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package jalview.gui; |
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import static org.testng.Assert.assertEquals; |
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import static org.testng.Assert.assertNull; |
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import static org.testng.Assert.assertTrue; |
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import jalview.api.AlignViewportI; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.commands.EditCommand; |
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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.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.SeqPanel.MousePos; |
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import jalview.io.DataSourceType; |
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import jalview.io.FileLoader; |
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import jalview.util.MessageManager; |
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import jalview.viewmodel.ViewportRanges; |
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import java.awt.EventQueue; |
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import java.awt.event.MouseEvent; |
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import java.lang.reflect.InvocationTargetException; |
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import javax.swing.JLabel; |
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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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| 94.6% |
Uncovered Elements: 24 (442) |
Complexity: 18 |
Complexity Density: 0.04 |
|
56 |
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public class SeqPanelTest |
57 |
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{ |
58 |
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AlignFrame af; |
59 |
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|
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
60 |
1 |
@BeforeClass(alwaysRun = true)... |
61 |
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public void setUpJvOptionPane() |
62 |
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{ |
63 |
1 |
JvOptionPane.setInteractiveMode(false); |
64 |
1 |
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
65 |
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} |
|
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
|
|
66 |
1 |
@Test(groups = "Functional")... |
67 |
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public void testSetStatusReturnsNearestResiduePosition() |
68 |
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{ |
69 |
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SequenceI seq1 = new Sequence("Seq1", "AACDE"); |
70 |
1 |
SequenceI seq2 = new Sequence("Seq2", "AA--E"); |
71 |
1 |
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
72 |
1 |
AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), |
73 |
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al.getHeight()); |
74 |
1 |
AlignmentI visAl = alignFrame.getViewport().getAlignment(); |
75 |
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76 |
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77 |
1 |
assertEquals( |
78 |
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alignFrame.alignPanel.getSeqPanel().setStatusMessage( |
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visAl.getSequenceAt(1), 1, 1), 2); |
80 |
1 |
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(), |
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"Sequence 2 ID: Seq2 Residue: ALA (2)"); |
82 |
1 |
assertEquals( |
83 |
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alignFrame.alignPanel.getSeqPanel().setStatusMessage( |
84 |
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visAl.getSequenceAt(1), 4, 1), 3); |
85 |
1 |
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(), |
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"Sequence 2 ID: Seq2 Residue: GLU (3)"); |
87 |
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|
88 |
1 |
assertEquals( |
89 |
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alignFrame.alignPanel.getSeqPanel().setStatusMessage( |
90 |
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visAl.getSequenceAt(1), 2, 1), 3); |
91 |
1 |
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(), |
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"Sequence 2 ID: Seq2"); |
93 |
1 |
assertEquals( |
94 |
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alignFrame.alignPanel.getSeqPanel().setStatusMessage( |
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visAl.getSequenceAt(1), 3, 1), 3); |
96 |
1 |
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(), |
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"Sequence 2 ID: Seq2"); |
98 |
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} |
99 |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
|
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100 |
1 |
@Test(groups = "Functional")... |
101 |
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public void testAmbiguousAminoAcidGetsStatusMessage() |
102 |
