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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.analysis

File SecStrConsensus.java

 

Coverage histogram

../../img/srcFileCovDistChart1.png
56% of files have more coverage

Code metrics

38
75
13
2
254
187
32
0.43
5.77
6.5
2.46

Classes

Class Line # Actions
SecStrConsensus 26 68 25
0.00%
SecStrConsensus.SimpleBP 35 7 7
0.550%
 

Contributing tests

This file is covered by 15 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 java.util.ArrayList;
24    import java.util.Hashtable;
25   
 
26    public class SecStrConsensus
27    {
28   
29    /**
30    * Internal class to represent a simple base-pair.
31    *
32    * @author Yawn [JBPNote: ^^ is that Anne Menard or Ya(w)nn Ponty, I wonder !
33    * ]
34    */
 
35    public static class SimpleBP
36    {
37    int bp5;
38   
39    int bp3;
40   
 
41  0 toggle public SimpleBP()
42    {
43   
44    }
45   
 
46  18835 toggle public SimpleBP(int i5, int i3)
47    {
48  18835 bp5 = i5;
49  18835 bp3 = i3;
50    }
51   
 
52  0 toggle public void setBP5(int i5)
53    {
54  0 bp5 = i5;
55    }
56   
 
57  0 toggle public void setBP3(int i3)
58    {
59  0 bp3 = i3;
60    }
61   
 
62  443539 toggle public int getBP5()
63    {
64  443539 return bp5;
65    }
66   
 
67  18825 toggle public int getBP3()
68    {
69  18825 return bp3;
70    }
71   
 
72  0 toggle public String toString()
73    {
74  0 return "(" + bp5 + "," + bp3 + ")";
75    }
76   
77    }
78   
 
79  0 toggle public static int[] extractConsensus(ArrayList<ArrayList<SimpleBP>> bps)
80    {
81    // We do not currently know the length of the alignment
82    // => Estimate it as the biggest index of a base-pair plus one.
83  0 int maxlength = 0;
84  0 for (ArrayList<SimpleBP> strs : bps)
85    {
86  0 for (SimpleBP bp : strs)
87    {
88   
89  0 maxlength = Math.max(1 + Math.max(bp.bp5, bp.bp3), maxlength);
90   
91    }
92    }
93    // Now we have a good estimate for length, allocate and initialize data
94    // to be fed to the dynamic programming procedure.
95  0 ArrayList<Hashtable<Integer, Double>> seq = new ArrayList<Hashtable<Integer, Double>>();
96  0 for (int i = 0; i < maxlength; i++)
97    {
98  0 seq.add(new Hashtable<Integer, Double>());
99    }
100  0 for (ArrayList<SimpleBP> strs : bps)
101    {
102  0 for (SimpleBP bp : strs)
103    {
104  0 int i = bp.bp5;
105  0 int j = bp.bp3;
106  0 Hashtable<Integer, Double> h = seq.get(i);
107  0 if (!h.containsKey(j))
108    {
109  0 h.put(j, 0.0);
110    }
111  0 h.put(j, h.get(j) + 1.);
112    }
113    }
114    // At this point, seq contains, at each position i, a hashtable which
115    // associates,
116    // to each possible end j, the number of time a base-pair (i,j) occurs in
117    // the alignment
118   
119    // We can now run the dynamic programming procedure on this data
120  0 double[][] mat = fillMatrix(seq);
121  0 ArrayList<SimpleBP> res = backtrack(mat, seq);
122   
123    // Convert it to an array, ie finalres[i] = j >= 0 iff a base-pair (i,j) is
124    // present
125    // in the consensus, or -1 otherwise
126  0 int[] finalres = new int[seq.size()];
127  0 for (int i = 0; i < seq.size(); i++)
128    {
129  0 finalres[i] = -1;
130    }
131  0 for (SimpleBP bp : res)
132    {
133  0 finalres[bp.bp5] = bp.bp3;
134  0 finalres[bp.bp3] = bp.bp5;
135    }
136   
137  0 return finalres;
138    }
139   
 
140  0 toggle private static boolean canBasePair(
141    ArrayList<Hashtable<Integer, Double>> seq, int i, int k)
142    {
143  0 return seq.get(i).containsKey(k);
144    }
145   
146    // Returns the score of a potential base-pair, ie the number of structures in
147    // which it is found.
 
148  0 toggle private static double basePairScore(
149    ArrayList<Hashtable<Integer, Double>> seq, int i, int k)
150    {
151  0 return seq.get(i).get(k);
152    }
153   
 
154  0 toggle private static double[][] fillMatrix(
155    ArrayList<Hashtable<Integer, Double>> seq)
156    {
157  0 int n = seq.size();
158  0 double[][] tab = new double[n][n];
159  0 for (int m = 1; m <= n; m++)
160    {
161  0 for (int i = 0; i < n - m + 1; i++)
162    {
163  0 int j = i + m - 1;
164  0 tab[i][j] = 0;
165  0 if (i < j)
166    {
167  0 tab[i][j] = Math.max(tab[i][j], tab[i + 1][j]);
168  0 for (int k = i + 1; k <= j; k++)
169    {
170  0 if (canBasePair(seq, i, k))
171    {
172  0 double fact1 = 0;
173  0 if (k > i + 1)
174    {
175  0 fact1 = tab[i + 1][k - 1];
176    }
177  0 double fact2 = 0;
178  0 if (k < j)
179    {
180  0 fact2 = tab[k + 1][j];
181    }
182  0 tab[i][j] = Math.max(tab[i][j],
183    basePairScore(seq, i, k) + fact1 + fact2);
184    }
185    }
186    }
187    }
188    }
189  0 return tab;
190    }
191   
 
192  0 toggle private static ArrayList<SimpleBP> backtrack(double[][] tab,
193    ArrayList<Hashtable<Integer, Double>> seq)
194    {
195  0 return backtrack(tab, seq, 0, seq.size() - 1);
196    }
197   
 
198  0 toggle private static ArrayList<SimpleBP> backtrack(double[][] tab,
199    ArrayList<Hashtable<Integer, Double>> seq, int i, int j)
200    {
201  0 ArrayList<SimpleBP> result = new ArrayList<SimpleBP>();
202  0 if (i < j)
203    {
204  0 ArrayList<Integer> indices = new ArrayList<Integer>();
205  0 indices.add(-1);
206  0 for (int k = i + 1; k <= j; k++)
207    {
208  0 indices.add(k);
209    }
210  0 for (int k : indices)
211    {
212  0 if (k == -1)
213    {
214  0 if (tab[i][j] == tab[i + 1][j])
215    {
216  0 result = backtrack(tab, seq, i + 1, j);
217    }
218    }
219    else
220    {
221  0 if (canBasePair(seq, i, k))
222    {
223  0 double fact1 = 0;
224  0 if (k > i + 1)
225    {
226  0 fact1 = tab[i + 1][k - 1];
227    }
228  0 double fact2 = 0;
229  0 if (k < j)
230    {
231  0 fact2 = tab[k + 1][j];
232    }
233  0 if (tab[i][j] == basePairScore(seq, i, k) + fact1 + fact2)
234    {
235  0 result = backtrack(tab, seq, i + 1, k - 1);
236  0 result.addAll(backtrack(tab, seq, k + 1, j));
237  0 result.add(new SimpleBP(i, k));
238    }
239    }
240    }
241    }
242    }
243  0 else if (i == j)
244    {
245   
246    }
247    else
248    {
249   
250    }
251  0 return result;
252    }
253   
254    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.