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package jalview.analysis; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertSame; |
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import static org.testng.Assert.assertTrue; |
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import jalview.api.AlignViewportI; |
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import jalview.api.FinderI; |
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import jalview.bin.Cache; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.ColumnSelection; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.SearchResultMatchI; |
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import jalview.datamodel.SearchResultsI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.AlignViewport; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import java.util.List; |
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import org.testng.annotations.AfterMethod; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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import junit.extensions.PA; |
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| 100% |
Uncovered Elements: 0 (387) |
Complexity: 17 |
Complexity Density: 0.05 |
|
52 |
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public class FinderTest |
53 |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
54 |
1 |
@BeforeClass(alwaysRun = true)... |
55 |
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public void setUpJvOptionPane() |
56 |
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{ |
57 |
1 |
JvOptionPane.setInteractiveMode(false); |
58 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
59 |
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} |
60 |
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61 |
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private AlignFrame af; |
62 |
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63 |
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private AlignmentI al; |
64 |
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65 |
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private AlignViewportI av; |
66 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
67 |
1 |
@BeforeClass(groups = "Functional")... |
68 |
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public void setUp() |
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{ |
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Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
71 |
1 |
Cache.applicationProperties.setProperty("PAD_GAPS", |
72 |
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Boolean.FALSE.toString()); |
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String seqData = "seq1seq1/8-18 ABCD--EF-GHIJI\n" + "seq2 A--BCDefHI\n" |
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+ "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n"; |
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af = new FileLoader().LoadFileWaitTillLoaded(seqData, |
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DataSourceType.PASTE); |
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av = af.getViewport(); |
79 |
1 |
al = av.getAlignment(); |
80 |
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} |
81 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
82 |
14 |
@AfterMethod(alwaysRun = true)... |
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public void tearDownAfterTest() |
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{ |
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av.setSelectionGroup(null); |
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} |
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88 |
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89 |
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90 |
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| 100% |
Uncovered Elements: 0 (19) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
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1 |
@Test(groups = "Functional")... |
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public void testFind_regex() |
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{ |
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96 |
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Finder f = new Finder(av); |
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f.findNext("E.H", false, false); |
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SearchResultsI sr = f.getSearchResults(); |
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assertEquals(sr.getSize(), 1); |
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List<SearchResultMatchI> matches = sr.getResults(); |
