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Coverage Report

  1. Project Clover database Mon Nov 11 2024 20:42:03 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
330
162
35
0.73
2.18
11
1.59

Classes

Class Line # Actions
JalviewDataset 35 38 29
0.00%
JalviewDataset.AlignmentSet 106 10 6
0.00%
 

Contributing tests

No tests hitting this source file were found.

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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.packed;
22   
23    import jalview.analysis.TreeModel;
24    import jalview.api.FeatureColourI;
25    import jalview.datamodel.AlignmentI;
26    import jalview.datamodel.SequenceI;
27    import jalview.io.NewickFile;
28   
29    import java.util.ArrayList;
30    import java.util.HashMap;
31    import java.util.Hashtable;
32    import java.util.List;
33    import java.util.Map;
34   
 
35    public class JalviewDataset
36    {
37    /**
38    * dataset that new data (sequences, alignments) will be added to
39    */
40    AlignmentI parentDataset;
41   
42    /**
43    * @return the parentDataset
44    */
 
45  0 toggle public AlignmentI getParentDataset()
46    {
47  0 return parentDataset;
48    }
49   
50    /**
51    * @param parentDataset
52    * the parentDataset to set
53    */
 
54  0 toggle public void setParentDataset(AlignmentI parentDataset)
55    {
56  0 this.parentDataset = parentDataset;
57    }
58   
59    /**
60    * @return the featureColours
61    */
 
62  0 toggle public Map<String, FeatureColourI> getFeatureColours()
63    {
64  0 return featureColours;
65    }
66   
67    /**
68    * @param featureColours
69    * the featureColours to set
70    */
 
71  0 toggle public void setFeatureColours(Map<String, FeatureColourI> featureColours)
72    {
73  0 this.featureColours = featureColours;
74    }
75   
76    /**
77    * @return the seqDetails
78    */
 
79  0 toggle public Hashtable getSeqDetails()
80    {
81  0 return seqDetails;
82    }
83   
84    /**
85    * @param seqDetails
86    * the seqDetails to set
87    */
 
88  0 toggle public void setSeqDetails(Hashtable seqDetails)
89    {
90  0 this.seqDetails = seqDetails;
91    }
92   
93    /**
94    * @return the al
95    */
 
96  0 toggle public List<AlignmentSet> getAl()
97    {
98  0 return (al == null) ? new ArrayList<AlignmentSet>() : al;
99    }
100   
101    /**
102    * current alignment being worked on.
103    */
104    List<AlignmentSet> al;
105   
 
106    public class AlignmentSet
107    {
108    public AlignmentI al;
109   
110    public List<jalview.io.NewickFile> trees;
111   
 
112  0 toggle AlignmentSet(AlignmentI a)
113    {
114  0 al = a;
115  0 trees = new ArrayList<jalview.io.NewickFile>();
116    }
117   
118    /**
119    * deuniquify the current alignment in the context, merging any new
120    * annotation/features with the existing set
121    *
122    * @param context
123    */
 
124  0 toggle void deuniquifyAlignment()
125    {
126  0 if (seqDetails == null || seqDetails.size() == 0)
127    {
128    // nothing to do
129  0 return;
130    }
131    // 1. recover correct names and attributes for each sequence in alignment.
132    /*
133    * TODO: housekeeping w.r.t. recovery of dataset and annotation references
134    * for input sequences, and then dataset sequence creation for new
135    * sequences retrieved from service // finally, attempt to de-uniquify to
136    * recover input sequence identity, and try to map back onto dataset Note:
137    * this jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true);
138    * will NOT WORK - the returned alignment may contain multiple versions of
139    * the input sequence, each being a subsequence of the original.
140    * deuniquify also removes existing annotation and features added in the
141    * previous step... al.setDataset(dataset); // add in new sequences
142    * retrieved from sequence search which are not already in dataset. //
143    * trigger a 'fetchDBids' to annotate sequences with database ids...
144    */
145    // jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
146    // seqDetails, al,true);
147   
148  0 jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
149    al.getSequencesArray(), true);
150    // 2. Update names of associated nodes in any trees
151  0 for (NewickFile nf : trees)
152    {
153    // the following works because all trees are already had node/SequenceI
154    // associations created.
155  0 TreeModel njt = new TreeModel(al.getSequencesArray(), null, nf,null);
156    // this just updates the displayed leaf name on the tree according to
157    // the SequenceIs.
158  0 njt.renameAssociatedNodes();
159    }
160   
161    }
162   
163    /**
164    * set modification flag. If anything modifies the alignment in the current
165    * set, this flag should be true
166    */
167    private boolean modified = false;
168   
169    /**
170    * @return the modified
171    */
 
