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Coverage Report

  1. Project Clover database Wed Nov 6 2024 00:56:24 GMT
  2. Package jalview.analysis

File SeqsetUtils.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

52
87
7
1
313
195
39
0.45
12.43
7
5.57

Classes

Class Line # Actions
SeqsetUtils 33 87 39
0.623287762.3%
 

Contributing tests

This file is covered by 20 tests. .

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.analysis;
22   
23    import jalview.datamodel.PDBEntry;
24    import jalview.datamodel.Sequence;
25    import jalview.datamodel.SequenceFeature;
26    import jalview.datamodel.SequenceI;
27   
28    import java.util.Enumeration;
29    import java.util.Hashtable;
30    import java.util.List;
31    import java.util.Vector;
32   
 
33    public class SeqsetUtils
34    {
35   
36    /**
37    * Store essential properties of a sequence in a hashtable for later recovery
38    * Keys are Name, Start, End, SeqFeatures, PdbId
39    *
40    * @param seq
41    * SequenceI
42    * @return Hashtable
43    */
 
44  237 toggle public static Hashtable SeqCharacterHash(SequenceI seq)
45    {
46  237 Hashtable sqinfo = new Hashtable();
47  237 sqinfo.put("Name", seq.getName());
48  237 sqinfo.put("Start", Integer.valueOf(seq.getStart()));
49  237 sqinfo.put("End", Integer.valueOf(seq.getEnd()));
50  237 if (seq.getDescription() != null)
51    {
52  34 sqinfo.put("Description", seq.getDescription());
53    }
54   
55  237 Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
56  237 List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
57  237 sfeat.addAll(sfs);
58   
59  237 if (seq.getDatasetSequence() == null)
60    {
61  17 sqinfo.put("SeqFeatures", sfeat);
62  17 sqinfo.put("PdbId",
63  17 (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
64    : new Vector<PDBEntry>());
65    }
66    else
67    {
68  220 sqinfo.put("datasetSequence",
69  220 (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
70    : new Sequence("THISISAPLACEHOLDER", ""));
71    }
72  237 return sqinfo;
73    }
74   
75    /**
76    * Recover essential properties of a sequence from a hashtable TODO: replace
77    * these methods with something more elegant.
78    *
79    * @param sq
80    * SequenceI
81    * @param sqinfo
82    * Hashtable
83    * @return boolean true if name was not updated from sqinfo Name entry
84    */
 
85  174 toggle public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
86    {
87  174 boolean namePresent = true;
88  174 if (sqinfo == null)
89    {
90  0 return false;
91    }
92  174 String oldname = (String) sqinfo.get("Name");
93  174 Integer start = (Integer) sqinfo.get("Start");
94  174 Integer end = (Integer) sqinfo.get("End");
95  174 Vector<SequenceFeature> sfeatures = (Vector<SequenceFeature>) sqinfo
96    .get("SeqFeatures");
97  174 Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
98  174 String description = (String) sqinfo.get("Description");
99  174 Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
100  174 if (oldname == null)
101    {
102  0 namePresent = false;
103    }
104    else
105    {
106  174 sq.setName(oldname);
107    }
108  174 if (pdbid != null && pdbid.size() > 0)
109    {
110  0 sq.setPDBId(pdbid);
111    }
112   
113  174 if ((start != null) && (end != null))
114    {
115  174 sq.setStart(start.intValue());
116  174 sq.setEnd(end.intValue());
117    }
118   
119  174 if (sfeatures != null && !sfeatures.isEmpty())
120    {
121  0 sq.setSequenceFeatures(sfeatures);
122    }
123  174 if (description != null)
124    {
125  2 sq.setDescription(description);
126    }
127  174 if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
128    && seqds.getLength() == 0))
129    {
130  172 if (sfeatures != null)
131    {
132  0 jalview.bin.Console.errPrintln(
133    "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
134    }
135  172 sq.setDatasetSequence(seqds);
136    }
137   
138  174 return namePresent;
139    }
140   
141    /**
142    * Form of the unique name used in uniquify for the i'th sequence in an
143    * ordered vector of sequences.
144    *
145    * @param i
146    * int
147    * @return String
148    */
 
149  101 toggle public static String unique_name(int i)
150    {
151  101 return new String("Sequence" + i);
152    }
153   
154    /**
155    * Generates a hash of SeqCharacterHash properties for each sequence in a
156    * sequence set, and optionally renames the sequences to an unambiguous 'safe'
157    * name.
158    *
159    * @param sequences
160    * SequenceI[]
161    * @param write_names
162    * boolean set this to rename each of the sequences to its
163    * unique_name(index) name
164    * @return Hashtable to be passed to
165    * @see deuniquify to recover original names (and properties) for renamed
166    * sequences
167    */
 