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assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); |
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assertEquals(matches.get(0).getStart(), 5); |
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assertEquals(matches.get(0).getEnd(), 7); |
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f = new Finder(av); |
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f.findAll("E.H", false, false); |
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sr = f.getSearchResults(); |
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assertEquals(sr.getSize(), 2); |
112 |
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matches = sr.getResults(); |
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assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); |
114 |
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assertSame(matches.get(1).getSequence(), al.getSequenceAt(2)); |
115 |
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assertEquals(matches.get(0).getStart(), 5); |
116 |
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assertEquals(matches.get(0).getEnd(), 7); |
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1 |
assertEquals(matches.get(1).getStart(), 4); |
118 |
1 |
assertEquals(matches.get(1).getEnd(), 6); |
119 |
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} |
120 |
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121 |
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122 |
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123 |
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| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
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124 |
1 |
@Test(groups = "Functional")... |
125 |
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public void testFind_residueNumber() |
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{ |
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1 |
Finder f = new Finder(av); |
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130 |
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131 |
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f.findNext("9", false, false); |
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SearchResultsI sr = f.getSearchResults(); |
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assertEquals(sr.getSize(), 1); |
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List<SearchResultMatchI> matches = sr.getResults(); |
136 |
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assertSame(matches.get(0).getSequence(), al.getSequenceAt(0)); |
137 |
1 |
assertEquals(matches.get(0).getStart(), 9); |
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1 |
assertEquals(matches.get(0).getEnd(), 9); |
139 |
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140 |
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141 |
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142 |
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143 |
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f = new Finder(av); |
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1 |
f.findAll("9", false, false); |
145 |
1 |
sr = f.getSearchResults(); |
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1 |
assertEquals(sr.getSize(), 2); |
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matches = sr.getResults(); |
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1 |
assertSame(matches.get(0).getSequence(), al.getSequenceAt(0)); |
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assertSame(matches.get(1).getSequence(), al.getSequenceAt(3)); |
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1 |
assertEquals(matches.get(0).getStart(), 9); |
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assertEquals(matches.get(0).getEnd(), 9); |
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assertEquals(matches.get(1).getStart(), 9); |
153 |
1 |
assertEquals(matches.get(1).getEnd(), 9); |
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155 |
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156 |
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157 |
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158 |
1 |
f = new Finder(av); |
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1 |
f.findNext(" 9", false, false); |
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1 |
assertTrue(f.getSearchResults().isEmpty()); |
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} |
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164 |
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165 |
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| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
