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package jalview.commands; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertNull; |
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import static org.testng.AssertJUnit.assertSame; |
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import jalview.commands.EditCommand.Action; |
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import jalview.commands.EditCommand.Edit; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.SequenceFeatures; |
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import jalview.gui.JvOptionPane; |
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import java.util.List; |
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import java.util.Map; |
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import org.testng.Assert; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.BeforeMethod; |
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import org.testng.annotations.Test; |
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@author |
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| 87.2% |
Uncovered Elements: 54 (422) |
Complexity: 40 |
Complexity Density: 0.11 |
|
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public class EditCommandTest |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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7 |
private static int func(int i)... |
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{ |
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return i * (i + 1) / 2; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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1 |
@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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private EditCommand testee; |
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private SequenceI[] seqs; |
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private Alignment al; |
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| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
|
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@BeforeMethod(alwaysRun = true)... |
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public void setUp() |
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{ |
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testee = new EditCommand(); |
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seqs = new SequenceI[4]; |
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seqs[0] = new Sequence("seq0", "abcdefghjk"); |
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seqs[0].setDatasetSequence(new Sequence("seq0ds", "abcdefghjk")); |
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seqs[1] = new Sequence("seq1", "fghjklmnopq"); |
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seqs[1].setDatasetSequence(new Sequence("seq1ds", "fghjklmnopq")); |
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seqs[2] = new Sequence("seq2", "qrstuvwxyz"); |
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seqs[2].setDatasetSequence(new Sequence("seq2ds", "qrstuvwxyz")); |
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seqs[3] = new Sequence("seq3", "1234567890"); |
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seqs[3].setDatasetSequence(new Sequence("seq3ds", "1234567890")); |
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al = new Alignment(seqs); |
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al.setGapCharacter('?'); |
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} |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testAppendEdit_insertGap() |
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{ |
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testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true); |
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assertEquals("abcd???efghjk", seqs[0].getSequenceAsString()); |
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assertEquals("fghj???klmnopq", seqs[1].getSequenceAsString()); |
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assertEquals("qrst???uvwxyz", seqs[2].getSequenceAsString()); |
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assertEquals("1234???567890", seqs[3].getSequenceAsString()); |
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} |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testAppendEdit_deleteGap() |
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{ |
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testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); |
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assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
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assertEquals("fghjnopq", seqs[1].getSequenceAsString()); |
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assertEquals("qrstxyz", seqs[2].getSequenceAsString()); |