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{ |
103 |
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SequenceI seq1 = new Sequence("Seq1", "ABCDE"); |
104 |
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SequenceI seq2 = new Sequence("Seq2", "AB--E"); |
105 |
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AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); |
106 |
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AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), |
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al.getHeight()); |
108 |
1 |
AlignmentI visAl = alignFrame.getViewport().getAlignment(); |
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110 |
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assertEquals( |
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alignFrame.alignPanel.getSeqPanel().setStatusMessage( |
112 |
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visAl.getSequenceAt(1), 1, 1), 2); |
113 |
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assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(), |
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"Sequence 2 ID: Seq2 Residue: B (2)"); |
115 |
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} |
116 |
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| 100% |
Uncovered Elements: 0 (21) |
Complexity: 1 |
Complexity Density: 0.05 |
1PASS
|
|
117 |
1 |
@Test(groups = "Functional")... |
118 |
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public void testGetEditStatusMessage() |
119 |
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{ |
120 |
1 |
assertNull(SeqPanel.getEditStatusMessage(null)); |
121 |
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|
122 |
1 |
EditCommand edit = new EditCommand(); |
123 |
1 |
assertNull(SeqPanel.getEditStatusMessage(edit)); |
124 |
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125 |
1 |
SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") }; |
126 |
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127 |
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128 |
1 |
edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-')); |
129 |
1 |
String expected = MessageManager.formatMessage("label.insert_gap", "1"); |
130 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
131 |
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132 |
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133 |
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edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 3, '-')); |
134 |
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expected = MessageManager.formatMessage("label.insert_gaps", "4"); |
135 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
136 |
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137 |
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138 |
1 |
edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-')); |
139 |
1 |
expected = MessageManager.formatMessage("label.insert_gaps", "2"); |
140 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
141 |
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142 |
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143 |
1 |
edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-')); |
144 |
1 |
assertNull(SeqPanel.getEditStatusMessage(edit)); |
145 |
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146 |
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147 |
1 |
edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-')); |
148 |
1 |
expected = MessageManager.formatMessage("label.delete_gap", "1"); |
149 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
150 |
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151 |
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152 |
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edit.addEdit(edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-')); |
153 |
1 |
expected = MessageManager.formatMessage("label.delete_gaps", "2"); |
154 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
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} |
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157 |
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158 |
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159 |
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|
160 |
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| 100% |
Uncovered Elements: 0 (44) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
161 |
1 |
@Test(groups = "Functional")... |
162 |
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public void testGetEditStatusMessage_lockedEditing() |
163 |
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{ |
164 |
1 |
EditCommand edit = new EditCommand(); |
165 |
1 |
SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") }; |
166 |
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167 |
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|
168 |
1 |
Edit e1 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-'); |
169 |
1 |
edit.addEdit(e1); |
170 |
1 |
Edit e2 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 1, '-'); |
171 |
1 |
e2.setSystemGenerated(true); |
172 |
1 |
edit.addEdit(e2); |
173 |
1 |
