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;
30 import java.io.PrintStream;
32 import org.testng.annotations.BeforeMethod;
33 import org.testng.annotations.Test;
36 * Test the alignment -> Mapping routines
41 public class TestAlignSeq
47 * @throws java.lang.Exception
49 @BeforeMethod(alwaysRun = true)
50 public void setUp() throws Exception
52 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
55 s2 = new Sequence("Seq2", "ASDFA");
58 s3 = new Sequence("Seq1", "SDFAQQQSSS");
62 @Test(groups = { "Functional" })
64 * simple test that mapping from alignment corresponds identical positions.
66 public void testGetMappingForS1()
68 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
69 System.out.println("s1: " + as.getAStr1());
70 System.out.println("s2: " + as.getAStr2());
72 // aligned results match
73 assertEquals("ASDFA", as.getAStr1());
74 assertEquals(as.getAStr1(), as.getAStr2());
76 Mapping s1tos2 = as.getMappingFromS1(false);
77 System.out.println(s1tos2.getMap().toString());
78 for (int i = s2.getStart(); i < s2.getEnd(); i++)
80 System.out.println("Position in s2: " + i
81 + " maps to position in s1: " + s1tos2.getPosition(i));
82 // TODO fails: getCharAt doesn't allow for the start position??
83 // assertEquals(String.valueOf(s2.getCharAt(i)),
84 // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
88 @Test(groups = { "Functional" })
89 public void testExtractGaps()
91 assertNull(AlignSeq.extractGaps(null, null));
92 assertNull(AlignSeq.extractGaps(". -", null));
93 assertNull(AlignSeq.extractGaps(null, "AB-C"));
95 assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
98 @Test(groups = { "Functional" })
99 public void testPrintAlignment()
101 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
102 final StringBuilder baos = new StringBuilder();
103 PrintStream ps = new PrintStream(System.out)
106 public void print(String x)
112 public void println()
118 as.printAlignment(ps);
119 String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 : 3 - 18 (Sequence length = 14)\nSequence Seq1 : 1 - 10 (Sequence length = 10)\n\n"
120 + "Seq1 SDFAQQQRRR\n"
122 + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n";
123 assertEquals(expected, baos.toString());