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assertEquals("1234890", seqs[3].getSequenceAsString()); |
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} |
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| 100% |
Uncovered Elements: 0 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testCut() |
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{ |
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Edit ec = testee.new Edit(Action.CUT, seqs, 4, 3, al); |
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EditCommand.cut(ec, new AlignmentI[] { al }); |
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assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
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assertEquals("fghjnopq", seqs[1].getSequenceAsString()); |
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assertEquals("qrstxyz", seqs[2].getSequenceAsString()); |
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assertEquals("1234890", seqs[3].getSequenceAsString()); |
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assertEquals("efg", new String(ec.string[0])); |
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assertEquals("klm", new String(ec.string[1])); |
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assertEquals("uvw", new String(ec.string[2])); |
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assertEquals("567", new String(ec.string[3])); |
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} |
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| 0% |
Uncovered Elements: 9 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
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@Test(groups = { "Functional" }, enabled = false)... |
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public void testPaste_addToAlignment() |
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{ |
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SequenceI[] newSeqs = new SequenceI[2]; |
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newSeqs[0] = new Sequence("newseq0", "ACEFKL"); |
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newSeqs[1] = new Sequence("newseq1", "JWMPDH"); |
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Edit ec = testee.new Edit(Action.PASTE, newSeqs, 0, al.getWidth(), al); |
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EditCommand.paste(ec, new AlignmentI[] { al }); |
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assertEquals(6, al.getSequences().size()); |
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assertEquals("1234567890", seqs[3].getSequenceAsString()); |
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assertEquals("ACEFKL", seqs[4].getSequenceAsString()); |
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assertEquals("JWMPDH", seqs[5].getSequenceAsString()); |
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} |
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164 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testUndo_insertGap() |
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{ |
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testee.appendEdit(Action.INSERT_GAP, seqs, 4, 3, al, true); |
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assertEquals("abcd???efghjk", seqs[0].getSequenceAsString()); |
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testee.undoCommand(new AlignmentI[] { al }); |
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assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
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assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
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assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
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assertEquals("1234567890", seqs[3].getSequenceAsString()); |
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} |
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180 |
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181 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testUndo_deleteGap() |
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{ |
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testee.appendEdit(Action.DELETE_GAP, seqs, 4, 3, al, true); |
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assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
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testee.undoCommand(new AlignmentI[] { al }); |
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assertEquals("abcd???hjk", seqs[0].getSequenceAsString()); |
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assertEquals("fghj???nopq", seqs[1].getSequenceAsString()); |
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assertEquals("qrst???xyz", seqs[2].getSequenceAsString()); |
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assertEquals("1234???890", seqs[3].getSequenceAsString()); |
