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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.analysis

File Rna.java

 

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40
148
13
1
480
284
68
0.46
11.38
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5.23

Classes

Class Line # Actions
Rna 40 148 68 6
0.970149397%
 

Contributing tests

This file is covered by 22 tests. .

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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  104529 toggle public static boolean isOpeningParenthesis(char c)
51    {
52  104529 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  78938 toggle public static boolean isClosingParenthesis(char c)
77    {
78  78938 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  18779 toggle public static char getMatchingOpeningParenthesis(char c)
104    {
105  18779 if ('a' <= c && c <= 'z')
106    {
107  26 return (char) (c + 'A' - 'a');
108    }
109  18753 switch (c)
110    {
111  18432 case ')':
112  18432 return '(';
113  76 case ']':
114  76 return '[';
115  44 case '}':
116  44 return '{';
117  201 case '>':
118  201 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  1285 toggle protected static List<SimpleBP> getSimpleBPs(CharSequence line)
139    throws WUSSParseException
140    {
141  1285 Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
142  1285 List<SimpleBP> pairs = new ArrayList<SimpleBP>();
143  1285 int i = 0;
144  95522 while (i < line.length())
145    {
146  94239 char base = line.charAt(i);
147   
148  94239 if (isOpeningParenthesis(base))
149    {
150  20840 if (!stacks.containsKey(base))
151    {
152  1329 stacks.put(base, new Stack<Integer>());
153    }
154  20840 stacks.get(base).push(i);
155   
156    }
157  73399 else if (isClosingParenthesis(base))
158    {
159   
160  18749 char opening = getMatchingOpeningParenthesis(base);
161   
162  18749 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  18748 Stack<Integer> stack = stacks.get(opening);
170  18748 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  18747 int temp = stack.pop();
178   
179  18747 pairs.add(new SimpleBP(temp, i));
180    }
181  94237 i++;
182    }
183  1283 for (char opening : stacks.keySet())
184    {
185  1323 Stack<Integer> stack = stacks.get(opening);
186  1323 if (!stack.empty())
187    {
188    /*
189    * we have an unmatched opening bracket; report error as at
190    * i (length of input string)
191    */
192  320 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  963 return pairs;
199    }
200   
201   
202   
203   
204   
205    /**
206    * Function to get the end position corresponding to a given start position
207    *
208    * @param indice
209    * - start position of a base pair
210    * @return - end position of a base pair
211    */
212    /*
213    * makes no sense at the moment :( public int findEnd(int indice){ //TODO:
214    * Probably extend this to find the start to a given end? //could be done by
215    * putting everything twice to the hash ArrayList<Integer> pair = new
216    * ArrayList<Integer>(); return pairHash.get(indice); }
217    */
218   
219    /**
220    * Answers true if the character is a recognised symbol for RNA secondary
221    * structure. Currently accepts a-z, A-Z, ()[]{}<>.
222    *
223    * @param c
224    * @return
225    */
 
226  8981 toggle public static boolean isRnaSecondaryStructureSymbol(char c)
227    {
228  8981 return isOpeningParenthesis(c) || isClosingParenthesis(c);
229    }
230   
231    /**
232    * Answers true if the string is a recognised symbol for RNA secondary
233    * structure. Currently accepts a-z, A-Z, ()[]{}<>.
234    *
235    * @param s
236    * @return
237    */
 
238  513 toggle public static boolean isRnaSecondaryStructureSymbol(String s)
239    {
240  513 return isOpeningParenthesis(s) || isClosingParenthesis(s);
241    }
242   
243    /**
244    * Translates a string to RNA secondary structure representation. Returns the
245    * string with any non-SS characters changed to spaces. Accepted characters
246    * are a-z, A-Z, and (){}[]<> brackets.
247    *
248    * @param ssString
249    * @return
250    */
 
251  8707 toggle public static String getRNASecStrucState(String ssString)
252    {
253  8707 if (ssString == null)
254    {
255  1 return null;
256    }
257  8706 StringBuilder result = new StringBuilder(ssString.length());
258  17431 for (int i = 0; i < ssString.length(); i++)
259    {
260  8725 char c = ssString.charAt(i);
261  8725 result.append(isRnaSecondaryStructureSymbol(c) ? c : " ");
262    }
263  8706 return result.toString();
264    }
265   
266    /**
267    * Answers true if the base-pair is either a Watson-Crick (A:T/U, C:G) or a
268    * wobble (G:T/U) pair (either way round), else false
269    *
270    * @param first
271    * @param second
272    * @return
273    */
 
