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Coverage Report

  1. Project Clover database Mon Nov 18 2024 09:56:54 GMT
  2. Package jalview.analysis

File Rna.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

40
147
13
1
477
283
68
0.46
11.31
13
5.23

Classes

Class Line # Actions
Rna 40 147 68
0.9797%
 

Contributing tests

This file is covered by 24 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    /* Author: Lauren Michelle Lui
22    * Methods are based on RALEE methods http://personalpages.manchester.ac.uk/staff/sam.griffiths-jones/software/ralee/
23    * Additional Author: Jan Engelhart (2011) - Structure consensus and bug fixing
24    * Additional Author: Anne Menard (2012) - Pseudoknot support and secondary structure consensus
25    * */
26   
27    package jalview.analysis;
28   
29    import jalview.analysis.SecStrConsensus.SimpleBP;
30    import jalview.datamodel.SequenceFeature;
31    import jalview.util.MessageManager;
32   
33    import java.util.ArrayList;
34    import java.util.HashMap;
35    import java.util.Hashtable;
36    import java.util.List;
37    import java.util.Map;
38    import java.util.Stack;
39   
 
40    public class Rna
41    {
42   
43    /**
44    * Answers true if the character is a valid open pair rna secondary structure
45    * symbol. Currently accepts A-Z, ([{<
46    *
47    * @param c
48    * @return
49    */
 
50  106839 toggle public static boolean isOpeningParenthesis(char c)
51    {
52  106839 return ('A' <= c && c <= 'Z' || c == '(' || c == '[' || c == '{'
53    || c == '<');
54    }
55   
56    /**
57    * Answers true if the string is a valid open pair rna secondary structure
58    * symbol. Currently accepts A-Z, ([{<
59    *
60    * @param s
61    * @return
62    */
 
63  1025 toggle public static boolean isOpeningParenthesis(String s)
64    {
65  1025 return s != null && s.length() == 1
66    && isOpeningParenthesis(s.charAt(0));
67    }
68   
69    /**
70    * Answers true if the character is a valid close pair rna secondary structure
71    * symbol. Currently accepts a-z, )]}>
72    *
73    * @param c
74    * @return
75    */
 
76  80352 toggle public static boolean isClosingParenthesis(char c)
77    {
78  80352 return ('a' <= c && c <= 'z' || c == ')' || c == ']' || c == '}'
79    || c == '>');
80    }
81   
82    /**
83    * Answers true if the string is a valid close pair rna secondary structure
84    * symbol. Currently accepts a-z, )]}>
85    *
86    * @param s
87    * @return
88    */
 
89  996 toggle public static boolean isClosingParenthesis(String s)
90    {
91  996 return s != null && s.length() == 1
92    && isClosingParenthesis(s.charAt(0));
93    }
94   
95    /**
96    * Returns the matching open pair symbol for the given closing symbol.
97    * Currently returns A-Z for a-z, or ([{< for )]}>, or the input symbol if it
98    * is not a valid closing symbol.
99    *
100    * @param c
101    * @return
102    */
 
103  18867 toggle public static char getMatchingOpeningParenthesis(char c)
104    {
105  18867 if ('a' <= c && c <= 'z')
106    {
107  74 return (char) (c + 'A' - 'a');
108    }
109  18793 switch (c)
110    {
111  18459 case ')':
112  18459 return '(';
113  76 case ']':
114  76 return '[';
115  44 case '}':
116  44 return '{';
117  214 case '>':
118  214 return '<';
119  0 default:
120  0 return c;
121    }
122    }
123   
124    /**
125    * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
126    * positions in "stack" vector. When a close bracket is reached, pair this
127    * with the last matching element in the "stack" vector and store in "pairs"
128    * vector. Remove last element in the "stack" vector. Continue in this manner
129    * until the whole string is processed. Parse errors are thrown as exceptions
130    * wrapping the error location - position of the first unmatched closing
131    * bracket, or string length if there is an unmatched opening bracket.
132    *
133    * @param line
134    * Secondary structure line of an RNA Stockholm file
135    * @return
136    * @throw {@link WUSSParseException}
137    */
 
