of an EnzymeCrossReference.
163    * </em>
164    * @return A new instance of an EnzymeCrossReference.
165    * @throws uk.ac.ebi.interfaces.sptr.SPTRException Needs to be implemented by individual application.
166    */
167   public SPTRCrossReference newEnzymeCrossReference(String type) throws SPTRException {
168     // Check database name (type).
169     if(!type.equals(EnzymeCrossReference.SWISSPROT) &&
170        !type.equals(EnzymeCrossReference.PROSITE) &&
171        !type.equals(EnzymeCrossReference.MIM)) throw new EnzymeCrossReferenceException("The database name given is not supported.");
172 
173     return new EnzymeCrossReference(type);
174   }
175 
176   public SPTRCrossReference newSPTRCrossReference(String type) throws SPTRException {
177     return null;
178   }
179 
180   public SPTRCrossReference copySPTRCrossReference(SPTRCrossReference sptrCrossReference) throws SPTRException {
181     return null;
182   }
183 
184   public ProteomeEntry copyProteomeEntryInstance(ProteomeEntry proteomeEntry) throws Integr8Exception {
185     return null;  //To change body of implemented methods use File | Settings | File Templates.
186   }
187 
188   public SPINSubmission newSPINSubmissionInstance() throws CitationException {
189     return null;  //To change body of implemented methods use File | Settings | File Templates.
190   }
191 
192   public SPINSubmission copySPINSubmissionInstance(SPINSubmission spinSubmission) throws CitationException {
193     return null;  //To change body of implemented methods use File | Settings | File Templates.
194   }
195 
196   public SPTRCrossReference newSPTRCrossReferenceInstance(String s) throws SPTRException {
197     return null;  //To change body of implemented methods use File | Settings | File Templates.
198   }
199 
200   public SPTRCrossReference copySPTRCrossReferenceInstance(SPTRCrossReference sptrCrossReference) throws SPTRException {
201     return null;  //To change body of implemented methods use File | Settings | File Templates.
202   }
203 
204   public PythiaEntry newPythiaEntryInstance(int i) throws PythiaException {
205     return null;  //To change body of implemented methods use File | Settings | File Templates.
206   }
207 
208   public PythiaEntry copyPythiaEntryInstance(PythiaEntry pythiaEntry) throws PythiaException {
209     return null;  //To change body of implemented methods use File | Settings | File Templates.
210   }
211 
212   public PredictiveInstance newPredictiveInstance(String s) throws PythiaException {
213     return null;  //To change body of implemented methods use File | Settings | File Templates.
214   }
215 
216   public PredictiveInstance copyPredictiveInstance(PredictiveInstance predictiveInstance) throws PythiaException {
217     return null;  //To change body of implemented methods use File | Settings | File Templates.
218   }
219 
220   public InterProProteinData newInterProProteinData(SPTREntry sptrEntry) throws InterProException {
221     return null;  //To change body of implemented methods use File | Settings | File Templates.
222   }
223 
224   public InterProProteinData copyInterProProteinData(InterProProteinData interProProteinData) throws InterProException {
225     return null;  //To change body of implemented methods use File | Settings | File Templates.
226   }
227 
228   public InterProStructure newInterProStructure(InterProEntry interProEntry) throws InterProException {
229     return null;  //To change body of implemented methods use File | Settings | File Templates.
230   }
231 
232   public InterProStructure copyInterProStructure(InterProStructure interProStructure) throws InterProException {
233     return null;  //To change body of implemented methods use File | Settings | File Templates.
234   }
235 
236   public InterProEntry newInterProEntry() throws InterProException {
237     return null;  //To change body of implemented methods use File | Settings | File Templates.
238   }
239 
240   public InterProEntry copyInterProEntry(InterProEntry interProEntry) throws InterProException {
241     return null;  //To change body of implemented methods use File | Settings | File Templates.
242   }
243 
244   public SignatureDBHit newSignatureDBHit() throws InterProException {
245     return null;  //To change body of implemented methods use File | Settings | File Templates.
246   }
247 
248   public SignatureDBHit copySignaturDBHit(SignatureDBHit signatureDBHit) throws InterProException {
249     return null;  //To change body of implemented methods use File | Settings | File Templates.
250   }
251 
252   public SignatureDBEntry newSignatureDBEntry(int i) throws InterProException {
253     return null;  //To change body of implemented methods use File | Settings | File Templates.
254   }
255 
256   public SignatureDBEntry copySignatureDBEntry(SignatureDBEntry signatureDBEntry) throws InterProException {
257     return null;  //To change body of implemented methods use File | Settings | File Templates.