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} |
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196 |
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197 |
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198 |
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| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
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199 |
1 |
@Test(groups = { "Functional" })... |
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public void testUndo_multipleCommands() |
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{ |
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203 |
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testee.appendEdit(Action.DELETE_GAP, seqs, 2, 3, al, true); |
204 |
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assertEquals("abfghjk", seqs[0].getSequenceAsString()); |
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assertEquals("1267890", seqs[3].getSequenceAsString()); |
206 |
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207 |
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208 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 2, 2, al, true); |
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assertEquals("ab??fghjk", seqs[0].getSequenceAsString()); |
210 |
1 |
assertEquals("12??67890", seqs[3].getSequenceAsString()); |
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1 |
testee.appendEdit(Action.DELETE_GAP, seqs, 3, 3, al, true); |
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assertEquals("ab?hjk", seqs[0].getSequenceAsString()); |
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assertEquals("12?890", seqs[3].getSequenceAsString()); |
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1 |
testee.undoCommand(new AlignmentI[] { al }); |
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assertEquals("ab?????hjk", seqs[0].getSequenceAsString()); |
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assertEquals("12?????890", seqs[3].getSequenceAsString()); |
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} |
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225 |
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226 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
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227 |
1 |
@Test(groups = { "Functional" })... |
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public void testUndo_multipleInsertGaps() |
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{ |
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testee.appendEdit(Action.INSERT_GAP, seqs, 4, 1, al, true); |
231 |
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testee.appendEdit(Action.INSERT_GAP, seqs, 5, 1, al, true); |
232 |
1 |
testee.appendEdit(Action.INSERT_GAP, seqs, 6, 1, al, true); |
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235 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
236 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
237 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
238 |
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239 |
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} |
240 |
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241 |
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242 |
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243 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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244 |
1 |
@Test(groups = { "Functional" })... |
245 |
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public void testUndo_cut() |
246 |
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{ |
247 |
1 |
testee.appendEdit(Action.CUT, seqs, 4, 3, al, true); |
248 |
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249 |
1 |
assertEquals("abcdhjk", seqs[0].getSequenceAsString()); |
250 |
1 |
testee.undoCommand(new AlignmentI[] { al }); |
251 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
252 |
1 |
assertEquals("fghjklmnopq", seqs[1].getSequenceAsString()); |
253 |
1 |
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
254 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
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} |
256 |
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257 |
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258 |
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259 |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
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260 |
1 |
@Test(groups = { "Functional" })... |
261 |
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public void testReplace() |
262 |
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{ |
263 |
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264 |
1 |
seqs[1].createDatasetSequence(); |
265 |
1 |
new EditCommand("", Action.REPLACE, "ZXY", new SequenceI[] { seqs[1] }, |
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4, 8, al); |
