2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.io.vamsas;
21 import jalview.datamodel.DBRefEntry;
22 import jalview.datamodel.SequenceI;
23 import uk.ac.vamsas.objects.core.DataSet;
24 import uk.ac.vamsas.objects.core.DbRef;
25 import uk.ac.vamsas.objects.core.Map;
26 import uk.ac.vamsas.objects.core.Sequence;
27 import jalview.io.VamsasAppDatastore;
29 public class Dbref extends Rangetype
31 jalview.datamodel.SequenceI sq = null;
33 uk.ac.vamsas.objects.core.Sequence sequence = null;
37 public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
38 jalview.datamodel.SequenceI sq2,
39 uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
41 super(datastore, dbentry, DbRef.class);
42 // initialise object specific attributes
51 public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
54 super(datastore, ref, jalview.datamodel.DBRefEntry.class);
57 ds = (DataSet) vdseq.getV_parent();
61 public void updateToDoc()
63 DbRef dbref = (DbRef) this.vobj;
64 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
65 dbref.setAccessionId(jvobj.getAccessionId());
66 dbref.setSource(jvobj.getSource());
67 dbref.setVersion(jvobj.getVersion());
68 if (jvobj.getMap() != null)
70 // Record mapping to external database coordinate system.
71 jalview.datamodel.Mapping mp = jvobj.getMap();
72 if (mp.getMap() != null)
75 if (dbref.getMapCount() == 0)
78 initMapType(vMap, mp.getMap(), true);
83 // we just update the data anyway.
84 vMap = dbref.getMap(0);
85 initMapType(vMap, mp.getMap(), true);
92 jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
93 + jvobj.getSrcAccString());
98 * ugly hack to try to get the embedded sequences within a database reference to be stored in the document's dataset.
101 private void updateMapTo(jalview.datamodel.Mapping mp)
103 log.info("Performing updateMapTo remove this message when we know what we're doing.");
104 // TODO determine how sequences associated with database mappings are stored in the document
105 if (mp!=null && mp.getTo() != null)
107 if (mp.getTo().getDatasetSequence() == null)
109 if (!dsReg.isInvolvedInDsitem(mp.getTo()))
111 // sync the dataset sequence, if it hasn't been done already.
112 Datasetsequence dssync = new Datasetsequence(
113 datastore, mp.getTo(),
114 (mp.getMappedWidth() == mp.getWidth()) ? sequence
116 : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA
117 : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA),
119 // add a mapping between new dataset sequence and sequence associated with the database reference
123 log.debug("Ignoring non-dataset sequence mapping.");
127 public void updateFromDoc()
129 DbRef vobj = (DbRef) this.vobj;
130 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
131 jvobj.setAccessionId(vobj.getAccessionId());
132 jvobj.setSource(vobj.getSource());
133 jvobj.setVersion(vobj.getVersion());
135 if (vobj.getMapCount() > 0)
137 // TODO: Jalview ignores all the other maps
138 if (vobj.getMapCount() > 1)
140 jalview.bin.Cache.log
141 .debug("Ignoring additional mappings on DbRef: "
142 + jvobj.getSource() + ":" + jvobj.getAccessionId());
144 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
145 parsemapType(vobj.getMap(0)));
146 if (jvobj.getMap()==null || !mp.equals(jvobj.getMap()))
153 public void conflict()
155 DbRef vobj = (DbRef) this.vobj;
156 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
157 jalview.bin.Cache.log.debug("Conflict in dbentry update for "
158 + vobj.getAccessionId() + vobj.getSource() + " "
159 + vobj.getVorbaId());
160 // TODO Auto-generated method stub
164 public void addFromDocument()
166 DbRef vobj = (DbRef) this.vobj;
167 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
169 sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
170 .toString(), vobj.getVersion().toString(), vobj
171 .getAccessionId().toString()));
172 if (vobj.getMapCount() > 0)
174 // TODO: Jalview ignores all the other maps
175 if (vobj.getMapCount() > 1)
177 jalview.bin.Cache.log
178 .debug("Ignoring additional mappings on DbRef: "
179 + jvobj.getSource() + ":" + jvobj.getAccessionId());
181 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
182 parsemapType(vobj.getMap(0)));
185 // TODO: jalview ignores links and properties because it doesn't know what
188 bindjvvobj(jvobj, vobj);
191 public void addToDocument()
193 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
194 DbRef dbref = new DbRef();
195 bindjvvobj(jvobj, dbref);
196 dbref.setAccessionId(jvobj.getAccessionId());
197 dbref.setSource(jvobj.getSource());
198 dbref.setVersion(jvobj.getVersion());
199 if (jvobj.getMap() != null)
201 jalview.datamodel.Mapping mp = jvobj.getMap();
202 if (mp.getMap() != null)
204 Map vMap = new Map();
205 initMapType(vMap, mp.getMap(), true);
210 jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
211 + jvobj.getSrcAccString());
214 sequence.addDbRef(dbref);