166 |
1 |
@Test(groups = "Functional")... |
167 |
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public void testFindNext() |
168 |
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{ |
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170 |
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171 |
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172 |
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173 |
1 |
Finder f = new Finder(av); |
174 |
1 |
PA.setValue(f, "sequenceIndex", 1); |
175 |
1 |
PA.setValue(f, "columnIndex", -1); |
176 |
1 |
f.findNext("e", false, false); |
177 |
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|
178 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
179 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
180 |
1 |
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); |
181 |
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182 |
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183 |
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184 |
1 |
assertEquals(PA.getValue(f, "columnIndex"), 0); |
185 |
1 |
f = new Finder(av); |
186 |
1 |
PA.setValue(f, "sequenceIndex", 1); |
187 |
1 |
PA.setValue(f, "columnIndex", 0); |
188 |
1 |
f.findNext("e", false, false); |
189 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
190 |
1 |
assertEquals(f.getSearchResults().getSize(), 1); |
191 |
1 |
List<SearchResultMatchI> matches = f.getSearchResults().getResults(); |
192 |
1 |
assertEquals(matches.get(0).getStart(), 5); |
193 |
1 |
assertEquals(matches.get(0).getEnd(), 5); |
194 |
1 |
assertSame(matches.get(0).getSequence(), al.getSequenceAt(1)); |
195 |
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|
196 |
1 |
assertEquals(PA.getValue(f, "sequenceIndex"), 1); |
197 |
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|
198 |
1 |
assertEquals(PA.getValue(f, "columnIndex"), 7); |
199 |
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200 |
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201 |
1 |
f = new Finder(av); |
202 |
1 |
PA.setValue(f, "sequenceIndex", 1); |
203 |
1 |
PA.setValue(f, "columnIndex", 7); |
204 |
1 |
f.findNext("e", false, false); |
205 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
206 |
1 |
assertSame(f.getIdMatches().get(0), al.getSequenceAt(2)); |
207 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
208 |
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} |
209 |
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210 |
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211 |
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212 |
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| 100% |
Uncovered Elements: 0 (37) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
213 |
1 |
@Test(groups = "Functional")... |
214 |
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public void testFind_inDescription() |
215 |
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{ |
216 |
1 |
AlignmentI al2 = new Alignment(al); |
217 |
1 |
al2.getSequenceAt(0).setDescription("BRAF"); |
218 |
1 |
al2.getSequenceAt(1).setDescription("braf"); |
219 |
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220 |
1 |
AlignViewportI av2 = new AlignViewport(al2); |
221 |
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222 |
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223 |
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224 |
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225 |
1 |
Finder f = new Finder(av2); |
226 |
1 |
f.findNext("rAF", false, true); |
227 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
228 |
1 |
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); |
229 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
230 |
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231 |
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232 |
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233 |
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|
234 |
1 |
f = new Finder(av2); |
235 |
1 |
f.findAll("rAF", false, true); |
236 |
1 |
assertEquals(f.getIdMatches().size(), 2); |
237 |
1 |
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); |
238 |
1 |
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); |
239 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
240 |
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|
241 |
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242 |
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243 |
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|
244 |
1 |
f = new Finder(av2); |
245 |
1 |
f.findAll("RAF", true, true); |
246 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
247 |
1 |
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); |
