+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.analysis;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.AssertJUnit.fail;
-
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.SequenceFeature;
-import jalview.gui.JvOptionPane;
-
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class RnaTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = { "Functional" })
- public void testGetSimpleBPs() throws WUSSParseException
- {
- String rna = "([{})]"; // JAL-1081 example
- List<SimpleBP> bps = Rna.getSimpleBPs(rna);
- assertEquals(3, bps.size());
-
- /*
- * the base pairs are added in the order in which the matching base is found
- * (popping the stack of unmatched opening brackets)
- */
- assertEquals(2, bps.get(0).bp5); // {
- assertEquals(3, bps.get(0).bp3); // }
- assertEquals(0, bps.get(1).bp5); // (
- assertEquals(4, bps.get(1).bp3); // )
- assertEquals(1, bps.get(2).bp5); // [
- assertEquals(5, bps.get(2).bp3); // ]
- }
-
- @Test(groups = { "Functional" })
- public void testGetSimpleBPs_unmatchedOpener()
- {
- String rna = "(([{})]";
- try
- {
- Rna.getSimpleBPs(rna);
- fail("expected exception");
- } catch (WUSSParseException e)
- {
- // error reported as after end of input string
- assertEquals(rna.length(), e.getProblemPos());
- }
- }
-
- @Test(groups = { "Functional" })
- public void testGetSimpleBPs_unmatchedCloser()
- {
- String rna = "([{})]]]";
- try
- {
- Rna.getSimpleBPs(rna);
- fail("expected exception");
- } catch (WUSSParseException e)
- {
- // error reported as at first unmatched close
- assertEquals(6, e.getProblemPos());
- }
-
- /*
- * a variant where we have no opening bracket of the same type
- * as the unmatched closing bracket (no stack rather than empty stack)
- */
- rna = "((()])";
- try
- {
- Rna.getSimpleBPs(rna);
- fail("expected exception");
- } catch (WUSSParseException e)
- {
- assertEquals(4, e.getProblemPos());
- }
- }
-
- @Test(groups = { "Functional" })
- public void testGetRNASecStrucState()
- {
- assertNull(Rna.getRNASecStrucState(null));
- for (int i = 0; i <= 255; i++)
- {
- String s = String.valueOf((char) i);
- String ss = Rna.getRNASecStrucState(s);
-
- /*
- * valid SS chars are a-z, A-Z, and various brackets;
- * anything else is returned as a space
- */
- if ((i >= 'a' && i <= 'z') || (i >= 'A' && i <= 'Z')
- || "()[]{}<>".indexOf(s) > -1)
- {
- assertEquals("" + i, s, ss);
- }
- else
- {
- assertEquals(" ", ss);
- }
- }
-
- /*
- * a string is processed character by character
- */
- assertEquals("a [K ]z} {Q b(w)p><i",
- Rna.getRNASecStrucState("a.[K-]z}?{Q b(w)p><i"));
- }
-
- /**
- * Tests for isClosingParenthesis with char or String argument
- */
- @Test(groups = { "Functional" })
- public void testIsClosingParenthesis()
- {
- assertFalse(Rna.isClosingParenthesis(null));
-
- /*
- * only a-z, )]}> are closing bracket symbols
- */
- for (int i = 0; i <= 255; i++)
- {
- boolean isClosingChar = Rna.isClosingParenthesis((char) i);
- boolean isClosingString = Rna.isClosingParenthesis(String
- .valueOf((char) i));
- if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
- || i == '>')
- {
- assertTrue(String.format("close base pair %c", i), isClosingChar);
- assertTrue(String.format("close base pair %c", i), isClosingString);
- }
- else
- {
- assertFalse(String.format("close base pair %c", i), isClosingChar);
- assertFalse(String.format("close base pair %c", i), isClosingString);
- }
- assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
- }
- }
-
- @Test(groups = { "Functional" })
- public void testIsCanonicalOrWobblePair()
- {
- String bases = "acgtuACGTU";
- for (int i = 0; i < bases.length(); i++)
- {
- for (int j = 0; j < bases.length(); j++)
- {
- char first = bases.charAt(i);
- char second = bases.charAt(j);
- boolean result = Rna.isCanonicalOrWobblePair(first, second);
- String pair = new String(new char[] { first, second })
- .toUpperCase();
- if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
- || pair.equals("UA") || pair.equals("GC")
- || pair.equals("CG") || pair.equals("GT")
- || pair.equals("TG") || pair.equals("GU")
- || pair.equals("UG"))
- {
- assertTrue(pair + " should be valid", result);
- }
- else
- {
- assertFalse(pair + " should be invalid", result);
- }
- }
- }
- }
-
- @Test(groups = { "Functional" })
- public void testIsCanonicalPair()
- {
- String bases = "acgtuACGTU";
- for (int i = 0; i < bases.length(); i++)
- {
- for (int j = 0; j < bases.length(); j++)
- {
- char first = bases.charAt(i);
- char second = bases.charAt(j);
- boolean result = Rna.isCanonicalPair(first, second);