274  5580 toggle public static boolean isCanonicalOrWobblePair(char first, char second)
275    {
276  5580 if (first > 'Z')
277    {
278  50 first -= 32;
279    }
280  5580 if (second > 'Z')
281    {
282  50 second -= 32;
283    }
284   
285  5580 switch (first)
286    {
287  950 case 'A':
288  950 switch (second)
289    {
290  4 case 'T':
291  809 case 'U':
292  813 return true;
293    }
294  137 break;
295  1570 case 'C':
296  1570 switch (second)
297    {
298  1359 case 'G':
299  1359 return true;
300    }
301  211 break;
302  20 case 'T':
303  1480 case 'U':
304  1500 switch (second)
305    {
306  988 case 'A':
307  318 case 'G':
308  1306 return true;
309    }
310  194 break;
311  1560 case 'G':
312  1560 switch (second)
313    {
314  1179 case 'C':
315  4 case 'T':
316  244 case 'U':
317  1427 return true;
318    }
319  133 break;
320    }
321  675 return false;
322    }
323   
324    /**
325    * Answers true if the base-pair is Watson-Crick - (A:T/U or C:G, either way
326    * round), else false
327    *
328    * @param first
329    * @param second
330    * @return
331    */
 
332  4965 toggle public static boolean isCanonicalPair(char first, char second)
333    {
334   
335  4965 if (first > 'Z')
336    {
337  50 first -= 32;
338    }
339  4965 if (second > 'Z')
340    {
341  50 second -= 32;
342    }
343   
344  4965 switch (first)
345    {
346  825 case 'A':
347  825 switch (second)
348    {
349  4 case 'T':
350  809 case 'U':
351  813 return true;
352    }
353  12 break;
354  1435 case 'G':
355  1435 switch (second)
356    {
357  1179 case 'C':
358  1179 return true;
359    }
360  256 break;
361  1375 case 'C':
362  1375 switch (second)
363    {
364  1359 case 'G':
365  1359 return true;
366    }
367  16 break;
368  20 case 'T':
369  1310 case 'U':
370  1330 switch (second)
371    {
372  988 case 'A':
373  988 return true;
374    }
375  342 break;
376    }
377  626 return false;
378    }
379   
380    /**
381    * Returns the matching close pair symbol for the given opening symbol.
382    * Currently returns a-z for A-Z, or )]}> for ([{<, or the input symbol if it
383    * is not a valid opening symbol.
384    *
385    * @param c
386    * @return
387    */
 
388  52 toggle public static char getMatchingClosingParenthesis(char c)
389    {
390  52 if ('A' <= c && c <= 'Z')
391    {
392  2 return (char) (c + 'a' - 'A');
393    }
394  50 switch (c)
395    {
396  13 case '(':
397  13 return ')';
398  13 case '[':
399  13 return ']';
400  11 case '{':
401  11 return '}';
402  13 case '<':
403  13 return '>';
404  0 default:
405  0 return c;
406    }
407    }
408   
 
409  1281 toggle public static SequenceFeature[] getHelixMap(CharSequence rnaAnnotation)
410    throws WUSSParseException
411    {
412  1281 List<SequenceFeature> result = new ArrayList<SequenceFeature>();
413   
414  1281 int helix = 0; // Number of helices/current helix
415  1281 int lastopen = 0; // Position of last open bracket reviewed
416  1281 int lastclose = 9999999; // Position of last close bracket reviewed
417   
418  1281 Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
419    // Keep track of helix number for each position
420   
421    // Go through each base pair and assign positions a helix
422  1281 List<SimpleBP> bps = getSimpleBPs(rnaAnnotation);
423  962 for (SimpleBP basePair : bps)
424    {
425  18737 final int open = basePair.getBP5();
426  18737 final int close = basePair.getBP3();
427   
428    // System.out.println("open " + open + " close " + close);
429    // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
430   
431    // we're moving from right to left based on closing pair
432    /*
433    * catch things like <<..>>..<<..>> |
434    */
435  18737 if (open > lastclose)
436    {
437  206 helix++;
438    }
439   
440    /*
441    * catch things like <<..<<..>>..<<..>>>> |
442    */
443  18737 int j = bps.size() - 1;
444  442837 while (j >= 0)
445    {
446  424179 int popen = bps.get(j).getBP5();
447   
448    // System.out.println("j " + j + " popen " + popen + " lastopen "
449    // +lastopen + " open " + open);
450  424179 if ((popen < lastopen) && (popen > open))
451    {
452  79 if (helices.containsValue(popen)
453    && ((helices.get(popen)) == helix))
454    {
455  0 continue;
456    }
457    else
458    {
459  79 helix++;
460  79 break;
461    }
462    }
463  424100 j -= 1;
464    }
465   
466    // Put positions and helix information into the hashtable
467  18737 helices.put(open, helix);
468  18737 helices.put(close, helix);
469   
470    // Record helix as featuregroup
471  18737 result.add(new SequenceFeature("RNA helix", "", open, close,
472    String.valueOf(helix)));
473   
474  18737 lastopen = open;
475  18737 lastclose = close;
476    }
477   
478  962 return result.toArray(new SequenceFeature[result.size()]);
479    }
480    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.