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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 GMT
  2. Package jalview.io.packed

File JalviewDataset.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

20
48
22
2
331
163
35
0.73
2.18
11
1.59

Classes

Class Line # Actions
JalviewDataset 36 38 29
0.00%
JalviewDataset.AlignmentSet 107 10 6
0.00%
 

Contributing tests

No tests hitting this source file were found.

Source view

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.packed;
22   
23    import jalview.analysis.SeqsetUtils.SequenceInfo;
24    import jalview.analysis.TreeModel;
25    import jalview.api.FeatureColourI;
26    import jalview.datamodel.AlignmentI;
27    import jalview.datamodel.SequenceI;
28    import jalview.io.NewickFile;
29   
30    import java.util.ArrayList;
31    import java.util.HashMap;
32    import java.util.Hashtable;
33    import java.util.List;
34    import java.util.Map;
35   
 
36    public class JalviewDataset
37    {
38    /**
39    * dataset that new data (sequences, alignments) will be added to
40    */
41    AlignmentI parentDataset;
42   
43    /**
44    * @return the parentDataset
45    */
 
46  0 toggle public AlignmentI getParentDataset()
47    {
48  0 return parentDataset;
49    }
50   
51    /**
52    * @param parentDataset
53    * the parentDataset to set
54    */
 
55  0 toggle public void setParentDataset(AlignmentI parentDataset)
56    {
57  0 this.parentDataset = parentDataset;
58    }
59   
60    /**
61    * @return the featureColours
62    */
 
63  0 toggle public Map<String, FeatureColourI> getFeatureColours()
64    {
65  0 return featureColours;
66    }
67   
68    /**
69    * @param featureColours
70    * the featureColours to set
71    */
 
72  0 toggle public void setFeatureColours(Map<String, FeatureColourI> featureColours)
73    {
74  0 this.featureColours = featureColours;
75    }
76   
77    /**
78    * @return the seqDetails
79    */
 
80  0 toggle public Map<String, SequenceInfo> getSeqDetails()
81    {
82  0 return seqDetails;
83    }
84   
85    /**
86    * @param seqDetails
87    * the seqDetails to set
88    */
 
89  0 toggle public void setSeqDetails(Hashtable seqDetails)
90    {
91  0 this.seqDetails = seqDetails;
92    }
93   
94    /**
95    * @return the al
96    */
 
97  0 toggle public List<AlignmentSet> getAl()
98    {
99  0 return (al == null) ? new ArrayList<AlignmentSet>() : al;
100    }
101   
102    /**
103    * current alignment being worked on.
104    */
105    List<AlignmentSet> al;
106   
 
107    public class AlignmentSet
108    {
109    public AlignmentI al;
110   
111    public List<jalview.io.NewickFile> trees;
112   
 
113  0 toggle AlignmentSet(AlignmentI a)
114    {
115  0 al = a;
116  0 trees = new ArrayList<jalview.io.NewickFile>();
117    }
118   
119    /**
120    * deuniquify the current alignment in the context, merging any new
121    * annotation/features with the existing set
122    *
123    * @param context
124    */
 
125  0 toggle void deuniquifyAlignment()
126    {
127  0 if (seqDetails == null || seqDetails.size() == 0)
128    {
129    // nothing to do
130  0 return;
131    }
132    // 1. recover correct names and attributes for each sequence in alignment.
133    /*
134    * TODO: housekeeping w.r.t. recovery of dataset and annotation references
135    * for input sequences, and then dataset sequence creation for new
136    * sequences retrieved from service // finally, attempt to de-uniquify to
137    * recover input sequence identity, and try to map back onto dataset Note:
138    * this jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
139    * will NOT WORK - the returned alignment may contain multiple versions of
140    * the input sequence, each being a subsequence of the original.
141    * deuniquify also removes existing annotation and features added in the
142    * previous step... al.setDataset(dataset); // add in new sequences
143    * retrieved from sequence search which are not already in dataset. //
144    * trigger a 'fetchDBids' to annotate sequences with database ids...
145    */
146    // jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
147    // seqDetails, al,true);
148   
149  0 jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
150    al.getSequencesArray(), true);
151    // 2. Update names of associated nodes in any trees
152  0 for (NewickFile nf : trees)
153    {
154    // the following works because all trees are already had node/SequenceI
155    // associations created.
156  0 TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf,null);
157    // this just updates the displayed leaf name on the tree according to
158    // the SequenceIs.
159  0 njt.renameAssociatedNodes();
160    }
161   
162    }
163   
164    /**
165    * set modification flag. If anything modifies the alignment in the current
166    * set, this flag should be true
167    */
168    private boolean modified = false;
169   
170    /**
171    * @return the modified
172    */
 
