2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.io.vamsas;
20 import jalview.datamodel.DBRefEntry;
21 import jalview.datamodel.SequenceI;
22 import uk.ac.vamsas.objects.core.DataSet;
23 import uk.ac.vamsas.objects.core.DbRef;
24 import uk.ac.vamsas.objects.core.Map;
25 import uk.ac.vamsas.objects.core.Sequence;
26 import jalview.io.VamsasAppDatastore;
28 public class Dbref extends Rangetype
30 jalview.datamodel.SequenceI sq = null;
32 uk.ac.vamsas.objects.core.Sequence sequence = null;
36 public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
37 jalview.datamodel.SequenceI sq2,
38 uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
40 super(datastore, dbentry, DbRef.class);
41 // initialise object specific attributes
50 public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
53 super(datastore, ref, jalview.datamodel.DBRefEntry.class);
56 ds = (DataSet) vdseq.getV_parent();
60 public void updateToDoc()
62 DbRef dbref = (DbRef) this.vobj;
63 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
64 dbref.setAccessionId(jvobj.getAccessionId());
65 dbref.setSource(jvobj.getSource());
66 dbref.setVersion(jvobj.getVersion());
67 if (jvobj.getMap() != null)
69 // Record mapping to external database coordinate system.
70 jalview.datamodel.Mapping mp = jvobj.getMap();
71 if (mp.getMap() != null)
74 if (dbref.getMapCount() == 0)
77 initMapType(vMap, mp.getMap(), true);
82 // we just update the data anyway.
83 vMap = dbref.getMap(0);
84 initMapType(vMap, mp.getMap(), true);
91 jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
92 + jvobj.getSrcAccString());
98 * ugly hack to try to get the embedded sequences within a database reference
99 * to be stored in the document's dataset.
103 private void updateMapTo(jalview.datamodel.Mapping mp)
105 log.info("Performing updateMapTo remove this message when we know what we're doing.");
106 // TODO determine how sequences associated with database mappings are stored
108 if (mp != null && mp.getTo() != null)
110 if (mp.getTo().getDatasetSequence() == null)
112 // TODO: fix this hinky sh!t
113 DatastoreItem dssync = dsReg.getDatastoreItemFor(mp.getTo());
116 // sync the dataset sequence, if it hasn't been done already.
117 // TODO: ensure real dataset sequence corresponding to getTo is
119 dssync = new Datasetsequence(
122 (mp.getMappedWidth() == mp.getWidth()) ? sequence
124 : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
125 : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
129 // TODO: NOW add a mapping between new dataset sequence and sequence
130 // associated with the database reference
132 // dna mappings only...
133 // new jalview.io.vamsas.Sequencemapping(datastore, mp, sequence, ds);
140 log.debug("Ignoring non-dataset sequence mapping.");
144 public void updateFromDoc()
146 DbRef vobj = (DbRef) this.vobj;
147 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
148 jvobj.setAccessionId(vobj.getAccessionId());
149 jvobj.setSource(vobj.getSource());
150 jvobj.setVersion(vobj.getVersion());
152 if (vobj.getMapCount() > 0)
154 // TODO: Jalview ignores all the other maps
155 if (vobj.getMapCount() > 1)
157 jalview.bin.Cache.log
158 .debug("Ignoring additional mappings on DbRef: "
159 + jvobj.getSource() + ":" + jvobj.getAccessionId());
161 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
162 parsemapType(vobj.getMap(0)));
163 if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
170 public void conflict()
172 DbRef vobj = (DbRef) this.vobj;
173 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
174 jalview.bin.Cache.log.debug("Conflict in dbentry update for "
175 + vobj.getAccessionId() + vobj.getSource() + " "
176 + vobj.getVorbaId());
177 // TODO Auto-generated method stub
181 public void addFromDocument()
183 DbRef vobj = (DbRef) this.vobj;
184 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
186 sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
187 .toString(), vobj.getVersion().toString(), vobj
188 .getAccessionId().toString()));
189 if (vobj.getMapCount() > 0)
191 // TODO: Jalview ignores all the other maps
192 if (vobj.getMapCount() > 1)
194 jalview.bin.Cache.log
195 .debug("Ignoring additional mappings on DbRef: "
196 + jvobj.getSource() + ":" + jvobj.getAccessionId());
198 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
199 parsemapType(vobj.getMap(0)));
202 // TODO: jalview ignores links and properties because it doesn't know what
205 bindjvvobj(jvobj, vobj);
208 public void addToDocument()
210 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
211 DbRef dbref = new DbRef();
212 bindjvvobj(jvobj, dbref);
213 dbref.setAccessionId(jvobj.getAccessionId());
214 dbref.setSource(jvobj.getSource());
215 dbref.setVersion(jvobj.getVersion());
216 sequence.addDbRef(dbref);
217 if (jvobj.getMap() != null)
219 jalview.datamodel.Mapping mp = jvobj.getMap();
220 if (mp.getMap() != null)
222 Map vMap = new Map();
223 initMapType(vMap, mp.getMap(), true);
229 jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
230 + jvobj.getSrcAccString());