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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:38:20 GMT
  2. Package jalview.io.gff

File SequenceOntologyLite.java

 

Coverage histogram

../../../img/srcFileCovDistChart8.png
13% of files have more coverage

Code metrics

14
35
7
1
251
138
15
0.43
5
7
2.14

Classes

Class Line # Actions
SequenceOntologyLite 41 35 15
0.803571480.4%
 

Contributing tests

This file is covered by 19 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.io.gff;
22   
23    import java.util.ArrayList;
24    import java.util.Collections;
25    import java.util.HashMap;
26    import java.util.List;
27    import java.util.Map;
28   
29    /**
30    * An implementation of SequenceOntologyI that hard codes terms of interest.
31    *
32    * Use this in unit testing by calling SequenceOntology.setInstance(new
33    * SequenceOntologyLite()).
34    *
35    * May also become a stand-in for SequenceOntology in the applet if we want to
36    * avoid the additional jars needed for parsing the full SO.
37    *
38    * @author gmcarstairs
39    *
40    */
 
41    public class SequenceOntologyLite implements SequenceOntologyI
42    {
43    /*
44    * initial selection of types of interest when processing Ensembl features
45    * NB unlike the full SequenceOntology we don't traverse indirect
46    * child-parent relationships here so e.g. need to list every sub-type
47    * (direct or indirect) that is of interest
48    */
49    // @formatter:off
50    private final String[][] TERMS = new String[][] {
51   
52    /*
53    * gene sub-types:
54    */
55    { "gene", "gene" },
56    { "ncRNA_gene", "gene" },
57    { "snRNA_gene", "gene" },
58    { "miRNA_gene", "gene" },
59    { "lincRNA_gene", "gene" },
60    { "rRNA_gene", "gene" },
61   
62    /*
63    * transcript sub-types:
64    */
65    { "transcript", "transcript" },
66    { "mature_transcript", "transcript" },
67    { "processed_transcript", "transcript" },
68    { "aberrant_processed_transcript", "transcript" },
69    { "ncRNA", "transcript" },
70    { "snRNA", "transcript" },
71    { "miRNA", "transcript" },
72    { "lincRNA", "transcript" },
73    { "lnc_RNA", "transcript" },
74    { "rRNA", "transcript" },
75    { "mRNA", "transcript" },
76    // there are many more sub-types of ncRNA...
77   
78    /*
79    * sequence_variant sub-types
80    */
81    { "sequence_variant", "sequence_variant" },
82    { "structural_variant", "sequence_variant" },
83    { "feature_variant", "sequence_variant" },
84    { "gene_variant", "sequence_variant" },
85    { "transcript_variant", "sequence_variant" },
86    // NB Ensembl uses NMD_transcript_variant as if a 'transcript'
87    // but we model it here correctly as per the SO
88    { "NMD_transcript_variant", "sequence_variant" },
89    { "missense_variant", "sequence_variant" },
90    { "synonymous_variant", "sequence_variant" },
91    { "frameshift_variant", "sequence_variant" },
92    { "5_prime_UTR_variant", "sequence_variant" },
93    { "3_prime_UTR_variant", "sequence_variant" },
94    { "stop_gained", "sequence_variant" },
95    { "stop_lost", "sequence_variant" },
96    { "inframe_deletion", "sequence_variant" },
97    { "inframe_insertion", "sequence_variant" },
98    { "splice_region_variant", "sequence_variant" },
99   
100    /*
101    * no sub-types of exon or CDS yet seen in Ensembl
102    * some added here for testing purposes
103    */
104    { "exon", "exon" },
105    { "coding_exon", "exon" },
106    { "CDS", "CDS" },
107    { "CDS_predicted", "CDS" },
108   
109    /*
110    * terms used in exonerate or PASA GFF
111    */
112    { "protein_match", "protein_match"},
113    { "nucleotide_match", "nucleotide_match"},
114    { "cDNA_match", "nucleotide_match"},
115   
116    /*
117    * used in InterProScan GFF
118    */
119    { "polypeptide", "polypeptide" }
120    };
121    // @formatter:on
122   
123    /*
124    * hard-coded list of any parents (direct or indirect)
125    * that we care about for a term
126    */
127    private Map<String, List<String>> parents;
128   
129    private List<String> termsFound;
130   
131    private List<String> termsNotFound;
132   
 
133  6 toggle public SequenceOntologyLite()
134    {
135  6 termsFound = new ArrayList<>();
136  6 termsNotFound = new ArrayList<>();
137  6 loadStaticData();
138    }
139   
140    /**
141    * Loads hard-coded data into a lookup table of {term, {list_of_parents}}
142    */
 
143  6 toggle private void loadStaticData()
144    {
145  6 parents = new HashMap<>();
146  6 for (String[] pair : TERMS)
147    {
148  246 List<String> p = parents.get(pair[0]);
149  246 if (p == null)
150    {
151  246 p = new ArrayList<>();
152  246 parents.put(pair[0], p);
153    }
154  246 p.add(pair[1]);
155    }
156    }
157   
158    /**
159    * Answers true if 'child' isA 'parent' (including equality). In this
160    * implementation, based only on hard-coded values.
161    */
 
162  80 toggle @Override
163    public boolean isA(String child, String parent)
164    {
165  80 if (child == null || parent == null)
166    {
167  0 return false;
168    }
169  80 if (child.equals(parent))
170    {
171  11 termFound(child);
172  11 return true;
173    }
174   
175  69 List<String> p = parents.get(child);
176  69 if (p == null)
177    {
178  13 termNotFound(child);
179  13 return false;
180    }
181  56 termFound(child);
182  56 if (p.contains(parent))
183    {
184  22 return true;
185    }
186  34 return false;
187    }
188   
189    /**
190    * Records a valid term queried for, for reporting purposes
191    *
192    * @param term
193    */
 
194  67 toggle private void termFound(String term)
195    {
196  67 if (!termsFound.contains(term))
197    {
198  27 synchronized (termsFound)
199    {
200  27 termsFound.add(term);
201    }
202    }
203    }
204   
205    /**
206    * Records an invalid term queried for, for reporting purposes
207    *
208    * @param term
209    */
 
210  13 toggle private void termNotFound(String term)
211    {
212  13 synchronized (termsNotFound)
213    {
214  13 if (!termsNotFound.contains(term))
215    {
216    // suppress logging here as it reports Uniprot sequence features
217    // (which do not use SO terms) when auto-configuring feature colours
218    // jalview.bin.Console.outPrintln("SO term " + term
219    // + " not known - add to model if needed in "
220    // + getClass().getName());
221  7 termsNotFound.add(term);
222    }
223    }
224    }
225   
226    /**
227    * Sorts (case-insensitive) and returns the list of valid terms queried for
228    */
 
229  0 toggle @Override
230    public List<String> termsFound()
231    {
232  0 synchronized (termsFound)
233    {
234  0 Collections.sort(termsFound, String.CASE_INSENSITIVE_ORDER);
235  0 return termsFound;
236    }
237    }
238   
239    /**
240    * Sorts (case-insensitive) and returns the list of invalid terms queried for
241    */
 
242  0 toggle @Override
243    public List<String> termsNotFound()
244    {
245  0 synchronized (termsNotFound)
246    {
247  0 Collections.sort(termsNotFound, String.CASE_INSENSITIVE_ORDER);
248  0 return termsNotFound;
249    }
250    }
251    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 09:54:26 GMT using coverage data from Mon Nov 18 2024 09:54:15 GMT.
  • OpenClover is free and open-source software.