Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SecStrConsensus	26	68	25	0.00%	Show methods
SecStrConsensus.SimpleBP	35	7	7	0.550%	Show methods

Class SecStrConsensus

Class SecStrConsensus	Line # 26	Total Statements 68	Complexity 25	TOTAL Coverage 0.00%
extractConsensus(ArrayList<ArrayList<SimpleBP>>) : int[]   extractConsensus(ArrayList<ArrayList<SimpleBP>>) : int[]	7979	24.024	4.04	0.0 0.00%
canBasePair(ArrayList<Hashtable<Integer, Double>>,int,int) : boolean   canBasePair(ArrayList<Hashtable<Integer, Double>>,int,int) : boolean	140140	1.01	1.01	0.0 0.00%
basePairScore(ArrayList<Hashtable<Integer, Double>>,int,int) : double   basePairScore(ArrayList<Hashtable<Integer, Double>>,int,int) : double	148148	1.01	1.01	0.0 0.00%
fillMatrix(ArrayList<Hashtable<Integer, Double>>) : double[][]   fillMatrix(ArrayList<Hashtable<Integer, Double>>) : double[][]	154154	18.018	8.08	0.0 0.00%
backtrack(double[][],ArrayList<Hashtable<Integer, Double>>) : ArrayList<SimpleBP>   backtrack(double[][],ArrayList<Hashtable<Integer, Double>>) : ArrayList<SimpleBP>	192192	1.01	1.01	0.0 0.00%
backtrack(double[][],ArrayList<Hashtable<Integer, Double>>,int,int) : ArrayList<SimpleBP>   backtrack(double[][],ArrayList<Hashtable<Integer, Double>>,int,int) : ArrayList<SimpleBP>	198198	23.023	10.010	0.0 0.00%

 

Class SecStrConsensus.SimpleBP

Class SecStrConsensus.SimpleBP	Line # 35	Total Statements 7	Complexity 7	TOTAL Coverage 0.550%
SimpleBP()   SimpleBP()	4141	0.00	1.01	-1.0 -1.0 -
SimpleBP(int,int)   SimpleBP(int,int)	4646	2.02	1.01	1.0 1.0100%
setBP5(int) : void   setBP5(int) : void	5252	1.01	1.01	0.0 0.00%
setBP3(int) : void   setBP3(int) : void	5757	1.01	1.01	0.0 0.00%
getBP5() : int   getBP5() : int	6262	1.01	1.01	1.0 1.0100%
getBP3() : int   getBP3() : int	6767	1.01	1.01	1.0 1.0100%
toString() : String   toString() : String	7272	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.055555556	jalview.io.StockholmFileTest.secondaryStructureForRNASequencejalview.io.StockholmFileTest.secondaryStructureForRNASequence	1PASS
	0.055555556	jalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequence	1PASS
	0.055555556	jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO	1PASS
	0.055555556	jalview.io.StockholmFileTest.stockholmFileRnaSSSpaceCharsjalview.io.StockholmFileTest.stockholmFileRnaSSSpaceChars	1PASS
	0.055555556	jalview.io.StockholmFileTest.stockholmFileRnaSSAlphaCharsjalview.io.StockholmFileTest.stockholmFileRnaSSAlphaChars	1PASS
	0.055555556	jalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequence	1PASS
	0.055555556	jalview.io.RNAMLfileTest.testRnamlSeqImportjalview.io.RNAMLfileTest.testRnamlSeqImport	1PASS
	0.055555556	jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO	1PASS

 

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
		0% Uncovered Elements: 112 (112) Complexity: 25 Complexity Density: 0.37
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		*/
		50% Uncovered Elements: 7 (14) Complexity: 7 Complexity Density: 1
35		public static class SimpleBP
36		{
37		int bp5;
38
39		int bp3;
40
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
41	0	public SimpleBP()...
42		{
43
44		}
45
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
46	9493	public SimpleBP(int i5, int i3)...
47		{
48	9493	bp5 = i5;
49	9493	bp3 = i3;
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	public void setBP5(int i5)...
53		{
54	0	bp5 = i5;
55		}
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public void setBP3(int i3)...
58		{
59	0	bp3 = i3;
60		}
61
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
62	254105	public int getBP5()...
63		{
64	254105	return bp5;
65		}
66
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
67	9493	public int getBP3()...
68		{
69	9493	return bp3;
70		}
71
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	public String toString()...
73		{
74	0	return "(" + bp5 + "," + bp3 + ")";
75		}
76
77		}
78
		0% Uncovered Elements: 30 (30) Complexity: 4 Complexity Density: 0.17
79	0	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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	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.
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	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
		0% Uncovered Elements: 32 (32) Complexity: 8 Complexity Density: 0.44
154	0	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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
192	0	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
		0% Uncovered Elements: 41 (41) Complexity: 10 Complexity Density: 0.43
198	0	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		}