172  0 toggle public boolean isModified()
173    {
174  0 return modified;
175    }
176   
177    /**
178    * or the modification state with the given state
179    *
180    * @param modifiedFromAction
181    */
 
182  0 toggle public void updateSetModified(boolean modifiedFromAction)
183    {
184  0 modified |= modifiedFromAction;
185    }
186    }
187   
188    /**
189    * current set of feature colours
190    */
191    Map<String, FeatureColourI> featureColours;
192   
193    /**
194    * original identity of each sequence in results
195    */
196    Hashtable seqDetails;
197   
198    public boolean relaxedIdMatching = false;
199   
 
200  0 toggle public JalviewDataset()
201    {
202  0 seqDetails = new Hashtable();
203  0 al = new ArrayList<AlignmentSet>();
204  0 parentDataset = null;
205  0 featureColours = new HashMap<String, FeatureColourI>();
206    }
207   
208    /**
209    * context created from an existing alignment.
210    *
211    * @param parentAlignment
212    */
 
213  0 toggle public JalviewDataset(AlignmentI aldataset,
214    Map<String, FeatureColourI> fc, Hashtable seqDets)
215    {
216    // TODO not used - remove?
217  0 this(aldataset, fc, seqDets, null);
218    }
219   
220    /**
221    *
222    * @param aldataset
223    * - parent dataset for any new alignment/sequence data (must not be
224    * null)
225    * @param fc
226    * (may be null) feature settings for the alignment where new feature
227    * renderstyles are stored
228    * @param seqDets
229    * - (may be null) anonymised sequence information created by
230    * Sequence uniquifier
231    * @param parentAlignment
232    * (may be null) alignment to associate new annotation and trees
233    * with.
234    */
 
235  0 toggle public JalviewDataset(AlignmentI aldataset,
236    Map<String, FeatureColourI> fc, Hashtable seqDets,
237    AlignmentI parentAlignment)
238    {
239  0 this();
240  0 parentDataset = aldataset;
241  0 if (parentAlignment != null)
242    {
243  0 parentDataset = parentAlignment.getDataset();
244  0 if (parentDataset == null)
245    {
246  0 parentDataset = parentAlignment;
247    }
248    else
249    {
250  0 addAlignment(parentAlignment);
251    }
252    }
253  0 if (seqDets != null)
254    {
255  0 seqDetails = seqDets;
256    }
257  0 if (fc != null)
258    {
259  0 featureColours = fc;
260    }
261   
262    }
263   
 
264  0 toggle public boolean hasAlignments()
265    {
266  0 return al != null && al.size() > 0;
267    }
268   
 
269  0 toggle public AlignmentI getLastAlignment()
270    {
271  0 return (al == null || al.size() < 1) ? null : al.get(al.size() - 1).al;
272    }
273   
 
274  0 toggle public AlignmentSet getLastAlignmentSet()
275    {
276  0 return (al == null || al.size() < 1) ? null : al.get(al.size() - 1);
277    }
278   
279    /**
280    * post process (deuniquify) the current alignment and its dependent data, and
281    * then add newal to the dataset.
282    *
283    * @param newal
284    */
 
285  0 toggle public void addAlignment(AlignmentI newal)
286    {
287  0 if (!hasAlignments())
288    {
289  0 al = new ArrayList<AlignmentSet>();
290    }
291  0 AlignmentSet last = getLastAlignmentSet();
292  0 if (last != null)
293    {
294  0 jalview.bin.Console.errPrintln("Deuniquifying last alignment set.");
295  0 last.deuniquifyAlignment();
296    }
297  0 al.add(new AlignmentSet(newal));
298    }
299   
 
300  0 toggle public void addTreeFromFile(NewickFile nf)
301    {
302  0 AlignmentSet lal = getLastAlignmentSet();
303  0 lal.trees.add(nf);
304    }
305   
 
306  0 toggle public boolean hasSequenceAssoc()
307    {
308    // TODO: discover where sequence associated data should be put.
309  0 return false;
310    }
311   
 
312  0 toggle public SequenceI getLastAssociatedSequence()
313    {
314    // TODO: delineate semantics for associating uniquified data with
315    // potentially de-uniquified sequence.
316  0 return null;
317    }
318   
319    /**
320    * update the modified state flag for the current set with the given
321    * modification state
322    *
323    * @param modified
324    * - this will be ored with current modification state
325    */
 
326  0 toggle public void updateSetModified(boolean modified)
327    {
328  0 getLastAlignmentSet().updateSetModified(modified);
329    }
330    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 20:49:40 GMT using coverage data from Mon Nov 11 2024 20:49:29 GMT.
  • OpenClover is free and open-source software.