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.datamodel;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
26 import jalview.util.Comparison;
28 import org.testng.annotations.Test;
31 * Unit tests for SeqCigar
33 public class SeqCigarTest
35 @Test(groups = { "Functional" })
36 public void testFindPosition()
38 SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
39 oseq.createDatasetSequence();
40 SeqCigar cs = new SeqCigar(oseq);
41 assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
42 for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
44 int os_p = oseq.findPosition(c);
45 int cigar_p = cs.findPosition(c);
46 if (Comparison.isGap(oseq.getCharAt(c)))
48 assertEquals("Expected gap at position " + os_p + " column " + c,
53 assertEquals("Positions don't match for at column " + c, os_p,
60 * refactored 'as is' from main method
62 * TODO: split into separate tests
64 @Test(groups = { "Functional" })
65 public void testSomething() throws Exception
67 String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
68 Sequence s = new Sequence("MySeq", o_seq, 39, 80);
69 String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
70 Sequence s_gapped = new Sequence("MySeq", orig_gapped, 39, 80);
71 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
72 s_gapped.setDatasetSequence(s);
73 String sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh";
74 Sequence s_subsequence_gapped = new Sequence("MySeq", sub_gapped_s, 43,
76 s_subsequence_gapped.setDatasetSequence(s);
78 SeqCigar c_null = new SeqCigar(s);
79 String cs_null = c_null.getCigarstring();
80 assertEquals("Failed to recover ungapped sequence cigar operations",
82 testCigar_string(s_gapped, ex_cs_gapped);
83 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
84 assertEquals("Failed parseCigar", ex_cs_gapped,
85 gen_sgapped.getCigarstring());
87 testSeqRecovery(gen_sgapped, s_gapped);
90 * Test dataset resolution
92 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
93 testSeqRecovery(sub_gapped, s_subsequence_gapped);
96 * Test width functions
98 assertEquals("Failed getWidth", sub_gapped_s.length(),
99 sub_gapped.getWidth());
101 sub_gapped.getFullWidth();
102 assertFalse("hasDeletedRegions is incorrect",
103 sub_gapped.hasDeletedRegions());
105 // Test start-end region SeqCigar
106 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
108 "SeqCigar(seq, start, end) not properly clipped alignsequence",
109 41, sub_se_gp.getWidth());
112 * TODO: can we add assertions to the sysouts that follow?
114 System.out.println("Original sequence align:\n" + sub_gapped_s
115 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
116 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
117 + sub_se_gp.getCigarstring() + "\n");
118 SequenceI ssgp = sub_se_gp.getSeq('-');
119 System.out.println("\t " + ssgp.getSequenceAsString());
120 for (int r = 0; r < 10; r++)
122 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
123 int sl = sub_se_gp.getWidth();
125 for (int rs = 0; rs < 10; rs++)
128 sub_se_gp.deleteRange(st, e);
129 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
130 System.out.println(st + "," + e + "\t:" + ssgapedseq);
135 SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
136 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
137 Alignment al = new Alignment(set);
138 for (int i = 0; i < al.getHeight(); i++)
140 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
141 + al.getSequenceAt(i).getStart() + "\t"
142 + al.getSequenceAt(i).getEnd() + "\t"
143 + al.getSequenceAt(i).getSequenceAsString());
146 System.out.println("Gapped.");
147 set = new SeqCigar[] { new SeqCigar(s),
148 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
149 set[0].deleteRange(20, 25);
150 al = new Alignment(set);
151 for (int i = 0; i < al.getHeight(); i++)
153 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
154 + al.getSequenceAt(i).getStart() + "\t"
155 + al.getSequenceAt(i).getEnd() + "\t"
156 + al.getSequenceAt(i).getSequenceAsString());
159 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
160 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
164 * non rigorous testing
168 * @param ex_cs_gapped
173 protected void testCigar_string(Sequence seq, String ex_cs_gapped)
175 SeqCigar c_sgapped = new SeqCigar(seq);
176 String cs_gapped = c_sgapped.getCigarstring();
177 assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
180 protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
182 // this is non-rigorous - start and end recovery is not tested.
183 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
184 // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
186 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
188 // TODO: investigate errors reported here, to allow full conversion to
189 // passing JUnit assertion form
190 System.err.println("Couldn't reconstruct sequence.\n"
191 + gen_sgapped_s.getSequenceAsString() + "\n"
192 + s_gapped.getSequenceAsString());