138  1392 toggle protected static List<SimpleBP> getSimpleBPs(CharSequence line)
139    throws WUSSParseException
140    {
141  1392 Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
142  1392 List<SimpleBP> pairs = new ArrayList<SimpleBP>();
143  1392 int i = 0;
144  97745 while (i < line.length())
145    {
146  96355 char base = line.charAt(i);
147   
148  96355 if (isOpeningParenthesis(base))
149    {
150  21562 if (!stacks.containsKey(base))
151    {
152  1490 stacks.put(base, new Stack<Integer>());
153    }
154  21562 stacks.get(base).push(i);
155   
156    }
157  74793 else if (isClosingParenthesis(base))
158    {
159   
160  18837 char opening = getMatchingOpeningParenthesis(base);
161   
162  18837 if (!stacks.containsKey(opening))
163    {
164  1 throw new WUSSParseException(MessageManager.formatMessage(
165    "exception.mismatched_unseen_closing_char", new String[]
166    { String.valueOf(base) }), i);
167    }
168   
169  18836 Stack<Integer> stack = stacks.get(opening);
170  18836 if (stack.isEmpty())
171    {
172    // error whilst parsing i'th position. pass back
173  1 throw new WUSSParseException(MessageManager.formatMessage(
174    "exception.mismatched_closing_char", new String[]
175    { String.valueOf(base) }), i);
176    }
177  18835 int temp = stack.pop();
178   
179  18835 pairs.add(new SimpleBP(temp, i));
180    }
181  96353 i++;
182    }
183  1390 for (char opening : stacks.keySet())
184    {
185  1484 Stack<Integer> stack = stacks.get(opening);
186  1484 if (!stack.empty())
187    {
188    /*
189    * we have an unmatched opening bracket; report error as at
190    * i (length of input string)
191    */
192  413 throw new WUSSParseException(MessageManager.formatMessage(
193    "exception.mismatched_opening_char", new String[]
194    { String.valueOf(opening), String.valueOf(stack.pop()) }),
195    i);
196    }
197    }
198  977 return pairs;
199    }
200   
201    /**
202    * Function to get the end position corresponding to a given start position
203    *
204    * @param indice
205    * - start position of a base pair
206    * @return - end position of a base pair
207    */
208    /*
209    * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
210    * Probably extend this to find the start to a given end? //could be done by
211    * putting everything twice to the hash ArrayList<Integer> pair = new
212    * ArrayList<Integer>(); return pairHash.get(indice); }
213    */
214   
215    /**
216    * Answers true if the character is a recognised symbol for RNA secondary
217    * structure. Currently accepts a-z, A-Z, ()[]{}<>.
218    *
219    * @param c
220    * @return
221    */
 
222  9175 toggle public static boolean isRnaSecondaryStructureSymbol(char c)
223    {
224  9175 return isOpeningParenthesis(c) || isClosingParenthesis(c);
225    }
226   
227    /**
228    * Answers true if the string is a recognised symbol for RNA secondary
229    * structure. Currently accepts a-z, A-Z, ()[]{}<>.
230    *
231    * @param s
232    * @return
233    */
 
234  513 toggle public static boolean isRnaSecondaryStructureSymbol(String s)
235    {
236  513 return isOpeningParenthesis(s) || isClosingParenthesis(s);
237    }
238   
239    /**
240    * Translates a string to RNA secondary structure representation. Returns the
241    * string with any non-SS characters changed to spaces. Accepted characters
242    * are a-z, A-Z, and (){}[]<> brackets.
243    *
244    * @param ssString
245    * @return
246    */
 
247  8901 toggle public static String getRNASecStrucState(String ssString)
248    {
249  8901 if (ssString == null)
250    {
251  1 return null;
252    }
253  8900 StringBuilder result = new StringBuilder(ssString.length());
254  17819 for (int i = 0; i < ssString.length(); i++)
255    {
256  8919 char c = ssString.charAt(i);
257  8919 result.append(isRnaSecondaryStructureSymbol(c) ? c : " ");
258    }
259  8900 return result.toString();
260    }
261   
262    /**
263    * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
264    * wobble (G:T/U) pair (either way round), else false
265    *
266    * @param first
267    * @param second
268    * @return
269    */
 
270  5580 toggle public static boolean isCanonicalOrWobblePair(char first, char second)
271    {
272  5580 if (first > 'Z')
273    {
274  50 first -= 32;
275    }
276  5580 if (second > 'Z')
277    {
278  50 second -= 32;
279    }
280   
281  5580 switch (first)
282    {
283  950 case 'A':
284  950 switch (second)
285    {
286  4 case 'T':
287  809 case 'U':
288  813 return true;
289    }
290  137 break;
291  1570 case 'C':
292  1570 switch (second)
293    {
294  1359 case 'G':
295  1359 return true;
296    }
297  211 break;
298  20 case 'T':
299  1480 case 'U':
300  1500 switch (second)
301    {
302  988 case 'A':
303  318 case 'G':
304  1306 return true;
305    }
306  194 break;
307  1560 case 'G':
308  1560 switch (second)
309    {
310  1179 case 'C':
311  4 case 'T':
312  244 case 'U':
313  1427 return true;
314    }
315  133 break;
316    }
317  675 return false;
318    }
319   
320    /**
321    * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
322    * round), else false
323    *
324    * @param first
325    * @param second
326    * @return
327    */
 