248 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
249 |
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|
250 |
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|
251 |
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252 |
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|
253 |
1 |
al2.getSequenceAt(0).setDescription("the efh sequence"); |
254 |
1 |
al2.getSequenceAt(0).setName("mouseEFHkinase"); |
255 |
1 |
al2.getSequenceAt(1).setName("humanEFHkinase"); |
256 |
1 |
f = new Finder(av2); |
257 |
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|
258 |
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|
259 |
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|
260 |
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|
261 |
1 |
f.findAll("EFH", false, true); |
262 |
1 |
assertEquals(f.getIdMatches().size(), 2); |
263 |
1 |
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0)); |
264 |
1 |
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1)); |
265 |
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|
266 |
1 |
assertEquals(f.getSearchResults().getSize(), 2); |
267 |
1 |
SearchResultMatchI match = f.getSearchResults().getResults().get(0); |
268 |
1 |
assertSame(match.getSequence(), al2.getSequenceAt(1)); |
269 |
1 |
assertEquals(match.getStart(), 5); |
270 |
1 |
assertEquals(match.getEnd(), 7); |
271 |
1 |
match = f.getSearchResults().getResults().get(1); |
272 |
1 |
assertSame(match.getSequence(), al2.getSequenceAt(2)); |
273 |
1 |
assertEquals(match.getStart(), 4); |
274 |
1 |
assertEquals(match.getEnd(), 6); |
275 |
|
} |
276 |
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|
277 |
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|
278 |
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|
279 |
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|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
280 |
1 |
@Test(groups = "Functional")... |
281 |
|
public void testFindAll_sequenceIds() |
282 |
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{ |
283 |
1 |
Finder f = new Finder(av); |
284 |
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285 |
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286 |
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287 |
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288 |
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|
289 |
1 |
f.findAll("SEQ1", false, false); |
290 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
291 |
1 |
assertSame(f.getIdMatches().get(0), al.getSequenceAt(0)); |
292 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
293 |
1 |
assertTrue(searchResults.isEmpty()); |
294 |
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|
295 |
|
|
296 |
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|
297 |
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|
298 |
1 |
f = new Finder(av); |
299 |
1 |
f.findAll("SEQ1", true, false); |
300 |
1 |
searchResults = f.getSearchResults(); |
301 |
1 |
assertTrue(searchResults.isEmpty()); |
302 |
|
|
303 |
|
|
304 |
|
|
305 |
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|
306 |
1 |
AlignmentI al2 = new Alignment(al); |
307 |
1 |
AlignViewportI av2 = new AlignViewport(al2); |
308 |
1 |
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ")); |
309 |
1 |
f = new Finder(av2); |
310 |
1 |
f.findAll("ABZ", false, false); |
311 |
1 |
assertEquals(f.getIdMatches().size(), 1); |
312 |
1 |
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4)); |
313 |
1 |
searchResults = f.getSearchResults(); |
314 |
1 |
assertEquals(searchResults.getSize(), 2); |
315 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
316 |
1 |
assertSame(match.getSequence(), al2.getSequenceAt(4)); |
317 |
1 |
assertEquals(match.getStart(), 4); |
318 |
1 |
assertEquals(match.getEnd(), 6); |
319 |
1 |
match = searchResults.getResults().get(1); |
320 |
1 |
assertSame(match.getSequence(), al2.getSequenceAt(4)); |
321 |
1 |
assertEquals(match.getStart(), 10); |
322 |
1 |
assertEquals(match.getEnd(), 12); |
323 |
|
} |
324 |
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|
325 |
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|
326 |
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|
327 |
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|
|
|
| 100% |
Uncovered Elements: 0 (39) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
328 |
1 |
@Test(groups = "Functional")... |
329 |
|
public void testFind_findNext() |
330 |
|
{ |
331 |
|
|
332 |
|
|
333 |
|
|
334 |
1 |
FinderI f = new Finder(av); |
335 |
1 |
f.findNext("EfH", false, false); |
336 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
337 |
1 |
assertEquals(searchResults.getSize(), 1); |