267 |
1 |
assertEquals("abcdefghjk", seqs[0].getSequenceAsString()); |
268 |
1 |
assertEquals("qrstuvwxyz", seqs[2].getSequenceAsString()); |
269 |
1 |
assertEquals("1234567890", seqs[3].getSequenceAsString()); |
270 |
1 |
seqs[1] = new Sequence("seq1", "fghjZXYnopq"); |
271 |
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} |
272 |
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273 |
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274 |
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275 |
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276 |
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| 100% |
Uncovered Elements: 0 (25) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
|
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277 |
1 |
@Test(groups = { "Functional" })... |
278 |
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public void testAddEdit_multipleInsertGap() |
279 |
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{ |
280 |
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281 |
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282 |
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283 |
1 |
Edit e = new EditCommand().new Edit(Action.INSERT_GAP, |
284 |
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new SequenceI[] { seqs[0] }, 1, 1, al); |
285 |
1 |
testee.addEdit(e); |
286 |
1 |
SequenceI edited = new Sequence("seq0", "a?bcdefghjk"); |
287 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
288 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
289 |
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new SequenceI[] { edited }, 2, 1, al); |
290 |
1 |
testee.addEdit(e); |
291 |
1 |
edited = new Sequence("seq0", "a??bcdefghjk"); |
292 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
293 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
294 |
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new SequenceI[] { edited }, 3, 1, al); |
295 |
1 |
testee.addEdit(e); |
296 |
1 |
assertEquals(1, testee.getSize()); |
297 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); |
298 |
1 |
assertEquals(1, testee.getEdit(0).getPosition()); |
299 |
1 |
assertEquals(3, testee.getEdit(0).getNumber()); |
300 |
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301 |
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302 |
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303 |
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304 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
305 |
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new SequenceI[] { edited }, 5, 2, al); |
306 |
1 |
testee.addEdit(e); |
307 |
1 |
assertEquals(2, testee.getSize()); |
308 |
1 |
assertEquals(5, testee.getEdit(1).getPosition()); |
309 |
1 |
assertEquals(2, testee.getEdit(1).getNumber()); |
310 |
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311 |
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312 |
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313 |
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314 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
315 |
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new SequenceI[] { edited }, 6, 2, al); |
316 |
1 |
testee.addEdit(e); |
317 |
1 |
assertEquals(3, testee.getSize()); |
318 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction()); |
319 |
1 |
assertEquals(6, testee.getEdit(2).getPosition()); |
320 |
1 |
assertEquals(2, testee.getEdit(2).getNumber()); |
321 |
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} |
322 |
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323 |
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324 |
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325 |
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326 |
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| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
327 |
1 |
@Test(groups = { "Functional" })... |
328 |
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public void testAddEdit_multipleDeleteGap() |
329 |
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{ |
330 |
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331 |
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332 |
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|
333 |
1 |
seqs[0].setSequence("a???bcdefghjk"); |
334 |
1 |
Edit e = new EditCommand().new Edit(Action.DELETE_GAP, |
335 |
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new SequenceI[] { seqs[0] }, 4, 1, al); |
336 |
1 |
testee.addEdit(e); |
337 |
1 |
assertEquals(1, testee.getSize()); |
338 |
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|
339 |
1 |
SequenceI edited = new Sequence("seq0", "a??bcdefghjk"); |
340 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
341 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
342 |
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new SequenceI[] { edited }, 3, 1, al); |
343 |