String expected = MessageManager.formatMessage("label.insert_gap", "1"); |
174 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
175 |
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|
176 |
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|
177 |
1 |
Edit e3 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-'); |
178 |
1 |
edit.addEdit(e3); |
179 |
1 |
Edit e4 = edit.new Edit(Action.DELETE_GAP, seqs, 5, 2, '-'); |
180 |
1 |
e4.setSystemGenerated(true); |
181 |
1 |
edit.addEdit(e4); |
182 |
1 |
expected = MessageManager.formatMessage("label.insert_gaps", "3"); |
183 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
184 |
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|
185 |
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|
186 |
1 |
Edit e5 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'); |
187 |
1 |
edit.addEdit(e5); |
188 |
1 |
Edit e6 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-'); |
189 |
1 |
e6.setSystemGenerated(true); |
190 |
1 |
edit.addEdit(e6); |
191 |
1 |
expected = MessageManager.formatMessage("label.insert_gap", "1"); |
192 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
193 |
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|
194 |
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|
195 |
1 |
Edit e7 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'); |
196 |
1 |
edit.addEdit(e7); |
197 |
1 |
Edit e8 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-'); |
198 |
1 |
e8.setSystemGenerated(true); |
199 |
1 |
edit.addEdit(e8); |
200 |
1 |
expected = MessageManager.formatMessage("label.insert_gaps", "2"); |
201 |
1 |
assertNull(SeqPanel.getEditStatusMessage(edit)); |
202 |
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|
203 |
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|
204 |
1 |
Edit e9 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-'); |
205 |
1 |
edit.addEdit(e9); |
206 |
1 |
Edit e10 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 1, '-'); |
207 |
1 |
e10.setSystemGenerated(true); |
208 |
1 |
edit.addEdit(e10); |
209 |
1 |
expected = MessageManager.formatMessage("label.delete_gap", "1"); |
210 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
211 |
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|
212 |
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|
213 |
1 |
Edit e11 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-'); |
214 |
1 |
edit.addEdit(e11); |
215 |
1 |
Edit e12 = edit.new Edit(Action.INSERT_GAP, seqs, 5, 2, '-'); |
216 |
1 |
e12.setSystemGenerated(true); |
217 |
1 |
edit.addEdit(e12); |
218 |
1 |
expected = MessageManager.formatMessage("label.delete_gaps", "3"); |
219 |
1 |
assertEquals(SeqPanel.getEditStatusMessage(edit), expected); |
220 |
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} |
221 |
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|
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|
| 0% |
Uncovered Elements: 18 (18) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
|
|
222 |
0 |
public void testFindMousePosition_unwrapped()... |
223 |
|
{ |
224 |
0 |
String seqData = ">Seq1\nAACDE\n>Seq2\nAA--E\n"; |
225 |
0 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seqData, |
226 |
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DataSourceType.PASTE); |
227 |
0 |
AlignViewportI av = alignFrame.getViewport(); |
228 |
0 |
av.setShowAnnotation(true); |
229 |
0 |
av.setWrapAlignment(false); |
230 |
0 |
final int charHeight = av.getCharHeight(); |
231 |
0 |
final int charWidth = av.getCharWidth(); |
232 |
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|
233 |
0 |
assertTrue(charHeight > 0); |
234 |
0 |
assertTrue(charWidth > 0); |
235 |
0 |
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0); |
236 |
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|
237 |
0 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
238 |
0 |
int x = 0; |
239 |
0 |
int y = 0; |
240 |
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|
241 |
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|
242 |
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|
243 |
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|
244 |
0 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, |
245 |
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0, 0, 0, false, 0); |
246 |
0 |
MousePos pos = testee.findMousePosition(evt); |
247 |
0 |
assertEquals(pos.column, 0); |
248 |
0 |
assertEquals(pos.seqIndex, 0); |
249 |
0 |
assertEquals(pos.annotationIndex, -1); |
250 |
|
} |
251 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
252 |
9 |
@AfterMethod(alwaysRun = true)... |
253 |
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public void tearDown() |
254 |
|
{ |
255 |
9 |
Desktop.instance.closeAll_actionPerformed(null); |
256 |
|
} |
257 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (91) |
Complexity: 2 |
Complexity Density: 0.02 |
1PASS
|
|
258 |
1 |
@Test(groups = "Functional")... |
259 |
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public void testFindMousePosition_wrapped_annotations() |
260 |
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{ |
261 |
1 |
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true"); |
262 |