338 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
339 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
340 |
1 |
assertEquals(match.getStart(), 5); |
341 |
1 |
assertEquals(match.getEnd(), 7); |
342 |
|
|
343 |
|
|
344 |
|
|
345 |
|
|
346 |
1 |
f = new Finder(av); |
347 |
1 |
f.findNext("I", false, false); |
348 |
1 |
searchResults = f.getSearchResults(); |
349 |
1 |
assertEquals(searchResults.getSize(), 1); |
350 |
1 |
match = searchResults.getResults().get(0); |
351 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
352 |
1 |
assertEquals(match.getStart(), 16); |
353 |
1 |
assertEquals(match.getEnd(), 16); |
354 |
|
|
355 |
1 |
f.findNext("I", false, false); |
356 |
1 |
searchResults = f.getSearchResults(); |
357 |
1 |
assertEquals(searchResults.getSize(), 1); |
358 |
1 |
match = searchResults.getResults().get(0); |
359 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
360 |
1 |
assertEquals(match.getStart(), 18); |
361 |
1 |
assertEquals(match.getEnd(), 18); |
362 |
|
|
363 |
1 |
f.findNext("I", false, false); |
364 |
1 |
searchResults = f.getSearchResults(); |
365 |
1 |
assertEquals(searchResults.getSize(), 1); |
366 |
1 |
match = searchResults.getResults().get(0); |
367 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
368 |
1 |
assertEquals(match.getStart(), 8); |
369 |
1 |
assertEquals(match.getEnd(), 8); |
370 |
|
|
371 |
1 |
f.findNext("I", false, false); |
372 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
373 |
|
|
374 |
|
|
375 |
|
|
376 |
|
|
377 |
1 |
f.findNext("I", false, false); |
378 |
1 |
searchResults = f.getSearchResults(); |
379 |
1 |
assertEquals(searchResults.getSize(), 1); |
380 |
1 |
match = searchResults.getResults().get(0); |
381 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
382 |
1 |
assertEquals(match.getStart(), 16); |
383 |
1 |
assertEquals(match.getEnd(), 16); |
384 |
|
} |
385 |
|
|
386 |
|
|
387 |
|
|
388 |
|
|
389 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
|
|
390 |
1 |
@Test(groups = "Functional")... |
391 |
|
public void testFind_maximalResultOnly() |
392 |
|
{ |
393 |
1 |
Finder f = new Finder(av); |
394 |
1 |
f.findAll("M+", false, false); |
395 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
396 |
1 |
assertEquals(searchResults.getSize(), 1); |
397 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
398 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(3)); |
399 |
1 |
assertEquals(match.getStart(), 4); |
400 |
1 |
assertEquals(match.getEnd(), 8); |
401 |
|
} |
402 |
|
|
403 |
|
|
404 |
|
|
405 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
406 |
1 |
@Test(groups = "Functional")... |
407 |
|
public void testFind_findAll() |
408 |
|
{ |
409 |
1 |
Finder f = new Finder(av); |
410 |
1 |
f.findAll("EfH", false, false); |
411 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
412 |
1 |
assertEquals(searchResults.getSize(), 2); |
413 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
414 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
415 |
1 |
assertEquals(match.getStart(), 5); |
416 |
1 |
assertEquals(match.getEnd(), 7); |
417 |
1 |
match = searchResults.getResults().get(1); |
418 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(2)); |
419 |
1 |
assertEquals(match.getStart(), 4); |
420 |
1 |
assertEquals(match.getEnd(), 6); |
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
|
425 |
1 |
f.findAll("I", false, false); |
426 |
1 |
searchResults = f.getSearchResults(); |
427 |
1 |
assertEquals(searchResults.getSize(), 3); |
428 |
1 |
match = searchResults.getResults().get(0); |
429 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
430 |
1 |
assertEquals(match.getStart(), 16); |
431 |
1 |
assertEquals(match.getEnd(), 16); |
432 |
1 |
match = searchResults.getResults().get(1); |
433 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
434 |
1 |
assertEquals(match.getStart(), 18); |
435 |
1 |
assertEquals(match.getEnd(), 18); |
436 |
1 |
match = searchResults.getResults().get(2); |
437 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
438 |
1 |
assertEquals(match.getStart(), 8); |
439 |
1 |
assertEquals(match.getEnd(), 8); |
440 |
|
} |
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
445 |
1 |
@Test(groups = "Functional")... |
446 |
|
public void testFind_findAllCaseSensitive() |
447 |
|
{ |
448 |
1 |
Finder f = new Finder(av); |
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
1 |
f.findAll("BC", true, false); |
454 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
455 |
1 |
assertEquals(searchResults.getSize(), 2); |
456 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
457 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
458 |
1 |
assertEquals(match.getStart(), 9); |
459 |
1 |