1 |
testee.addEdit(e); |
344 |
1 |
assertEquals(1, testee.getSize()); |
345 |
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|
346 |
1 |
edited = new Sequence("seq0", "a?bcdefghjk"); |
347 |
1 |
edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
348 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
349 |
|
new SequenceI[] { edited }, 2, 1, al); |
350 |
1 |
testee.addEdit(e); |
351 |
1 |
assertEquals(1, testee.getSize()); |
352 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); |
353 |
1 |
assertEquals(2, testee.getEdit(0).getPosition()); |
354 |
1 |
assertEquals(3, testee.getEdit(0).getNumber()); |
355 |
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|
356 |
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|
357 |
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|
358 |
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|
359 |
1 |
e = new EditCommand().new Edit(Action.DELETE_GAP, |
360 |
|
new SequenceI[] { edited }, 2, 1, al); |
361 |
1 |
testee.addEdit(e); |
362 |
1 |
assertEquals(2, testee.getSize()); |
363 |
1 |
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction()); |
364 |
1 |
assertEquals(2, testee.getEdit(1).getPosition()); |
365 |
1 |
assertEquals(1, testee.getEdit(1).getNumber()); |
366 |
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|
367 |
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|
368 |
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|
369 |
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|
370 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, |
371 |
|
new SequenceI[] { edited }, 1, 1, al); |
372 |
1 |
testee.addEdit(e); |
373 |
1 |
assertEquals(3, testee.getSize()); |
374 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction()); |
375 |
1 |
assertEquals(1, testee.getEdit(2).getPosition()); |
376 |
1 |
assertEquals(1, testee.getEdit(2).getNumber()); |
377 |
|
} |
378 |
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|
379 |
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|
380 |
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|
381 |
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|
382 |
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|
383 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
384 |
1 |
@Test(groups = { "Functional" })... |
385 |
|
public void testAddEdit_removeAllGaps() |
386 |
|
{ |
387 |
1 |
seqs[0].setSequence("a???bcdefghjk"); |
388 |
1 |
Edit e = new EditCommand().new Edit(Action.DELETE_GAP, |
389 |
|
new SequenceI[] { seqs[0] }, 4, 1, al); |
390 |
1 |
testee.addEdit(e); |
391 |
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|
392 |
1 |
seqs[1].setSequence("f??ghjklmnopq"); |
393 |
1 |
Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[] |
394 |
|
{ seqs[1] }, 3, 1, al); |
395 |
1 |
testee.addEdit(e2); |
396 |
1 |
assertEquals(2, testee.getSize()); |
397 |
1 |
assertSame(e, testee.getEdit(0)); |
398 |
1 |
assertSame(e2, testee.getEdit(1)); |
399 |
|
} |
400 |
|
|
401 |
|
|
402 |
|
|
403 |
|
|
404 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
|
|
405 |
1 |
@Test(groups = { "Functional" })... |
406 |
|
public void testAddEdit_groupInsertGaps() |
407 |
|
{ |
408 |
|
|
409 |
|
|
410 |
|
|
411 |
1 |
Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { |
412 |
|
seqs[0], seqs[1] }, 1, 1, al); |
413 |
1 |
testee.addEdit(e); |
414 |
1 |
SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk"); |
415 |
1 |
seq1edited.setDatasetSequence(seqs[0].getDatasetSequence()); |
416 |
1 |
SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq"); |
417 |
1 |
seq2edited.setDatasetSequence(seqs[1].getDatasetSequence()); |
418 |
1 |
e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] { |
419 |
|
seq1edited, seq2edited }, 2, 1, al); |
420 |
1 |
testee.addEdit(e); |
421 |
|
|
422 |
1 |
assertEquals(1, testee.getSize()); |
423 |
1 |
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction()); |
424 |
1 |
assertEquals(1, testee.getEdit(0).getPosition()); |
425 |
1 |
assertEquals(2, testee.getEdit(0).getNumber()); |
426 |
1 |
assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0) |
427 |
|
.getSequences()[0].getDatasetSequence()); |
428 |
1 |
assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0) |
429 |
|
.getSequences()[1].getDatasetSequence()); |
430 |
|
} |
431 |
|
|
432 |
|
|
433 |
|
|
434 |
|
|
435 |
|
|
436 |
|
|
437 |
|
|
438 |
|
|
439 |
|
|
440 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
441 |
1 |
@Test(groups = { "Functional" })... |
442 |
|
public void testPriorState_multipleInserts() |
443 |
|
{ |
444 |
1 |
EditCommand command = new EditCommand(); |
445 |
1 |
SequenceI seq = new Sequence("", "--A--B-CDEF"); |
446 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
447 |
1 |
seq.setDatasetSequence(ds); |
448 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
449 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 1, 2, '-'); |
450 |
1 |
command.addEdit(e); |
451 |
1 |
