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,
59 * refactored 'as is' from main method
61 * TODO: split into separate tests
63 @Test(groups = { "Functional" })
64 public void testSomething() throws Exception
66 String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
67 Sequence s = new Sequence("MySeq", o_seq, 39, 80);
68 String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
69 Sequence s_gapped = new Sequence("MySeq", orig_gapped, 39, 80);
70 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
71 s_gapped.setDatasetSequence(s);
72 String sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh";
73 Sequence s_subsequence_gapped = new Sequence("MySeq", sub_gapped_s, 43,
75 s_subsequence_gapped.setDatasetSequence(s);
77 SeqCigar c_null = new SeqCigar(s);
78 String cs_null = c_null.getCigarstring();
79 assertEquals("Failed to recover ungapped sequence cigar operations",
81 testCigar_string(s_gapped, ex_cs_gapped);
82 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
83 assertEquals("Failed parseCigar", ex_cs_gapped,
84 gen_sgapped.getCigarstring());
86 testSeqRecovery(gen_sgapped, s_gapped);
89 * Test dataset resolution
91 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
92 testSeqRecovery(sub_gapped, s_subsequence_gapped);
95 * Test width functions
97 assertEquals("Failed getWidth", sub_gapped_s.length(),
98 sub_gapped.getWidth());
100 sub_gapped.getFullWidth();
101 assertFalse("hasDeletedRegions is incorrect",
102 sub_gapped.hasDeletedRegions());
104 // Test start-end region SeqCigar
105 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
107 "SeqCigar(seq, start, end) not properly clipped alignsequence",
108 41, sub_se_gp.getWidth());
111 * TODO: can we add assertions to the sysouts that follow?
113 System.out.println("Original sequence align:\n" + sub_gapped_s
114 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
115 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
116 + sub_se_gp.getCigarstring() + "\n");
117 SequenceI ssgp = sub_se_gp.getSeq('-');
118 System.out.println("\t " + ssgp.getSequenceAsString());
119 for (int r = 0; r < 10; r++)
121 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
122 int sl = sub_se_gp.getWidth();
124 for (int rs = 0; rs < 10; rs++)
127 sub_se_gp.deleteRange(st, e);
128 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
129 System.out.println(st + "," + e + "\t:" + ssgapedseq);
134 SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
135 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
136 Alignment al = new Alignment(set);
137 for (int i = 0; i < al.getHeight(); i++)
139 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
140 + al.getSequenceAt(i).getStart() + "\t"
141 + al.getSequenceAt(i).getEnd() + "\t"
142 + al.getSequenceAt(i).getSequenceAsString());
145 System.out.println("Gapped.");
146 set = new SeqCigar[] { new SeqCigar(s),
147 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
148 set[0].deleteRange(20, 25);
149 al = new Alignment(set);
150 for (int i = 0; i < al.getHeight(); i++)
152 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
153 + al.getSequenceAt(i).getStart() + "\t"
154 + al.getSequenceAt(i).getEnd() + "\t"
155 + al.getSequenceAt(i).getSequenceAsString());
158 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
159 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
163 * non rigorous testing
167 * @param ex_cs_gapped
172 protected void testCigar_string(Sequence seq, String ex_cs_gapped)
174 SeqCigar c_sgapped = new SeqCigar(seq);
175 String cs_gapped = c_sgapped.getCigarstring();
176 assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
179 protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
181 // this is non-rigorous - start and end recovery is not tested.
182 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
183 // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
185 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
187 // TODO: investigate errors reported here, to allow full conversion to
188 // passing JUnit assertion form
189 System.err.println("Couldn't reconstruct sequence.\n"
190 + gen_sgapped_s.getSequenceAsString() + "\n"
191 + s_gapped.getSequenceAsString());