assertEquals(match.getEnd(), 10); |
460 |
1 |
match = searchResults.getResults().get(1); |
461 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
462 |
1 |
assertEquals(match.getStart(), 2); |
463 |
1 |
assertEquals(match.getEnd(), 3); |
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
468 |
1 |
f = new Finder(av); |
469 |
1 |
f.findAll("bc", true, false); |
470 |
1 |
searchResults = f.getSearchResults(); |
471 |
1 |
assertEquals(searchResults.getSize(), 1); |
472 |
1 |
match = searchResults.getResults().get(0); |
473 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(2)); |
474 |
1 |
assertEquals(match.getStart(), 1); |
475 |
1 |
assertEquals(match.getEnd(), 2); |
476 |
|
|
477 |
1 |
f.findAll("bC", true, false); |
478 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
479 |
|
} |
480 |
|
|
481 |
|
|
482 |
|
|
483 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (35) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
484 |
1 |
@Test(groups = "Functional")... |
485 |
|
public void testFind_inSelection() |
486 |
|
{ |
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
1 |
SequenceGroup sg = new SequenceGroup(); |
493 |
1 |
sg.setStartRes(3); |
494 |
1 |
sg.setEndRes(5); |
495 |
1 |
sg.addSequence(al.getSequenceAt(1), false); |
496 |
1 |
sg.addSequence(al.getSequenceAt(2), false); |
497 |
1 |
av.setSelectionGroup(sg); |
498 |
|
|
499 |
1 |
FinderI f = new Finder(av); |
500 |
1 |
f.findNext("b", false, false); |
501 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
502 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
503 |
1 |
assertEquals(searchResults.getSize(), 1); |
504 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
505 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
506 |
1 |
assertEquals(match.getStart(), 2); |
507 |
1 |
assertEquals(match.getEnd(), 2); |
508 |
|
|
509 |
|
|
510 |
|
|
511 |
|
|
512 |
1 |
f.findNext("b", false, false); |
513 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
514 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
515 |
|
|
516 |
1 |
f = new Finder(av); |
517 |
1 |
f.findNext("d", false, false); |
518 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
519 |
1 |
searchResults = f.getSearchResults(); |
520 |
1 |
assertEquals(searchResults.getSize(), 1); |
521 |
1 |
match = searchResults.getResults().get(0); |
522 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
523 |
1 |
assertEquals(match.getStart(), 4); |
524 |
1 |
assertEquals(match.getEnd(), 4); |
525 |
1 |
f.findNext("d", false, false); |
526 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
527 |
1 |
searchResults = f.getSearchResults(); |
528 |
1 |
assertEquals(searchResults.getSize(), 1); |
529 |
1 |
match = searchResults.getResults().get(0); |
530 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(2)); |
531 |
1 |
assertEquals(match.getStart(), 3); |
532 |
1 |
assertEquals(match.getEnd(), 3); |
533 |
|
} |
534 |
|
|
535 |
|
|
536 |
|
|
537 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
|
538 |
1 |
@Test(groups = "Functional")... |
539 |
|
public void testFind_findAllInSelection() |
540 |
|
{ |
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
1 |
SequenceGroup sg = new SequenceGroup(); |
547 |
1 |
sg.setStartRes(3); |
548 |
1 |
sg.setEndRes(5); |
549 |
1 |
sg.addSequence(al.getSequenceAt(1), false); |
550 |
1 |
sg.addSequence(al.getSequenceAt(2), false); |
551 |
1 |
av.setSelectionGroup(sg); |
552 |
|
|
553 |
|
|
554 |
|
|
555 |
|
|
556 |
1 |
Finder f = new Finder(av); |
557 |
1 |
f.findAll("e", false, false); |
558 |
1 |
assertEquals(f.getIdMatches().size(), 2); |
559 |
1 |
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); |
560 |
1 |
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); |
561 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
562 |
1 |
assertEquals(searchResults.getSize(), 1); |
563 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
564 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(2)); |
565 |
1 |
assertEquals(match.getStart(), 4); |
566 |
1 |
assertEquals(match.getEnd(), 4); |
567 |
|
|
568 |
|
|
569 |
|
|
570 |
|
|
571 |
1 |
f = new Finder(av); |
572 |
1 |
f.findAll("Q", false, false); |
573 |
1 |
assertEquals(f.getIdMatches().size(), 2); |
574 |
1 |
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1)); |
575 |
1 |
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2)); |
576 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
577 |
|
} |
578 |
|
|
579 |
|
|
580 |
|
|
581 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (21) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
582 |
1 |
@Test(groups = "Functional")... |
583 |
|
public void testFind_findAllInSelectionWithShortSequence() |
584 |
|
{ |
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
