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  1. Project Clover database Wed Nov 13 2024 16:21:17 GMT
  2. Package jalview.io.vamsas

File Dbref.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

30
73
8
1
237
169
25
0.34
9.12
8
3.12

Classes

Class Line # Actions
Dbref 33 73 25
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.io.vamsas;
22   
23    import jalview.bin.Console;
24    import jalview.datamodel.DBRefEntry;
25    import jalview.datamodel.SequenceI;
26    import jalview.io.VamsasAppDatastore;
27   
28    import uk.ac.vamsas.objects.core.DataSet;
29    import uk.ac.vamsas.objects.core.DbRef;
30    import uk.ac.vamsas.objects.core.Map;
31    import uk.ac.vamsas.objects.core.Sequence;
32   
 
33    public class Dbref extends Rangetype
34    {
35    jalview.datamodel.SequenceI sq = null;
36   
37    uk.ac.vamsas.objects.core.Sequence sequence = null;
38   
39    DataSet ds;
40   
 
41  0 toggle public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
42    jalview.datamodel.SequenceI sq2,
43    uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
44    {
45  0 super(datastore, dbentry, DbRef.class);
46    // initialise object specific attributes
47  0 sq = sq2;
48  0 sequence = sequence2;
49  0 this.jvobj = dbentry;
50  0 ds = dataset;
51    // call the accessors
52  0 doSync();
53    }
54   
 
55  0 toggle public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
56    SequenceI dsseq)
57    {
58  0 super(datastore, ref, jalview.datamodel.DBRefEntry.class);
59  0 sequence = vdseq;
60  0 sq = dsseq;
61  0 ds = (DataSet) vdseq.getV_parent();
62  0 doJvUpdate();
63    }
64   
 
65  0 toggle public void updateToDoc()
66    {
67  0 DbRef dbref = (DbRef) this.vobj;
68  0 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
69  0 dbref.setAccessionId(jvobj.getAccessionId());
70  0 dbref.setSource(jvobj.getSource());
71  0 dbref.setVersion(jvobj.getVersion());
72  0 if (jvobj.getMap() != null)
73    {
74    // Record mapping to external database coordinate system.
75  0 jalview.datamodel.Mapping mp = jvobj.getMap();
76  0 if (mp.getMap() != null)
77    {
78  0 Map vMap = null;
79  0 if (dbref.getMapCount() == 0)
80    {
81  0 vMap = new Map();
82  0 initMapType(vMap, mp.getMap(), true);
83  0 dbref.addMap(vMap);
84    }
85    else
86    {
87    // we just update the data anyway.
88  0 vMap = dbref.getMap(0);
89  0 initMapType(vMap, mp.getMap(), true);
90    }
91  0 updateMapTo(mp);
92    }
93    }
94    else
95    {
96  0 Console.debug(
97    "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
98    }
99   
100    }
101   
102    /**
103    * ugly hack to try to get the embedded sequences within a database reference
104    * to be stored in the document's dataset.
105    *
106    * @param mp
107    */
 
108  0 toggle private void updateMapTo(jalview.datamodel.Mapping mp)
109    {
110  0 log.info(
111    "Performing updateMapTo remove this message when we know what we're doing.");
112    // TODO determine how sequences associated with database mappings are stored
113    // in the document
114  0 if (mp != null && mp.getTo() != null)
115    {
116  0 if (mp.getTo().getDatasetSequence() == null)
117    {
118    // TODO: fix this hinky sh!t
119  0 DatastoreItem dssync = dsReg.getDatastoreItemFor(mp.getTo());
120  0 if (dssync == null)
121    {
122    // sync the dataset sequence, if it hasn't been done already.
123    // TODO: ensure real dataset sequence corresponding to getTo is
124    // recovered
125  0 dssync = new Datasetsequence(datastore, mp.getTo(),
126  0 (mp.getMappedWidth() == mp.getWidth())
127    ? sequence.getDictionary()
128  0 : ((mp.getMappedWidth() == 3)
129    ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
130    : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
131    ds);
132    }
133    //
134    // TODO: NOW add a mapping between new dataset sequence and sequence
135    // associated with the database reference
136   
137    // dna mappings only...
138    // new jalview.io.vamsas.Sequencemapping(datastore, mp, sequence, ds);
139   
140    }
141   
142    }
143    else
144    {
145  0 log.debug("Ignoring non-dataset sequence mapping.");
146    }
147    }
148   
 
149  0 toggle public void updateFromDoc()
150    {
151  0 DbRef vobj = (DbRef) this.vobj;
152  0 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
153  0 jvobj.setAccessionId(vobj.getAccessionId());
154  0 jvobj.setSource(vobj.getSource());
155  0 jvobj.setVersion(vobj.getVersion());
156    // add new dbref
157  0 if (vobj.getMapCount() > 0)
158    {
159    // TODO: Jalview ignores all the other maps
160  0 if (vobj.getMapCount() > 1)
161    {
162  0 Console.debug("Ignoring additional mappings on DbRef: "
163    + jvobj.getSource() + ":" + jvobj.getAccessionId());
164    }
165  0 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
166    parsemapType(vobj.getMap(0)));
167  0 if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
168    {
169  0 jvobj.setMap(mp);
170    }
171    }
172    }
173   
 
174  0 toggle public void conflict()
175    {
176  0 DbRef vobj = (DbRef) this.vobj;
177  0 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
178  0 Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
179    + vobj.getSource() + " " + vobj.getVorbaId());
180    // TODO Auto-generated method stub
181   
182    }
183   
 
184  0 toggle public void addFromDocument()
185    {
186  0 DbRef vobj = (DbRef) this.vobj;
187  0 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
188    // add new dbref
189  0 sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(
190    vobj.getSource().toString(), vobj.getVersion().toString(),
191    vobj.getAccessionId().toString()));
192  0 if (vobj.getMapCount() > 0)
193    {
194    // TODO: Jalview ignores all the other maps
195  0 if (vobj.getMapCount() > 1)
196    {
197  0 Console.debug("Ignoring additional mappings on DbRef: "
198    + jvobj.getSource() + ":" + jvobj.getAccessionId());
199    }
200  0 jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
201    parsemapType(vobj.getMap(0)));
202  0 jvobj.setMap(mp);
203    }
204    // TODO: jalview ignores links and properties because it doesn't know what
205    // to do with them.
206   
207  0 bindjvvobj(jvobj, vobj);
208    }
209   
 
210  0 toggle public void addToDocument()
211    {
212  0 DBRefEntry jvobj = (DBRefEntry) this.jvobj;
213  0 DbRef dbref = new DbRef();
214  0 bindjvvobj(jvobj, dbref);
215  0 dbref.setAccessionId(jvobj.getAccessionId());
216  0 dbref.setSource(jvobj.getSource());
217  0 dbref.setVersion(jvobj.getVersion());
218  0 sequence.addDbRef(dbref);
219  0 if (jvobj.getMap() != null)
220    {
221  0 jalview.datamodel.Mapping mp = jvobj.getMap();
222  0 if (mp.getMap() != null)
223    {
224  0 Map vMap = new Map();
225  0 initMapType(vMap, mp.getMap(), true);
226  0 dbref.addMap(vMap);
227  0 updateMapTo(mp);
228    }
229    else
230    {
231  0 Console.debug(
232    "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
233    }
234    }
235    }
236   
237    }