1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.util

File DnaUtils.java

 

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Classes

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DnaUtils 28 34 12
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Contributing tests

This file is covered by 7 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    package jalview.util;
22   
23    import java.text.ParseException;
24    import java.util.ArrayList;
25    import java.util.Collections;
26    import java.util.List;
27   
 
28    public class DnaUtils
29    {
30   
31    /**
32    * Parses an ENA/GenBank format location specifier and returns a list of
33    * [start, end] ranges. Throws an exception if not able to parse.
34    * <p>
35    * Currently we do not parse "order()" specifiers, or indeterminate ranges of
36    * the format "&lt;start..end" or "start..&gt;end" or "start.end" or
37    * "start^end"
38    *
39    * @param location
40    * @return
41    * @throws ParseException
42    * if unable to parse the location (the exception message is the
43    * location specifier being parsed); we use ParseException in
44    * preference to the unchecked IllegalArgumentException
45    * @see http://www.insdc.org/files/feature_table.html#3.4
46    */
 
47  86 toggle public static List<int[]> parseLocation(String location)
48    throws ParseException
49    {
50  86 location = location.trim(); // failsafe for untidy input data
51  85 if (location.startsWith("join("))
52    {
53  14 return parseJoin(location);
54    }
55  71 else if (location.startsWith("complement("))
56    {
57  14 return parseComplement(location);
58    }
59  57 if (location.startsWith("order("))
60    {
61  1 throw new ParseException(location, 0);
62    }
63   
64    /*
65    * try to parse m..n (or simply m)
66    */
67  56 String[] range = location.split("\\.\\.");
68  56 if (range.length == 1 || range.length == 2)
69    {
70  56 try
71    {
72  56 int start = Integer.valueOf(range[0]);
73  51 int end = range.length == 1 ? start : Integer.valueOf(range[1]);
74  50 return Collections.singletonList(new int[] { start, end });
75    } catch (NumberFormatException e)
76    {
77    /*
78    * could be a location like <1..888 or 1..>888
79    */
80  6 throw new ParseException(location, 0);
81    }
82    }
83    else
84    {
85    /*
86    * could be a location like 102.110 or 123^124
87    */
88  0 throw new ParseException(location, 0);
89    }
90    }
91   
92    /**
93    * Parses a complement(locationSpec) into a list of start-end ranges
94    *
95    * @param location
96    * @return
97    * @throws ParseException
98    */
 
99  14 toggle static List<int[]> parseComplement(String location) throws ParseException
100    {
101    /*
102    * take what is inside complement()
103    */
104  14 if (!location.endsWith(")"))
105    {
106  3 throw new ParseException(location, 0);
107    }
108  11 String toComplement = location.substring("complement(".length(),
109    location.length() - 1);
110  11 List<int[]> ranges = parseLocation(toComplement);
111   
112    /*
113    * reverse the order and direction of ranges
114    */
115  11 Collections.reverse(ranges);
116  11 for (int[] range : ranges)
117    {
118  12 int temp = range[0];
119  12 range[0] = range[1];
120  12 range[1] = temp;
121    }
122  11 return ranges;
123    }
124   
125    /**
126    * Parses a join(loc1,loc2,...,locn) into a list of start-end ranges
127    *
128    * @param location
129    * @return
130    * @throws ParseException
131    */
 
132  14 toggle static List<int[]> parseJoin(String location) throws ParseException
133    {
134  14 List<int[]> ranges = new ArrayList<int[]>();
135   
136    /*
137    * take what is inside join()
138    */
139  14 if (!location.endsWith(")"))
140    {
141  3 throw new ParseException(location, 0);
142    }
143  11 String joinedLocs = location.substring("join(".length(),
144    location.length() - 1);
145  11 String[] locations = joinedLocs.split(",");
146  11 for (String loc : locations)
147    {
148  25 List<int[]> range = parseLocation(loc);
149  23 ranges.addAll(range);
150    }
151  9 return ranges;
152    }
153   
154    }