258   }
259 
260    public Annotation newAnnotationInstance () throws InterProException {
261       return null;  //To change body of implemented methods use File | Settings | File Templates.
262    }
263 
264    public Annotation copyAnnotationInstance (Annotation annotation) throws InterProException {
265       return null;  //To change body of implemented methods use File | Settings | File Templates.
266    }
267 
268    public InterProCrossReference newInterProCrossReferenceInstance (String s) throws InterProException {
269       return null;  //To change body of implemented methods use File | Settings | File Templates.
270    }
271 
272    public InterProCrossReference copyInterProCrossReferenceInstance (InterProCrossReference interProCrossReference) throws InterProException {
273       return null;  //To change body of implemented methods use File | Settings | File Templates.
274    }
275 
276    public GOTerm newGOTerm() throws GOException {
277     return null;  //To change body of implemented methods use File | Settings | File Templates.
278   }
279 
280   public GOTerm copyGOTerm(GOTerm goTerm) throws GOException {
281     return null;  //To change body of implemented methods use File | Settings | File Templates.
282   }
283 
284   public GOEvidence newGOEvidence() throws GOException {
285     return null;  //To change body of implemented methods use File | Settings | File Templates.
286   }
287 
288   public GOEvidence copyGOEvidence(GOEvidence goEvidence) throws GOException {
289     return null;  //To change body of implemented methods use File | Settings | File Templates.
290   }
291 
292   public GOProteinData newGOProteinData(SPTREntry sptrEntry) throws GOException {
293     return null;  //To change body of implemented methods use File | Settings | File Templates.
294   }
295 
296   public GOProteinData copyGOProteinData(GOProteinData goProteinData) throws GOException {
297     return null;  //To change body of implemented methods use File | Settings | File Templates.
298   }
299 
300   public GOStructure newGOStructure() throws GOException {
301     return null;  //To change body of implemented methods use File | Settings | File Templates.
302   }
303 
304   public GOStructure copyGOStructure(GOStructure goStructure) throws GOException {
305     return null;  //To change body of implemented methods use File | Settings | File Templates.
306   }
307 
308   public CluSTrEntry newCluSTrEntry() throws CluSTrException {
309     return null;  //To change body of implemented methods use File | Settings | File Templates.
310   }
311 
312   public CluSTrEntry copyCluSTrEntry(CluSTrEntry cluSTrEntry) throws CluSTrException {
313     return null;  //To change body of implemented methods use File | Settings | File Templates.
314   }
315 
316   public UniParcEntry newUniParcEntry() throws UniParcException {
317     return null;  //To change body of implemented methods use File | Settings | File Templates.
318   }
319 
320   public UniParcEntry newUniParcEntry(SPTREntry sptrEntry, String s,
321                                       UniParcCrossReferenceMetaData uniParcCrossReferenceMetaData) throws UniParcException {
322     return null;  //To change body of implemented methods use File | Settings | File Templates.
323   }
324 
325   public UniParcEntry copyUniParcEntry(UniParcEntry uniParcEntry) throws UniParcException {
326     return null;  //To change body of implemented methods use File | Settings | File Templates.
327   }
328 
329   public UniParcCrossReference newUniParcCrossReference(String s) throws UniParcException {
330     return null;  //To change body of implemented methods use File | Settings | File Templates.
331   }
332 
333   public UniParcCrossReference copyUniParcCrossReference(UniParcCrossReference uniParcCrossReference) throws UniParcException {
334     return null;  //To change body of implemented methods use File | Settings | File Templates.
335   }
336 
337   public UniParcCrossReferenceMetaData newUniParcCrossReferenceMetaData() throws UniParcException {
338     return null;  //To change body of implemented methods use File | Settings | File Templates.
339   }
340 
341   public UniParcCrossReferenceMetaData copyUniParcCrossReferenceMetaData(
342           UniParcCrossReferenceMetaData uniParcCrossReferenceMetaData) throws UniParcException {
343     return null;  //To change body of implemented methods use File | Settings | File Templates.
344   }
345 
346   public UniRef100Entry newUniRef100Entry() throws UniRefException {
347     return null;  //To change body of implemented methods use File | Settings | File Templates.
348   }
349 
350   public UniRef100Entry newUniRef100Entry(SPTREntry sptrEntry) throws UniRefException {
351     return null;  //To change body of implemented methods use File | Settings | File Templates.
352   }
353 
354   public UniRef90Entry newUniRef90Entry() throws UniRefException {
355     return null;  //To change body of implemented methods use File | Settings | File Templates.
