2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.analysis;
23 import java.util.Locale;
25 import static org.testng.AssertJUnit.assertEquals;
26 import static org.testng.AssertJUnit.assertFalse;
27 import static org.testng.AssertJUnit.assertNull;
28 import static org.testng.AssertJUnit.assertTrue;
29 import static org.testng.AssertJUnit.fail;
31 import jalview.analysis.SecStrConsensus.SimpleBP;
32 import jalview.datamodel.SequenceFeature;
33 import jalview.gui.JvOptionPane;
35 import java.util.List;
37 import org.testng.annotations.BeforeClass;
38 import org.testng.annotations.Test;
43 @BeforeClass(alwaysRun = true)
44 public void setUpJvOptionPane()
46 JvOptionPane.setInteractiveMode(false);
47 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50 @Test(groups = { "Functional" })
51 public void testGetSimpleBPs() throws WUSSParseException
53 String rna = "([{})]"; // JAL-1081 example
54 List<SimpleBP> bps = Rna.getSimpleBPs(rna);
55 assertEquals(3, bps.size());
58 * the base pairs are added in the order in which the matching base is found
59 * (popping the stack of unmatched opening brackets)
61 assertEquals(2, bps.get(0).bp5); // {
62 assertEquals(3, bps.get(0).bp3); // }
63 assertEquals(0, bps.get(1).bp5); // (
64 assertEquals(4, bps.get(1).bp3); // )
65 assertEquals(1, bps.get(2).bp5); // [
66 assertEquals(5, bps.get(2).bp3); // ]
69 @Test(groups = { "Functional" })
70 public void testGetSimpleBPs_unmatchedOpener()
72 String rna = "(([{})]";
75 Rna.getSimpleBPs(rna);
76 fail("expected exception");
77 } catch (WUSSParseException e)
79 // error reported as after end of input string
80 assertEquals(rna.length(), e.getProblemPos());
84 @Test(groups = { "Functional" })
85 public void testGetSimpleBPs_unmatchedCloser()
87 String rna = "([{})]]]";
90 Rna.getSimpleBPs(rna);
91 fail("expected exception");
92 } catch (WUSSParseException e)
94 // error reported as at first unmatched close
95 assertEquals(6, e.getProblemPos());
99 * a variant where we have no opening bracket of the same type
100 * as the unmatched closing bracket (no stack rather than empty stack)
105 Rna.getSimpleBPs(rna);
106 fail("expected exception");
107 } catch (WUSSParseException e)
109 assertEquals(4, e.getProblemPos());
113 @Test(groups = { "Functional" })
114 public void testGetRNASecStrucState()
116 assertNull(Rna.getRNASecStrucState(null));
117 for (int i = 0; i <= 255; i++)
119 String s = String.valueOf((char) i);
120 String ss = Rna.getRNASecStrucState(s);
123 * valid SS chars are a-z, A-Z, and various brackets;
124 * anything else is returned as a space
126 if ((i >= 'a' && i <= 'z') || (i >= 'A' && i <= 'Z')
127 || "()[]{}<>".indexOf(s) > -1)
129 assertEquals("" + i, s, ss);
133 assertEquals(" ", ss);
138 * a string is processed character by character
140 assertEquals("a [K ]z} {Q b(w)p><i",
141 Rna.getRNASecStrucState("a.[K-]z}?{Q b(w)p><i"));
145 * Tests for isClosingParenthesis with char or String argument
147 @Test(groups = { "Functional" })
148 public void testIsClosingParenthesis()
150 assertFalse(Rna.isClosingParenthesis(null));
153 * only a-z, )]}> are closing bracket symbols
155 for (int i = 0; i <= 255; i++)
157 boolean isClosingChar = Rna.isClosingParenthesis((char) i);
158 boolean isClosingString = Rna.isClosingParenthesis(String
160 if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
163 assertTrue(String.format("close base pair %c", i), isClosingChar);
164 assertTrue(String.format("close base pair %c", i), isClosingString);
168 assertFalse(String.format("close base pair %c", i), isClosingChar);
169 assertFalse(String.format("close base pair %c", i), isClosingString);
171 assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
175 @Test(groups = { "Functional" })
176 public void testIsCanonicalOrWobblePair()
178 String bases = "acgtuACGTU";
179 for (int i = 0; i < bases.length(); i++)
181 for (int j = 0; j < bases.length(); j++)
183 char first = bases.charAt(i);
184 char second = bases.charAt(j);
185 boolean result = Rna.isCanonicalOrWobblePair(first, second);
186 String pair = new String(new char[] { first, second })
187 .toUpperCase(Locale.ROOT);
188 if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
189 || pair.equals("UA") || pair.equals("GC")
190 || pair.equals("CG") || pair.equals("GT")
191 || pair.equals("TG") || pair.equals("GU")
192 || pair.equals("UG"))
194 assertTrue(pair + " should be valid", result);
198 assertFalse(pair + " should be invalid", result);
204 @Test(groups = { "Functional" })
205 public void testIsCanonicalPair()