e = command.new Edit(Action.INSERT_GAP, sqs, 4, 1, '-'); |
452 |
1 |
command.addEdit(e); |
453 |
1 |
e = command.new Edit(Action.INSERT_GAP, sqs, 0, 2, '-'); |
454 |
1 |
command.addEdit(e); |
455 |
|
|
456 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
457 |
1 |
assertEquals("ABCDEF", unwound.get(ds).getSequenceAsString()); |
458 |
|
} |
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
468 |
1 |
@Test(groups = { "Functional" })... |
469 |
|
public void testPriorState_removeAllGaps() |
470 |
|
{ |
471 |
1 |
EditCommand command = new EditCommand(); |
472 |
1 |
SequenceI seq = new Sequence("", "ABC"); |
473 |
1 |
SequenceI ds = new Sequence("", "ABC"); |
474 |
1 |
seq.setDatasetSequence(ds); |
475 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
476 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-'); |
477 |
1 |
command.addEdit(e); |
478 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-'); |
479 |
1 |
command.addEdit(e); |
480 |
|
|
481 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
482 |
1 |
assertEquals("A-B-C", unwound.get(ds).getSequenceAsString()); |
483 |
|
} |
484 |
|
|
485 |
|
|
486 |
|
|
487 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 1 |
Complexity Density: 0.11 |
1PASS
|
|
488 |
1 |
@Test(groups = { "Functional" })... |
489 |
|
public void testPriorState_singleDelete() |
490 |
|
{ |
491 |
1 |
EditCommand command = new EditCommand(); |
492 |
1 |
SequenceI seq = new Sequence("", "ABCDEF"); |
493 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
494 |
1 |
seq.setDatasetSequence(ds); |
495 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
496 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 2, 2, '-'); |
497 |
1 |
command.addEdit(e); |
498 |
|
|
499 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
500 |
1 |
assertEquals("AB--CDEF", unwound.get(ds).getSequenceAsString()); |
501 |
|
} |
502 |
|
|
503 |
|
|
504 |
|
|
505 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
506 |
1 |
@Test(groups = { "Functional" })... |
507 |
|
public void testPriorState_singleInsert() |
508 |
|
{ |
509 |
1 |
EditCommand command = new EditCommand(); |
510 |
1 |
SequenceI seq = new Sequence("", "AB---CDEF"); |
511 |
1 |
SequenceI ds = new Sequence("", "ABCDEF"); |
512 |
1 |
seq.setDatasetSequence(ds); |
513 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
514 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-'); |
515 |
1 |
command.addEdit(e); |
516 |
|
|
517 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
518 |
1 |
SequenceI prior = unwound.get(ds); |
519 |
1 |
assertEquals("ABCDEF", prior.getSequenceAsString()); |
520 |
1 |
assertEquals(1, prior.getStart()); |
521 |
1 |
assertEquals(6, prior.getEnd()); |
522 |
|
} |
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
|
527 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
528 |
1 |
@Test(groups = { "Functional" })... |
529 |
|
public void testPriorState_singleInsertWithOffset() |
530 |
|
{ |
531 |
1 |
EditCommand command = new EditCommand(); |
532 |
1 |
SequenceI seq = new Sequence("", "AB---CDEF", 8, 13); |
533 |
|
|
534 |
|
|
535 |
1 |
seq.createDatasetSequence(); |
536 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
537 |
1 |
Edit e = command.new Edit(Action.INSERT_GAP, sqs, 2, 3, '-'); |
538 |
1 |
command.addEdit(e); |
539 |
|
|
540 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
541 |
1 |
SequenceI prior = unwound.get(seq.getDatasetSequence()); |
542 |
1 |
assertEquals("ABCDEF", prior.getSequenceAsString()); |
543 |
1 |
assertEquals(8, prior.getStart()); |
544 |
1 |
assertEquals(13, prior.getEnd()); |
545 |
|
} |
546 |
|
|
547 |
|
|
548 |
|
|
549 |
|
|
550 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (36) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
551 |
1 |
@Test(groups = { "Functional" })... |
552 |
|
public void testPriorState_removeGapsMultipleSeqs() |
553 |
|
{ |
554 |
1 |
EditCommand command = new EditCommand(); |
555 |
1 |
String original1 = "--ABC-DEF"; |
556 |
1 |
String original2 = "FG-HI--J"; |
557 |
1 |
String original3 = "M-NOPQ"; |
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
1 |
SequenceI seq = new Sequence("", "ABC-DEF"); |
563 |
1 |
SequenceI ds1 = new Sequence("", "ABCDEF"); |
564 |
1 |
seq.setDatasetSequence(ds1); |
565 |
1 |
SequenceI[] sqs = new SequenceI[] { seq }; |
566 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 2, '-'); |
567 |
1 |
command.addEdit(e); |
568 |
1 |
seq = new Sequence("", "ABCDEF"); |
569 |
1 |
seq.setDatasetSequence(ds1); |
570 |
1 |
sqs = new SequenceI[] { seq }; |
571 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 3, 1, '-'); |
572 |
1 |
command.addEdit(e); |
573 |
|
|
574 |
|
|
575 |
|
|
576 |
|
|
577 |
1 |
seq = new Sequence("", "FGHI--J"); |
578 |
1 |
SequenceI ds2 = new Sequence("", "FGHIJ"); |
579 |
1 |
seq.setDatasetSequence(ds2); |
580 |
1 |
sqs = new SequenceI[] { seq }; |
581 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 2, 1, '-'); |
