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;
25 import org.testng.annotations.Test;
26 import org.testng.annotations.BeforeMethod;
27 import java.io.PrintStream;
29 import jalview.datamodel.Mapping;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceI;
34 * Test the alignment -> Mapping routines
39 public class TestAlignSeq
45 * @throws java.lang.Exception
48 public void setUp() throws Exception
50 s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
53 s2 = new Sequence("Seq2", "ASDFA");
56 s3 = new Sequence("Seq1", "SDFAQQQSSS");
62 * simple test that mapping from alignment corresponds identical positions.
64 public void testGetMappingForS1()
66 AlignSeq as = AlignSeq
67 .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
68 System.out.println("s1: " + as.getAStr1());
69 System.out.println("s2: " + as.getAStr2());
71 // aligned results match
72 assertEquals("ASDFA", as.getAStr1());
73 assertEquals(as.getAStr1(), as.getAStr2());
75 Mapping s1tos2 = as.getMappingFromS1(false);
76 System.out.println(s1tos2.getMap().toString());
77 for (int i = s2.getStart(); i < s2.getEnd(); i++)
79 System.out.println("Position in s2: " + i
80 + " maps to position in s1: " + s1tos2.getPosition(i));
81 // TODO fails: getCharAt doesn't allow for the start position??
82 // assertEquals(String.valueOf(s2.getCharAt(i)),
83 // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
88 public void testExtractGaps()
90 assertNull(AlignSeq.extractGaps(null, null));
91 assertNull(AlignSeq.extractGaps(". -", null));
92 assertNull(AlignSeq.extractGaps(null, "AB-C"));
94 assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
98 public void testPrintAlignment()
100 AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
101 final StringBuilder baos = new StringBuilder();
102 PrintStream ps = new PrintStream(System.out)
105 public void print(String x)
111 public void println()
117 as.printAlignment(ps);
118 String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 : 3 - 18 (Sequence length = 14)\nSequence Seq1 : 1 - 10 (Sequence length = 10)\n\n"
119 + "Seq1 SDFAQQQRRR\n"
121 + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
122 assertEquals(expected, baos.toString());