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.Assert.assertTrue;
24 import static org.testng.AssertJUnit.assertEquals;
25 import static org.testng.AssertJUnit.assertFalse;
27 import jalview.gui.JvOptionPane;
28 import jalview.util.Comparison;
30 import org.testng.annotations.BeforeClass;
31 import org.testng.annotations.Test;
34 * Unit tests for SeqCigar
36 public class SeqCigarTest
39 @BeforeClass(alwaysRun = true)
40 public void setUpJvOptionPane()
42 JvOptionPane.setInteractiveMode(false);
43 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
46 @Test(groups = { "Functional" })
47 public void testFindPosition()
49 SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
50 oseq.createDatasetSequence();
51 SeqCigar cs = new SeqCigar(oseq);
52 assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
53 for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
55 int os_p = oseq.findPosition(c);
56 int cigar_p = cs.findPosition(c);
57 if (Comparison.isGap(oseq.getCharAt(c)))
59 assertEquals("Expected gap at position " + os_p + " column " + c,
64 assertEquals("Positions don't match for at column " + c, os_p,
71 * refactored 'as is' from main method
73 * TODO: split into separate tests
75 @Test(groups = { "Functional" })
76 public void testSomething() throws Exception
78 String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
79 Sequence s = new Sequence("MySeq", o_seq, 39, 80);
80 String orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt";
81 Sequence s_gapped = new Sequence("MySeq", orig_gapped, 39, 80);
82 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
83 s_gapped.setDatasetSequence(s);
84 String sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh";
85 Sequence s_subsequence_gapped = new Sequence("MySeq", sub_gapped_s, 43,
87 s_subsequence_gapped.setDatasetSequence(s);
89 SeqCigar c_null = new SeqCigar(s);
90 String cs_null = c_null.getCigarstring();
91 assertEquals("Failed to recover ungapped sequence cigar operations",
93 testCigar_string(s_gapped, ex_cs_gapped);
94 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
95 assertEquals("Failed parseCigar", ex_cs_gapped,
96 gen_sgapped.getCigarstring());
98 assertTrue(testSeqRecovery(gen_sgapped, s_gapped,true));
101 * Test dataset resolution
103 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
104 assertTrue(testSeqRecovery(sub_gapped, s_subsequence_gapped,true));
107 * Test width functions
109 assertEquals("Failed getWidth", sub_gapped_s.length(),
110 sub_gapped.getWidth());
112 sub_gapped.getFullWidth();
113 assertFalse("hasDeletedRegions is incorrect",
114 sub_gapped.hasDeletedRegions());
116 // Test start-end region SeqCigar
117 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
119 "SeqCigar(seq, start, end) not properly clipped alignsequence",
120 41, sub_se_gp.getWidth());
123 * TODO: can we add assertions to the sysouts that follow?
125 System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
126 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
127 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
128 + sub_se_gp.getCigarstring() + "\n");
129 SequenceI ssgp = sub_se_gp.getSeq('-');
130 System.out.println("\t " + ssgp.getSequenceAsString());
131 for (int r = 0; r < 10; r++)
133 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
134 int sl = sub_se_gp.getWidth();
136 for (int rs = 0; rs < 10; rs++)
139 sub_se_gp.deleteRange(st, e);
140 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
141 System.out.println(st + "," + e + "\t:" + ssgapedseq);
146 SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
147 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
148 Alignment al = new Alignment(set);
149 for (int i = 0; i < al.getHeight(); i++)
151 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
152 + al.getSequenceAt(i).getStart() + "\t"
153 + al.getSequenceAt(i).getEnd() + "\t"
154 + al.getSequenceAt(i).getSequenceAsString());
157 System.out.println("Gapped.");
158 set = new SeqCigar[] { new SeqCigar(s),
159 new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
160 set[0].deleteRange(20, 25);
161 al = new Alignment(set);
162 for (int i = 0; i < al.getHeight(); i++)
164 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
165 + al.getSequenceAt(i).getStart() + "\t"
166 + al.getSequenceAt(i).getEnd() + "\t"
167 + al.getSequenceAt(i).getSequenceAsString());
170 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
171 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
175 * non rigorous testing
179 * @param ex_cs_gapped
184 protected void testCigar_string(Sequence seq, String ex_cs_gapped)
186 SeqCigar c_sgapped = new SeqCigar(seq);
187 String cs_gapped = c_sgapped.getCigarstring();
188 assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
191 protected boolean testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped,boolean startEndCheck)
193 // this is non-rigorous - start and end recovery is not tested.
194 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
195 // assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
197 if (!gen_sgapped_s.getSequenceAsString().equals(
198 s_gapped.getSequenceAsString()))
200 // TODO: investigate errors reported here, to allow full conversion to
201 // passing JUnit assertion form
202 System.err.println("Couldn't reconstruct sequence.\n"
203 + gen_sgapped_s.getSequenceAsString() + "\n"
204 + s_gapped.getSequenceAsString());
209 assertEquals("Start not conserved in reconstructed sequence",s_gapped.getStart(),gen_sgapped_s.getStart());
210 assertEquals("End not conserved in reconstructed sequence",s_gapped.getEnd(),gen_sgapped_s.getEnd());