582 |
1 |
command.addEdit(e); |
583 |
1 |
seq = new Sequence("", "FGHIJ"); |
584 |
1 |
seq.setDatasetSequence(ds2); |
585 |
1 |
sqs = new SequenceI[] { seq }; |
586 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-'); |
587 |
1 |
command.addEdit(e); |
588 |
|
|
589 |
|
|
590 |
|
|
591 |
|
|
592 |
1 |
seq = new Sequence("", "MNOPQ"); |
593 |
1 |
SequenceI ds3 = new Sequence("", "MNOPQ"); |
594 |
1 |
seq.setDatasetSequence(ds3); |
595 |
1 |
sqs = new SequenceI[] { seq }; |
596 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 1, 1, '-'); |
597 |
1 |
command.addEdit(e); |
598 |
|
|
599 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
600 |
1 |
assertEquals(original1, unwound.get(ds1).getSequenceAsString()); |
601 |
1 |
assertEquals(original2, unwound.get(ds2).getSequenceAsString()); |
602 |
1 |
assertEquals(original3, unwound.get(ds3).getSequenceAsString()); |
603 |
|
} |
604 |
|
|
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (32) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
610 |
1 |
@Test(groups = { "Functional" })... |
611 |
|
public void testPriorState_removeGappedCols() |
612 |
|
{ |
613 |
1 |
EditCommand command = new EditCommand(); |
614 |
1 |
String original1 = "--ABC--DEF"; |
615 |
1 |
String original2 = "-G-HI--J"; |
616 |
1 |
String original3 = "-M-NO--PQ"; |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
1 |
SequenceI seq1 = new Sequence("", "-ABC--DEF"); |
622 |
1 |
SequenceI ds1 = new Sequence("", "ABCDEF"); |
623 |
1 |
seq1.setDatasetSequence(ds1); |
624 |
1 |
SequenceI seq2 = new Sequence("", "G-HI--J"); |
625 |
1 |
SequenceI ds2 = new Sequence("", "GHIJ"); |
626 |
1 |
seq2.setDatasetSequence(ds2); |
627 |
1 |
SequenceI seq3 = new Sequence("", "M-NO--PQ"); |
628 |
1 |
SequenceI ds3 = new Sequence("", "MNOPQ"); |
629 |
1 |
seq3.setDatasetSequence(ds3); |
630 |
1 |
SequenceI[] sqs = new SequenceI[] { seq1, seq2, seq3 }; |
631 |
1 |
Edit e = command.new Edit(Action.DELETE_GAP, sqs, 0, 1, '-'); |
632 |
1 |
command.addEdit(e); |
633 |
|
|
634 |
|
|
635 |
|
|
636 |
|
|
637 |
1 |
seq1 = new Sequence("", "-ABCDEF"); |
638 |
1 |
seq1.setDatasetSequence(ds1); |
639 |
1 |
seq2 = new Sequence("", "G-HIJ"); |
640 |
1 |
seq2.setDatasetSequence(ds2); |
641 |
1 |
seq3 = new Sequence("", "M-NOPQ"); |
642 |
1 |
seq3.setDatasetSequence(ds3); |
643 |
1 |
sqs = new SequenceI[] { seq1, seq2, seq3 }; |
644 |
1 |
e = command.new Edit(Action.DELETE_GAP, sqs, 4, 2, '-'); |
645 |
1 |
command.addEdit(e); |
646 |
|
|
647 |
1 |
Map<SequenceI, SequenceI> unwound = command.priorState(false); |
648 |
1 |
assertEquals(original1, unwound.get(ds1).getSequenceAsString()); |
649 |
1 |
assertEquals(original2, unwound.get(ds2).getSequenceAsString()); |
650 |
1 |
assertEquals(original3, unwound.get(ds3).getSequenceAsString()); |
651 |
1 |
assertEquals(ds1, unwound.get(ds1).getDatasetSequence()); |
652 |
1 |
assertEquals(ds2, unwound.get(ds2).getDatasetSequence()); |
653 |
1 |
assertEquals(ds3, unwound.get(ds3).getDatasetSequence()); |
654 |
|
} |
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
|
|
| 0% |
Uncovered Elements: 27 (27) |
Complexity: 1 |
Complexity Density: 0.04 |
3FAIL
|
|
659 |
0 |
@Test(groups = { "Functional" })... |
660 |
|
public void testCut_withFeatures() |
661 |
|
{ |
662 |
|
|
663 |
|
|
664 |
|
|
665 |
|
|
666 |
0 |
SequenceI seq0 = seqs[0]; |
667 |
0 |
seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f, |
668 |
|
null)); |
669 |
0 |
seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6, |
670 |
|
0f, null)); |
671 |
0 |
seq0.addSequenceFeature(new SequenceFeature("internal", "", 5, 6, 0f, |
672 |
|
null)); |
673 |
0 |
seq0.addSequenceFeature(new SequenceFeature("overlap right", "", 7, 8, |
674 |
|
0f, null)); |
675 |
0 |
seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f, |
676 |
|
null)); |
677 |
|
|
678 |
0 |
Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); |
679 |
0 |
EditCommand.cut(ec, new AlignmentI[] { al }); |
680 |
|
|
681 |
0 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
682 |
0 |
SequenceFeatures.sortFeatures(sfs, true); |
683 |
|
|
684 |
0 |
assertEquals(4, sfs.size()); |
685 |
0 |
SequenceFeature sf = sfs.get(0); |
686 |
0 |
assertEquals("before", sf.getType()); |
687 |
0 |
assertEquals(1, sf.getBegin()); |
688 |
0 |
assertEquals(3, sf.getEnd()); |
689 |
0 |
sf = sfs.get(1); |
690 |
0 |
assertEquals("overlap left", sf.getType()); |
691 |
0 |
assertEquals(2, sf.getBegin()); |
692 |
0 |
assertEquals(3, sf.getEnd()); |
693 |
0 |
sf = sfs.get(2); |
694 |
0 |
assertEquals("overlap right", sf.getType()); |
695 |
0 |
assertEquals(4, sf.getBegin()); |
696 |
0 |
assertEquals(5, sf.getEnd()); |
697 |
0 |
sf = sfs.get(3); |
698 |
0 |
assertEquals("after", sf.getType()); |
699 |
0 |
assertEquals(4, sf.getBegin()); |
700 |
0 |
assertEquals(6, sf.getEnd()); |
701 |
|
} |
702 |
|
|
703 |
|
|
704 |
|
|
705 |
|
|
706 |
|
|
|
|
| 92.1% |
Uncovered Elements: 3 (38) |
Complexity: 7 |
Complexity Density: 0.27 |