207 String bases = "acgtuACGTU";
208 for (int i = 0; i < bases.length(); i++)
210 for (int j = 0; j < bases.length(); j++)
212 char first = bases.charAt(i);
213 char second = bases.charAt(j);
214 boolean result = Rna.isCanonicalPair(first, second);
215 String pair = new String(new char[] { first, second })
216 .toUpperCase(Locale.ROOT);
217 if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
218 || pair.equals("UA") || pair.equals("GC")
219 || pair.equals("CG"))
221 assertTrue(pair + " should be valid", result);
225 assertFalse(pair + " should be invalid", result);
232 * Tests for isOpeningParenthesis with char or String argument
234 @Test(groups = { "Functional" })
235 public void testIsOpeningParenthesis()
238 * only A-Z, ([{< are opening bracket symbols
240 for (int i = 0; i <= 255; i++)
242 boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
243 boolean isOpeningString = Rna.isOpeningParenthesis(String
245 if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
248 assertTrue(String.format("Open base pair %c", i), isOpeningChar);
249 assertTrue(String.format("Open base pair %c", i), isOpeningString);
253 assertFalse(String.format("Open base pair %c", i), isOpeningChar);
254 assertFalse(String.format("Open base pair %c", i), isOpeningString);
256 assertFalse(Rna.isOpeningParenthesis(String.valueOf((char) i) + " "));
260 @Test(groups = { "Functional" })
261 public void testGetMatchingOpeningParenthesis() throws WUSSParseException
263 for (int i = 0; i <= 255; i++)
265 boolean isClosing = Rna.isClosingParenthesis((char) i);
268 char opening = Rna.getMatchingOpeningParenthesis((char) i);
269 if (i >= 'a' && i <= 'z')
271 assertEquals(i + 'A' - 'a', opening);
273 else if (i == ')' && opening == '(' || i == ']' && opening == '['
274 || i == '}' && opening == '{' || i == '>' && opening == '<')
280 fail("Got " + opening + " as opening bracket pair for "
288 * Tests for isRnaSecondaryStructureSymbol with char or String argument
290 @Test(groups = { "Functional" })
291 public void testIsRnaSecondaryStructureSymbol()
293 assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
296 * only A-Z, a-z, ()[]{}<> are valid symbols
298 for (int i = 0; i <= 255; i++)
300 boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
301 boolean isValidString = Rna.isRnaSecondaryStructureSymbol(String
303 if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
304 || i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
305 || i == '<' || i == '>')
307 assertTrue(String.format("close base pair %c", i), isValidChar);
308 assertTrue(String.format("close base pair %c", i), isValidString);
312 assertFalse(String.format("close base pair %c", i), isValidChar);
313 assertFalse(String.format("close base pair %c", i), isValidString);
315 assertFalse(Rna.isRnaSecondaryStructureSymbol(String
316 .valueOf((char) i) + " "));
320 @Test(groups = "Functional")
321 public void testGetHelixMap_oneHelix() throws WUSSParseException
323 String rna = ".(..[{.<..>}..].)";
324 SequenceFeature[] sfs = Rna.getHelixMap(rna);
325 assertEquals(4, sfs.length);
328 * pairs are added in the order in which the closing bracket is found
329 * (see testGetSimpleBPs)
331 assertEquals(7, sfs[0].getBegin());
332 assertEquals(10, sfs[0].getEnd());
333 assertEquals("0", sfs[0].getFeatureGroup());
334 assertEquals(5, sfs[1].getBegin());
335 assertEquals(11, sfs[1].getEnd());
336 assertEquals("0", sfs[1].getFeatureGroup());
337 assertEquals(4, sfs[2].getBegin());
338 assertEquals(14, sfs[2].getEnd());
339 assertEquals("0", sfs[2].getFeatureGroup());
340 assertEquals(1, sfs[3].getBegin());
341 assertEquals(16, sfs[3].getEnd());
342 assertEquals("0", sfs[3].getFeatureGroup());
345 @Test(groups = "Functional")
346 public void testGetHelixMap_twoHelices() throws WUSSParseException
348 String rna = ".([.)]..{.<}.>";
349 SequenceFeature[] sfs = Rna.getHelixMap(rna);
350 assertEquals(4, sfs.length);
353 * pairs are added in the order in which the closing bracket is found
354 * (see testGetSimpleBPs)
356 assertEquals(1, sfs[0].getBegin());
357 assertEquals(4, sfs[0].getEnd());
358 assertEquals("0", sfs[0].getFeatureGroup());
359 assertEquals(2, sfs[1].getBegin());
360 assertEquals(5, sfs[1].getEnd());
361 assertEquals("0", sfs[1].getFeatureGroup());
362 assertEquals(8, sfs[2].getBegin());
363 assertEquals(11, sfs[2].getEnd());
364 assertEquals("1", sfs[2].getFeatureGroup());
365 assertEquals(10, sfs[3].getBegin());
366 assertEquals(13, sfs[3].getEnd());
367 assertEquals("1", sfs[3].getFeatureGroup());