|
589 |
|
|
590 |
1 |
SequenceGroup sg = new SequenceGroup(); |
591 |
1 |
sg.setStartRes(9); |
592 |
1 |
sg.setEndRes(11); |
593 |
1 |
sg.addSequence(al.getSequenceAt(0), false); |
594 |
1 |
sg.addSequence(al.getSequenceAt(1), false); |
595 |
1 |
sg.addSequence(al.getSequenceAt(2), false); |
596 |
1 |
sg.addSequence(al.getSequenceAt(3), false); |
597 |
1 |
av.setSelectionGroup(sg); |
598 |
|
|
599 |
|
|
600 |
|
|
601 |
|
|
602 |
1 |
Finder f = new Finder(av); |
603 |
1 |
f.findAll("I", false, false); |
604 |
1 |
assertTrue(f.getIdMatches().isEmpty()); |
605 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
606 |
1 |
assertEquals(searchResults.getSize(), 2); |
607 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
608 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(0)); |
609 |
1 |
assertEquals(match.getStart(), 16); |
610 |
1 |
assertEquals(match.getEnd(), 16); |
611 |
1 |
match = searchResults.getResults().get(1); |
612 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
613 |
1 |
assertEquals(match.getStart(), 8); |
614 |
1 |
assertEquals(match.getEnd(), 8); |
615 |
|
} |
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (32) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
620 |
1 |
@Test(groups = "Functional")... |
621 |
|
public void testFind_withHiddenColumns() |
622 |
|
{ |
623 |
|
|
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
|
633 |
|
|
634 |
1 |
HiddenColumns hc = new HiddenColumns(); |
635 |
1 |
hc.hideColumns(2, 4); |
636 |
1 |
al.setHiddenColumns(hc); |
637 |
|
|
638 |
|
|
639 |
|
|
640 |
|
|
641 |
|
|
642 |
1 |
Finder f = new Finder(av); |
643 |
1 |
f.findAll("D", false, false); |
644 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
645 |
1 |
assertEquals(searchResults.getSize(), 1); |
646 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
647 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
648 |
1 |
assertEquals(match.getStart(), 4); |
649 |
1 |
assertEquals(match.getEnd(), 4); |
650 |
|
|
651 |
|
|
652 |
|
|
653 |
|
|
654 |
|
|
655 |
1 |
hc.hideColumns(2, 5); |
656 |
1 |
f = new Finder(av); |
657 |
1 |
f.findAll("aaa", false, false); |
658 |
1 |
searchResults = f.getSearchResults(); |
659 |
1 |
assertEquals(searchResults.getSize(), 1); |
660 |
1 |
match = searchResults.getResults().get(0); |
661 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(3)); |
662 |
1 |
assertEquals(match.getStart(), 9); |
663 |
1 |
assertEquals(match.getEnd(), 11); |
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
|
668 |
1 |
f.findAll("BE", false, false); |
669 |
1 |
assertTrue(f.getSearchResults().isEmpty()); |
670 |
|
|
671 |
|
|
672 |
|
|
673 |
|
|
674 |
|
|
675 |
1 |
hc.revealAllHiddenColumns(new ColumnSelection()); |
676 |
1 |
hc.hideColumns(8, 13); |
677 |
1 |
f = new Finder(av); |
678 |
1 |
f.findNext("H", false, false); |
679 |
1 |
searchResults = f.getSearchResults(); |
680 |
1 |
assertEquals(searchResults.getSize(), 1); |
681 |
1 |
match = searchResults.getResults().get(0); |
682 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(2)); |
683 |
1 |
assertEquals(match.getStart(), 6); |
684 |
1 |
assertEquals(match.getEnd(), 6); |
685 |
|
} |
686 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (22) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
687 |
1 |
@Test(groups = "Functional")... |
688 |
|
public void testFind_withHiddenColumnsAndSelection() |
689 |
|
{ |
690 |
|
|
691 |
|
|
692 |
|
|
693 |
|
|
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
|
698 |
|
|
699 |
|
|
700 |
|
|
701 |
1 |
HiddenColumns hc = new HiddenColumns(); |
702 |
1 |
hc.hideColumns(2, 4); |
703 |
1 |
hc.hideColumns(6, 7); |
704 |
1 |
al.setHiddenColumns(hc); |
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
|
709 |
1 |
SequenceGroup sg = new SequenceGroup(); |
710 |
1 |
sg.addSequence(al.getSequenceAt(1), false); |
711 |
1 |
sg.addSequence(al.getSequenceAt(2), false); |
712 |
1 |
sg.setStartRes(0); |
713 |
1 |
sg.setEndRes(13); |
714 |
1 |
av.setSelectionGroup(sg); |
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
|
719 |
|
|
720 |
1 |
Finder f = new Finder(av); |
721 |
1 |
f.findAll("[AH]", false, false); |
722 |
1 |
SearchResultsI searchResults = f.getSearchResults(); |
723 |
1 |
assertEquals(searchResults.getSize(), 2); |
724 |
1 |
SearchResultMatchI match = searchResults.getResults().get(0); |
725 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
726 |
1 |
assertEquals(match.getStart(), 1); |
727 |
1 |
assertEquals(match.getEnd(), 1); |
728 |
1 |
match = searchResults.getResults().get(1); |
729 |
1 |
assertSame(match.getSequence(), al.getSequenceAt(1)); |
730 |
1 |
assertEquals(match.getStart(), 7); |
731 |
1 |
assertEquals(match.getEnd(), 7); |
732 |
|
} |
733 |
|
} |