173  0 toggle public boolean isModified()
174    {
175  0 return modified;
176    }
177   
178    /**
179    * or the modification state with the given state
180    *
181    * @param modifiedFromAction
182    */
 
183  0 toggle public void updateSetModified(boolean modifiedFromAction)
184    {
185  0 modified |= modifiedFromAction;
186    }
187    }
188   
189    /**
190    * current set of feature colours
191    */
192    Map<String, FeatureColourI> featureColours;
193   
194    /**
195    * original identity of each sequence in results
196    */
197    Map<String, SequenceInfo> seqDetails;
198   
199    public boolean relaxedIdMatching = false;
200   
 
201  0 toggle public JalviewDataset()
202    {
203  0 seqDetails = new Hashtable();
204  0 al = new ArrayList<AlignmentSet>();
205  0 parentDataset = null;
206  0 featureColours = new HashMap<String, FeatureColourI>();
207    }
208   
209    /**
210    * context created from an existing alignment.
211    *
212    * @param parentAlignment
213    */
 
214  0 toggle public JalviewDataset(AlignmentI aldataset,
215    Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets)
216    {
217    // TODO not used - remove?
218  0 this(aldataset, fc, seqDets, null);
219    }
220   
221    /**
222    *
223    * @param aldataset
224    * - parent dataset for any new alignment/sequence data (must not be
225    * null)
226    * @param fc
227    * (may be null) feature settings for the alignment where new feature
228    * renderstyles are stored
229    * @param seqDets
230    * - (may be null) anonymised sequence information created by
231    * Sequence uniquifier
232    * @param parentAlignment
233    * (may be null) alignment to associate new annotation and trees
234    * with.
235    */
 
236  0 toggle public JalviewDataset(AlignmentI aldataset,
237    Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets,
238    AlignmentI parentAlignment)
239    {
240  0 this();
241  0 parentDataset = aldataset;
242  0 if (parentAlignment != null)
243    {
244  0 parentDataset = parentAlignment.getDataset();
245  0 if (parentDataset == null)
246    {
247  0 parentDataset = parentAlignment;
248    }
249    else
250    {
251  0 addAlignment(parentAlignment);
252    }
253    }
254  0 if (seqDets != null)
255    {
256  0 seqDetails = seqDets;
257    }
258  0 if (fc != null)
259    {
260  0 featureColours = fc;
261    }
262   
263    }
264   
 
265  0 toggle public boolean hasAlignments()
266    {
267  0 return al != null && al.size() > 0;
268    }
269   
 
270  0 toggle public AlignmentI getLastAlignment()
271    {
272  0 return (al == null || al.size() < 1) ? null : al.get(al.size() - 1).al;
273    }
274   
 
275  0 toggle public AlignmentSet getLastAlignmentSet()
276    {
277  0 return (al == null || al.size() < 1) ? null : al.get(al.size() - 1);
278    }
279   
280    /**
281    * post process (deuniquify) the current alignment and its dependent data, and
282    * then add newal to the dataset.
283    *
284    * @param newal
285    */
 
286  0 toggle public void addAlignment(AlignmentI newal)
287    {
288  0 if (!hasAlignments())
289    {
290  0 al = new ArrayList<AlignmentSet>();
291    }
292  0 AlignmentSet last = getLastAlignmentSet();
293  0 if (last != null)
294    {
295  0 jalview.bin.Console.errPrintln("Deuniquifying last alignment set.");
296  0 last.deuniquifyAlignment();
297    }
298  0 al.add(new AlignmentSet(newal));
299    }
300   
 
301  0 toggle public void addTreeFromFile(NewickFile nf)
302    {
303  0 AlignmentSet lal = getLastAlignmentSet();
304  0 lal.trees.add(nf);
305    }
306   
 
307  0 toggle public boolean hasSequenceAssoc()
308    {
309    // TODO: discover where sequence associated data should be put.
310  0 return false;
311    }
312   
 
313  0 toggle public SequenceI getLastAssociatedSequence()
314    {
315    // TODO: delineate semantics for associating uniquified data with
316    // potentially de-uniquified sequence.
317  0 return null;
318    }
319   
320    /**
321    * update the modified state flag for the current set with the given
322    * modification state
323    *
324    * @param modified
325    * - this will be ored with current modification state
326    */
 
327  0 toggle public void updateSetModified(boolean modified)
328    {
329  0 getLastAlignmentSet().updateSetModified(modified);
330    }
331    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.