356   }
357 
358   public UniRef90Entry newUniRef90Entry(SPTREntry sptrEntry) throws UniRefException {
359     return null;  //To change body of implemented methods use File | Settings | File Templates.
360   }
361 
362   public UniRef50Entry newUniRef50Entry() throws UniRefException {
363     return null;  //To change body of implemented methods use File | Settings | File Templates.
364   }
365 
366   public UniRef50Entry newUniRef50Entry(SPTREntry sptrEntry) throws UniRefException {
367     return null;  //To change body of implemented methods use File | Settings | File Templates.
368   }
369 
370   public ClusterMember newClusterMember(String s) throws UniRefException {
371     return null;  //To change body of implemented methods use File | Settings | File Templates.
372   }
373 
374   public Gene newGeneInstance() throws SPTRException {
375     return null;  //To change body of implemented methods use File | Settings | File Templates.
376   }
377 
378   public Gene copyGeneInstance(Gene gene) throws SPTRException {
379     return null;  //To change body of implemented methods use File | Settings | File Templates.
380   }
381 
382   public uk.ac.ebi.interfaces.integr8.SPTREntry newIntegr8SPTREntryInstance(int i) throws Integr8Exception {
383     return null;  //To change body of implemented methods use File | Settings | File Templates.
384   }
385 
386   public uk.ac.ebi.interfaces.integr8.SPTREntry newIntegr8SPTREntryInstance(SPTREntry sptrEntry) throws Integr8Exception {
387     return null;  //To change body of implemented methods use File | Settings | File Templates.
388   }
389 
390   public uk.ac.ebi.interfaces.integr8.SPTREntry copyIntegr8SPTREntryInstance(uk.ac.ebi.interfaces.integr8.SPTREntry sptrEntry) throws Integr8Exception {
391     return null;  //To change body of implemented methods use File | Settings | File Templates.
392   }
393 
394   public uk.ac.ebi.interfaces.integr8.Gene newIntegr8GeneInstance() throws Integr8Exception {
395     return null;  //To change body of implemented methods use File | Settings | File Templates.
396   }
397 
398   public uk.ac.ebi.interfaces.integr8.Gene copyIntegr8GeneInstance(Gene gene) throws Integr8Exception {
399     return null;  //To change body of implemented methods use File | Settings | File Templates.
400   }
401 
402   public uk.ac.ebi.interfaces.integr8.Gene copyIntegr8GeneInstance(uk.ac.ebi.interfaces.integr8.Gene gene) throws Integr8Exception {
403     return null;  //To change body of implemented methods use File | Settings | File Templates.
404   }
405 
406   public ProteomeEntry newProteomeEntryInstance() throws Integr8Exception {
407     return null;  //To change body of implemented methods use File | Settings | File Templates.
408   }
409 
410   public Absorption newAbsorptionInstance() throws SPTRException {
411     return null;  //To change body of implemented methods use File | Settings | File Templates.
412   }
413 
414   public Absorption copyAbsorptionInstance(Absorption absorption) throws SPTRException {
415     return null;  //To change body of implemented methods use File | Settings | File Templates.
416   }
417 
418   public KineticParameter newKineticParameterInstance() throws SPTRException {
419     return null;  //To change body of implemented methods use File | Settings | File Templates.
420   }
421 
422   public KineticParameter copyKineticParameterInstance(KineticParameter kineticParameter) throws SPTRException {
423     return null;  //To change body of implemented methods use File | Settings | File Templates.
424   }
425 
426   public MaximumVelocity newMaximumVelocityInstance() throws SPTRException {
427     return null;  //To change body of implemented methods use File | Settings | File Templates.
428   }
429 
430   public MaximumVelocity copyMaximumVelocityInstance(MaximumVelocity maximumVelocity) throws SPTRException {
431     return null;  //To change body of implemented methods use File | Settings | File Templates.
432   }
433 
434   public MichaelisConstant newMichaelisConstantInstance() throws SPTRException {
435     return null;  //To change body of implemented methods use File | Settings | File Templates.
436   }
437 
438   public MichaelisConstant copyMichaelisConstantInstance(MichaelisConstant michaelisConstant) throws SPTRException {
439     return null;  //To change body of implemented methods use File | Settings | File Templates.
440   }
441 
442   public MassSpectrometryRange newMassSpectrometryRangeInstance() throws SPTRException {
443     return null;  //To change body of implemented methods use File | Settings | File Templates.
444   }
445 
446   public MassSpectrometryRange copyMassSpectrometryRangeInstance(MassSpectrometryRange massSpectrometryRange) throws SPTRException {
447     return null;  //To change body of implemented methods use File | Settings | File Templates.
448   }
449 }