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 static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertNull;
26 import jalview.datamodel.Mapping;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.JvOptionPane;
31 import java.io.PrintStream;
32 import java.nio.charset.Charset;
33 import java.util.Locale;
35 import org.testng.annotations.BeforeClass;
36 import org.testng.annotations.BeforeMethod;
37 import org.testng.annotations.Test;
39 import com.google.common.base.Charsets;
42 * Test the alignment -> Mapping routines
47 public class TestAlignSeq
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60 * @throws java.lang.Exception
62 @BeforeMethod(alwaysRun = true)
63 public void setUp() throws Exception
65 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
68 s2 = new Sequence("Seq2", "ASDFA");
71 s3 = new Sequence("Seq3", "SDFAQQQSSS");
75 @Test(groups = { "Functional" })
77 * simple test that mapping from alignment corresponds identical positions.
79 public void testGetMappingForS1()
81 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
82 System.out.println("s1: " + as.getAStr1());
83 System.out.println("s2: " + as.getAStr2());
85 // aligned results match
86 assertEquals("ASDFA", as.getAStr1());
87 assertEquals(as.getAStr1(), as.getAStr2());
89 Mapping s1tos2 = as.getMappingFromS1(false);
90 checkMapping(s1tos2,s1,s2);
93 public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
95 System.out.println(s1tos2.getMap().toString());
96 for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
98 int p=s1tos2.getPosition(i);
99 char s2c=_s2.getCharAt(i-_s2.getStart());
100 char s1c=_s1.getCharAt(p-_s1.getStart());
101 System.out.println("Position in s2: " + i +s2c
102 + " maps to position in s1: " +p+s1c);
103 assertEquals(s1c,s2c);
106 @Test(groups = { "Functional" })
108 * simple test that mapping from alignment corresponds identical positions.
110 public void testGetMappingForS1_withLowerCase()
112 // make one of the sequences lower case
113 SequenceI ns2 = new Sequence(s2);
114 ns2.replace('D', 'd');
115 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
116 System.out.println("s1: " + as.getAStr1());
117 System.out.println("s2: " + as.getAStr2());
119 // aligned results match
120 assertEquals("ASDFA", as.getAStr1());
121 assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
123 Mapping s1tos2 = as.getMappingFromS1(false);
124 assertEquals("ASdFA",as.getAStr2());
125 // verify mapping is consistent between original all-caps sequences
126 checkMapping(s1tos2,s1,s2);
129 @Test(groups = { "Functional" })
130 public void testExtractGaps()
132 assertNull(AlignSeq.extractGaps(null, null));
133 assertNull(AlignSeq.extractGaps(". -", null));
134 assertNull(AlignSeq.extractGaps(null, "AB-C"));
136 assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
139 @Test(groups = { "Functional" })
140 public void testPrintAlignment()
142 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
143 final StringBuilder baos = new StringBuilder();
144 PrintStream ps = new PrintStream(System.out)
147 public void print(String x)
153 public void println()
159 as.printAlignment(ps);
160 String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
161 + "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
162 + "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
163 assertEquals(expected, baos.toString());