- String pair = new String(new char[] { first, second })
- .toUpperCase();
- if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
- || pair.equals("UA") || pair.equals("GC")
- || pair.equals("CG"))
- {
- assertTrue(pair + " should be valid", result);
- }
- else
- {
- assertFalse(pair + " should be invalid", result);
- }
- }
- }
- }
-
- /**
- * Tests for isOpeningParenthesis with char or String argument
- */
- @Test(groups = { "Functional" })
- public void testIsOpeningParenthesis()
- {
- /*
- * only A-Z, ([{< are opening bracket symbols
- */
- for (int i = 0; i <= 255; i++)
- {
- boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
- boolean isOpeningString = Rna.isOpeningParenthesis(String
- .valueOf((char) i));
- if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
- || i == '<')
- {
- assertTrue(String.format("Open base pair %c", i), isOpeningChar);
- assertTrue(String.format("Open base pair %c", i), isOpeningString);
- }
- else
- {
- assertFalse(String.format("Open base pair %c", i), isOpeningChar);
- assertFalse(String.format("Open base pair %c", i), isOpeningString);
- }
- assertFalse(Rna.isOpeningParenthesis(String.valueOf((char) i) + " "));
- }
- }
-
- @Test(groups = { "Functional" })
- public void testGetMatchingOpeningParenthesis() throws WUSSParseException
- {
- for (int i = 0; i <= 255; i++)
- {
- boolean isClosing = Rna.isClosingParenthesis((char) i);
- if (isClosing)
- {
- char opening = Rna.getMatchingOpeningParenthesis((char) i);
- if (i >= 'a' && i <= 'z')
- {
- assertEquals(i + 'A' - 'a', opening);
- }
- else if (i == ')' && opening == '(' || i == ']' && opening == '['
- || i == '}' && opening == '{' || i == '>' && opening == '<')
- {
- // ok
- }
- else
- {
- fail("Got " + opening + " as opening bracket pair for "
- + ((char) i));
- }
- }
- }
- }
-
- /**
- * Tests for isRnaSecondaryStructureSymbol with char or String argument
- */
- @Test(groups = { "Functional" })
- public void testIsRnaSecondaryStructureSymbol()
- {
- assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
-
- /*
- * only A-Z, a-z, ()[]{}<> are valid symbols
- */
- for (int i = 0; i <= 255; i++)
- {
- boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
- boolean isValidString = Rna.isRnaSecondaryStructureSymbol(String
- .valueOf((char) i));
- if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
- || i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
- || i == '<' || i == '>')
- {
- assertTrue(String.format("close base pair %c", i), isValidChar);
- assertTrue(String.format("close base pair %c", i), isValidString);
- }
- else
- {
- assertFalse(String.format("close base pair %c", i), isValidChar);
- assertFalse(String.format("close base pair %c", i), isValidString);
- }
- assertFalse(Rna.isRnaSecondaryStructureSymbol(String
- .valueOf((char) i) + " "));
- }
- }
-
- @Test(groups = "Functional")
- public void testGetHelixMap_oneHelix() throws WUSSParseException
- {
- String rna = ".(..[{.<..>}..].)";
- SequenceFeature[] sfs = Rna.getHelixMap(rna);
- assertEquals(4, sfs.length);
-
- /*
- * pairs are added in the order in which the closing bracket is found
- * (see testGetSimpleBPs)
- */
- assertEquals(7, sfs[0].getBegin());
- assertEquals(10, sfs[0].getEnd());
- assertEquals("0", sfs[0].getFeatureGroup());
- assertEquals(5, sfs[1].getBegin());
- assertEquals(11, sfs[1].getEnd());
- assertEquals("0", sfs[1].getFeatureGroup());
- assertEquals(4, sfs[2].getBegin());
- assertEquals(14, sfs[2].getEnd());
- assertEquals("0", sfs[2].getFeatureGroup());
- assertEquals(1, sfs[3].getBegin());
- assertEquals(16, sfs[3].getEnd());
- assertEquals("0", sfs[3].getFeatureGroup());
- }
-
- @Test(groups = "Functional")
- public void testGetHelixMap_twoHelices() throws WUSSParseException
- {
- String rna = ".([.)]..{.<}.>";
- SequenceFeature[] sfs = Rna.getHelixMap(rna);
- assertEquals(4, sfs.length);
-
- /*
- * pairs are added in the order in which the closing bracket is found
- * (see testGetSimpleBPs)
- */
- assertEquals(1, sfs[0].getBegin());
- assertEquals(4, sfs[0].getEnd());
- assertEquals("0", sfs[0].getFeatureGroup());
- assertEquals(2, sfs[1].getBegin());
- assertEquals(5, sfs[1].getEnd());
- assertEquals("0", sfs[1].getFeatureGroup());
- assertEquals(8, sfs[2].getBegin());
- assertEquals(11, sfs[2].getEnd());
- assertEquals("1", sfs[2].getFeatureGroup());
- assertEquals(10, sfs[3].getBegin());
- assertEquals(13, sfs[3].getEnd());
- assertEquals("1", sfs[3].getFeatureGroup());
- }
-}
git://source.jalview.org / jalview.git / blobdiff