328  4965 toggle public static boolean isCanonicalPair(char first, char second)
329    {
330   
331  4965 if (first > 'Z')
332    {
333  50 first -= 32;
334    }
335  4965 if (second > 'Z')
336    {
337  50 second -= 32;
338    }
339   
340  4965 switch (first)
341    {
342  825 case 'A':
343  825 switch (second)
344    {
345  4 case 'T':
346  809 case 'U':
347  813 return true;
348    }
349  12 break;
350  1435 case 'G':
351  1435 switch (second)
352    {
353  1179 case 'C':
354  1179 return true;
355    }
356  256 break;
357  1375 case 'C':
358  1375 switch (second)
359    {
360  1359 case 'G':
361  1359 return true;
362    }
363  16 break;
364  20 case 'T':
365  1310 case 'U':
366  1330 switch (second)
367    {
368  988 case 'A':
369  988 return true;
370    }
371  342 break;
372    }
373  626 return false;
374    }
375   
376    /**
377    * Returns the matching close pair symbol for the given opening symbol.
378    * Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it
379    * is not a valid opening symbol.
380    *
381    * @param c
382    * @return
383    */
 
384  52 toggle public static char getMatchingClosingParenthesis(char c)
385    {
386  52 if ('A' <= c && c <= 'Z')
387    {
388  2 return (char) (c + 'a' - 'A');
389    }
390  50 switch (c)
391    {
392  13 case '(':
393  13 return ')';
394  13 case '[':
395  13 return ']';
396  11 case '{':
397  11 return '}';
398  13 case '<':
399  13 return '>';
400  0 default:
401  0 return c;
402    }
403    }
404   
 
405  1388 toggle public static SequenceFeature[] getHelixMap(CharSequence rnaAnnotation)
406    throws WUSSParseException
407    {
408  1388 List<SequenceFeature> result = new ArrayList<SequenceFeature>();
409   
410  1388 int helix = 0; // Number of helices/current helix
411  1388 int lastopen = 0; // Position of last open bracket reviewed
412  1388 int lastclose = 9999999; // Position of last close bracket reviewed
413   
414  1388 Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
415    // Keep track of helix number for each position
416   
417    // Go through each base pair and assign positions a helix
418  1388 List<SimpleBP> bps = getSimpleBPs(rnaAnnotation);
419  976 for (SimpleBP basePair : bps)
420    {
421  18825 final int open = basePair.getBP5();
422  18825 final int close = basePair.getBP3();
423   
424    // jalview.bin.Console.outPrintln("open " + open + " close " + close);
425    // jalview.bin.Console.outPrintln("lastclose " + lastclose + " lastopen "
426    // + lastopen);
427   
428    // we're moving from right to left based on closing pair
429    /*
430    * catch things like <<..>>..<<..>> |
431    */
432  18825 if (open > lastclose)
433    {
434  220 helix++;
435    }
436   
437    /*
438    * catch things like <<..<<..>>..<<..>>>> |
439    */
440  18825 int j = bps.size();
441  443447 while (--j >= 0)
442    {
443  424714 int popen = bps.get(j).getBP5();
444   
445    // jalview.bin.Console.outPrintln("j " + j + " popen " + popen + "
446    // lastopen "
447    // +lastopen + " open " + open);
448  424714 if ((popen < lastopen) && (popen > open))
449    {
450  92 if (helices.containsValue(popen)
451    && ((helices.get(popen)) == helix))
452    {
453  0 continue;
454    }
455    else
456    {
457  92 helix++;
458  92 break;
459    }
460    }
461    }
462   
463    // Put positions and helix information into the hashtable
464  18825 helices.put(open, helix);
465  18825 helices.put(close, helix);
466   
467    // Record helix as featuregroup
468  18825 result.add(new SequenceFeature("RNA helix", "", open, close,
469    String.valueOf(helix)));
470   
471  18825 lastopen = open;
472  18825 lastclose = close;
473    }
474   
475  976 return result.toArray(new SequenceFeature[result.size()]);
476    }
477    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 18 2024 10:04:05 GMT using coverage data from Mon Nov 18 2024 10:03:47 GMT.
  • OpenClover is free and open-source software.