1PASS
|
|
707 |
1 |
@Test(groups = { "Functional" })... |
708 |
|
public void testCut_withFeatures_exhaustive() |
709 |
|
{ |
710 |
|
|
711 |
|
|
712 |
|
|
713 |
1 |
SequenceI seq0 = new Sequence("seq", "ABCDE"); |
714 |
1 |
AlignmentI alignment = new Alignment(new SequenceI[] { seq0 }); |
715 |
1 |
alignment.setDataset(null); |
716 |
6 |
for (int from = 1; from <= seq0.getLength(); from++) |
717 |
|
{ |
718 |
20 |
for (int to = from; to <= seq0.getLength(); to++) |
719 |
|
{ |
720 |
15 |
String desc = String.format("%d-%d", from, to); |
721 |
15 |
SequenceFeature sf = new SequenceFeature("test", desc, from, to, |
722 |
|
0f, |
723 |
|
null); |
724 |
15 |
sf.setValue("from", Integer.valueOf(from)); |
725 |
15 |
sf.setValue("to", Integer.valueOf(to)); |
726 |
15 |
seq0.addSequenceFeature(sf); |
727 |
|
} |
728 |
|
} |
729 |
|
|
730 |
1 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
731 |
1 |
assertEquals(func(5), sfs.size()); |
732 |
|
|
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
|
737 |
1 |
SequenceI[] sqs = new SequenceI[] { seq0 }; |
738 |
|
|
739 |
|
|
740 |
|
|
741 |
|
|
742 |
|
|
743 |
3 |
for (int from = 1; from < 3; from++) |
744 |
|
{ |
745 |
4 |
for (int to = 2; to < 3; to++) |
746 |
|
{ |
747 |
2 |
testee.appendEdit(Action.CUT, sqs, from, (to - from + 1), |
748 |
|
alignment, true); |
749 |
|
|
750 |
2 |
sfs = seq0.getSequenceFeatures(); |
751 |
|
|
752 |
|
|
753 |
|
|
754 |
|
|
755 |
|
|
756 |
|
|
757 |
2 |
String msg = String.format("Cut %d-%d ", from, to); |
758 |
2 |
if (to - from == 4) |
759 |
|
{ |
760 |
|
|
761 |
0 |
assertNull(sfs); |
762 |
|
} |
763 |
|
else |
764 |
|
{ |
765 |
2 |
assertEquals(msg + "wrong number of features left", func(5) |
766 |
|
- func(to - from + 1), sfs.size()); |
767 |
|
} |
768 |
|
|
769 |
|
|
770 |
|
|
771 |
|
|
772 |
2 |
if (sfs != null) |
773 |
|
{ |
774 |
2 |
for (SequenceFeature sf : sfs) |
775 |
|
{ |
776 |
26 |
checkFeatureRelocation(sf, from + 1, to + 1); |
777 |
|
} |
778 |
|
} |
779 |
|
|
780 |
|
|
781 |
|
|
782 |
2 |
testee.undoCommand(new AlignmentI[] { alignment }); |
783 |
2 |
assertEquals(func(5), seq0.getSequenceFeatures().size()); |
784 |
|
} |
785 |
|
} |
786 |
|
} |
787 |
|
|
788 |
|
|
789 |
|
|
790 |
|
|
791 |
|
@param |
792 |
|
@param |
793 |
|
|
794 |
|
@param |
795 |
|
|
796 |
|
|
|
|
| 93.1% |
Uncovered Elements: 2 (29) |
Complexity: 7 |
Complexity Density: 0.37 |
|
797 |
26 |
private void checkFeatureRelocation(SequenceFeature sf, int from, int to)... |
798 |
|
{ |
799 |
|
|
800 |
26 |
int cutSize = to - from + 1; |
801 |
26 |
int oldFrom = ((Integer) sf.getValue("from")).intValue(); |
802 |
26 |
int oldTo = ((Integer) sf.getValue("to")).intValue(); |
803 |
|
|
804 |
26 |
String msg = String.format( |
805 |
|
"Feature %s relocated to %d-%d after cut of %d-%d", |
806 |
|
sf.getDescription(), sf.getBegin(), sf.getEnd(), from, to); |
807 |
26 |
if (oldTo < from) |
808 |
|
{ |
809 |
|
|
810 |
4 |
assertEquals("1: " + msg, oldFrom, sf.getBegin()); |
811 |
4 |
assertEquals("2: " + msg, oldTo, sf.getEnd()); |
812 |
|
} |
813 |
22 |
else if (oldFrom > to) |
814 |
|
{ |
815 |
|
|
816 |
6 |
assertEquals("3: " + msg, oldFrom - cutSize, sf.getBegin()); |
817 |
6 |
assertEquals("4: " + msg, oldTo - cutSize, sf.getEnd()); |
818 |
|
} |
819 |
16 |
else if (oldFrom < from && oldTo > to) |
820 |
|
{ |
821 |
|
|
822 |
6 |
assertEquals("5: " + msg, oldFrom, sf.getBegin()); |
823 |
6 |
assertEquals("6: " + msg, oldTo - cutSize, sf.getEnd()); |
824 |
|
} |
825 |
10 |
else if (oldFrom < from) |
826 |
|
{ |
827 |
|
|
828 |
4 |
assertEquals("7: " + msg, from - 1, sf.getEnd()); |
829 |
|
} |
830 |
6 |
else if (oldTo > to) |
831 |
|
{ |
832 |
|
|
833 |
6 |
assertEquals("8: " + msg, from, sf.getBegin()); |
834 |
6 |
assertEquals("9: " + msg, from + oldTo - to - 1, sf.getEnd()); |
835 |
|
} |
836 |
|
else |
837 |
|
{ |
838 |
|
|
839 |
0 |
Assert.fail(msg + " - should have been deleted"); |
840 |
|
} |
841 |
|
} |
842 |
|
|
843 |
|
|
844 |
|
|
845 |
|
|
|
|
| 0% |
Uncovered Elements: 10 (10) |
Complexity: 1 |
Complexity Density: 0.1 |
3FAIL
|
|
846 |
0 |
@Test(groups = { "Functional" })... |
847 |
|
public void testCut_gappedWithFeatures() |
848 |
|
{ |
849 |
|
|
850 |
|
|
851 |
|
|
852 |
|
|
853 |
0 |
SequenceI seq0 = new Sequence("seq", "A-BCC"); |
854 |
0 |
seq0.addSequenceFeature(new SequenceFeature("", "", 3, 4, 0f, |
855 |
|
null)); |
856 |
0 |
AlignmentI alignment = new Alignment(new SequenceI[] { seq0 }); |
857 |
|
|
858 |
0 |
Edit ec = testee.new Edit(Action.CUT, seqs, 0, 3, alignment); |
859 |
|
|
860 |
0 |
EditCommand.cut(ec, new AlignmentI[] { alignment }); |
861 |
|
|
862 |
|
|
863 |
|
|
864 |
|
|
865 |
0 |
List<SequenceFeature> sfs = seq0.getSequenceFeatures(); |
866 |
0 |
assertEquals(1, sfs.size()); |
867 |
0 |
SequenceFeature sf = sfs.get(0); |
868 |
0 |
assertEquals(1, sf.getBegin()); |
869 |
0 |
assertEquals(2, sf.getEnd()); |
870 |
|
|
871 |
|
|
872 |
|
} |
873 |
|
} |