168  4 toggle public static Hashtable uniquify(SequenceI[] sequences,
169    boolean write_names)
170    {
171    // Generate a safely named sequence set and a hash to recover the sequence
172    // names
173  4 Hashtable map = new Hashtable();
174    // String[] un_names = new String[sequences.length];
175   
176  105 for (int i = 0; i < sequences.length; i++)
177    {
178  101 String safename = unique_name(i);
179  101 map.put(safename, SeqCharacterHash(sequences[i]));
180   
181  101 if (write_names)
182    {
183  101 sequences[i].setName(safename);
184    }
185    }
186   
187  4 return map;
188    }
189   
190    /**
191    * recover unsafe sequence names and original properties for a sequence set
192    * using a map generated by
193    *
194    * @see uniquify(sequences,true)
195    * @param map
196    * Hashtable
197    * @param sequences
198    * SequenceI[]
199    * @return boolean
200    */
 
201  1 toggle public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
202    {
203  1 return deuniquify(map, sequences, true);
204    }
205   
206    /**
207    * recover unsafe sequence names and original properties for a sequence set
208    * using a map generated by
209    *
210    * @see uniquify(sequences,true)
211    * @param map
212    * Hashtable
213    * @param sequences
214    * SequenceI[]
215    * @param quiet
216    * when false, don't complain about sequences without any data in the
217    * map.
218    * @return boolean
219    */
 
220  1 toggle public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
221    boolean quiet)
222    {
223  1 jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
224    sequences);
225  1 SequenceI msq = null;
226  1 Enumeration keys = map.keys();
227  1 Vector unmatched = new Vector();
228  3 for (int i = 0, j = sequences.length; i < j; i++)
229    {
230  2 unmatched.addElement(sequences[i]);
231    }
232  3 while (keys.hasMoreElements())
233    {
234  2 Object key = keys.nextElement();
235  2 if (key instanceof String)
236    {
237  ? if ((msq = matcher.findIdMatch((String) key)) != null)
238    {
239  2 Hashtable sqinfo = (Hashtable) map.get(key);
240  2 unmatched.removeElement(msq);
241  2 SeqCharacterUnhash(msq, sqinfo);
242    }
243    else
244    {
245  0 if (!quiet)
246    {
247  0 jalview.bin.Console.errPrintln("Can't find '" + ((String) key)
248    + "' in uniquified alignment");
249    }
250    }
251    }
252    }
253  1 if (unmatched.size() > 0 && !quiet)
254    {
255  0 jalview.bin.Console.errPrintln("Did not find matches for :");
256  0 for (Enumeration i = unmatched.elements(); i
257    .hasMoreElements(); System.out
258    .println(((SequenceI) i.nextElement()).getName()))
259    {
260  0 ;
261    }
262  0 return false;
263    }
264   
265  1 return true;
266    }
267   
268    /**
269    * returns a subset of the sequenceI seuqences, including only those that
270    * contain at least one residue.
271    *
272    * @param sequences
273    * SequenceI[]
274    * @return SequenceI[]
275    */
 
276  0 toggle public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
277    {
278    // Identify first row of alignment with residues for prediction
279  0 boolean ungapped[] = new boolean[sequences.length];
280  0 int msflen = 0;
281  0 for (int i = 0, j = sequences.length; i < j; i++)
282    {
283  0 String tempseq = jalview.analysis.AlignSeq.extractGaps(
284    jalview.util.Comparison.GapChars,
285    sequences[i].getSequenceAsString());
286   
287  0 if (tempseq.length() == 0)
288    {
289  0 ungapped[i] = false;
290    }
291    else
292    {
293  0 ungapped[i] = true;
294  0 msflen++;
295    }
296    }
297  0 if (msflen == 0)
298    {
299  0 return null; // no minimal set
300    }
301    // compose minimal set
302  0 SequenceI[] mset = new SequenceI[msflen];
303  0 for (int i = 0, j = sequences.length, k = 0; i < j; i++)
304    {
305  0 if (ungapped[i])
306    {
307  0 mset[k++] = sequences[i];
308    }
309    }
310  0 ungapped = null;
311  0 return mset;
312    }
313    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 6 2024 01:03:43 GMT using coverage data from Wed Nov 6 2024 01:03:32 GMT.
  • OpenClover is free and open-source software.