1 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true"); |
263 |
1 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( |
264 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
265 |
1 |
AlignViewportI av = alignFrame.getViewport(); |
266 |
1 |
av.setScaleAboveWrapped(false); |
267 |
1 |
av.setScaleLeftWrapped(false); |
268 |
1 |
av.setScaleRightWrapped(false); |
269 |
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|
270 |
1 |
alignFrame.alignPanel.updateLayout(); |
271 |
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|
272 |
1 |
final int charHeight = av.getCharHeight(); |
273 |
1 |
final int charWidth = av.getCharWidth(); |
274 |
1 |
final int alignmentHeight = av.getAlignment().getHeight(); |
275 |
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|
276 |
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|
277 |
1 |
assertTrue(charHeight > 0); |
278 |
1 |
assertTrue(charWidth > 0); |
279 |
1 |
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0); |
280 |
|
|
281 |
1 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
282 |
1 |
int x = 0; |
283 |
1 |
int y = 0; |
284 |
|
|
285 |
|
|
286 |
|
|
287 |
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|
288 |
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|
289 |
1 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, |
290 |
|
0, 0, 0, false, 0); |
291 |
1 |
MousePos pos = testee.findMousePosition(evt); |
292 |
1 |
assertEquals(pos.column, 0); |
293 |
1 |
assertEquals(pos.seqIndex, -1); |
294 |
1 |
assertEquals(pos.annotationIndex, -1); |
295 |
|
|
296 |
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|
297 |
|
|
298 |
|
|
299 |
1 |
y = charHeight - 1; |
300 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
301 |
|
false, 0); |
302 |
1 |
pos = testee.findMousePosition(evt); |
303 |
1 |
assertEquals(pos.seqIndex, -1); |
304 |
1 |
assertEquals(pos.annotationIndex, -1); |
305 |
|
|
306 |
|
|
307 |
|
|
308 |
|
|
309 |
1 |
y = charHeight; |
310 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
311 |
|
false, 0); |
312 |
1 |
pos = testee.findMousePosition(evt); |
313 |
1 |
assertEquals(pos.seqIndex, 0); |
314 |
1 |
assertEquals(pos.annotationIndex, -1); |
315 |
|
|
316 |
|
|
317 |
|
|
318 |
|
|
319 |
1 |
y = 2 * charHeight - 1; |
320 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
321 |
|
false, 0); |
322 |
1 |
pos = testee.findMousePosition(evt); |
323 |
1 |
assertEquals(pos.seqIndex, 0); |
324 |
1 |
assertEquals(pos.annotationIndex, -1); |
325 |
|
|
326 |
|
|
327 |
|
|
328 |
|
|
329 |
1 |
y = 2 * charHeight; |
330 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
331 |
|
false, 0); |
332 |
1 |
pos = testee.findMousePosition(evt); |
333 |
1 |
assertEquals(pos.seqIndex, 1); |
334 |
1 |
assertEquals(pos.annotationIndex, -1); |
335 |
|
|
336 |
|
|
337 |
|
|
338 |
|
|
339 |
1 |
y = 3 * charHeight - 1; |
340 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
341 |
|
false, 0); |
342 |
1 |
pos = testee.findMousePosition(evt); |
343 |
1 |
assertEquals(pos.seqIndex, 1); |
344 |
1 |
assertEquals(pos.annotationIndex, -1); |
345 |
|
|
346 |
|
|
347 |
|
|
348 |
|
|
349 |
1 |
y = charHeight * (1 + alignmentHeight) - 1; |
350 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
351 |
|
false, 0); |
352 |
1 |
pos = testee.findMousePosition(evt); |
353 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
354 |
1 |
assertEquals(pos.annotationIndex, -1); |
355 |
|
|
356 |
|
|
357 |
|
|
358 |
|
|
359 |
|
|
360 |
1 |
y += 1; |
361 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
362 |
|
false, 0); |
363 |
1 |
pos = testee.findMousePosition(evt); |
364 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
365 |
1 |
assertEquals(pos.annotationIndex, -1); |
366 |
|
|
367 |
|
|
368 |
|
|
369 |
|
|
370 |
1 |
y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; |
371 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
372 |
|
false, 0); |
373 |
1 |
pos = testee.findMousePosition(evt); |
374 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
375 |
1 |
assertEquals(pos.annotationIndex, -1); |
376 |
|
|
377 |
1 |
AlignmentAnnotation[] annotationRows = av.getAlignment() |
378 |
|
.getAlignmentAnnotation(); |
379 |
5 |
for (int n = 0; n < annotationRows.length; n++) |
380 |
|
{ |
381 |
|
|
382 |
|
|
383 |
|
|
384 |
4 |
y += 1; |
385 |
4 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
386 |
|
false, 0); |
387 |
4 |
pos = testee.findMousePosition(evt); |
388 |
4 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
389 |
4 |
assertEquals(pos.annotationIndex, n); |
390 |
|
|
391 |
|
|
392 |
|
|
393 |
|
|
394 |
4 |
y += annotationRows[n].height - 1; |
395 |
4 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
396 |
|
false, 0); |
397 |
4 |
pos = testee.findMousePosition(evt); |
398 |
4 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
399 |
4 |
assertEquals(pos.annotationIndex, n); |
400 |
|
} |
401 |
|
|
402 |
|
|
403 |
|
|
404 |
|
|
405 |
1 |
y += 1; |
406 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
407 |
|
false, 0); |
408 |
1 |
pos = testee.findMousePosition(evt); |
409 |
1 |
assertEquals(pos.seqIndex, -1); |
410 |
1 |
assertEquals(pos.annotationIndex, -1); |
411 |
|
|
412 |
|
|
413 |
|
|
414 |
|
|
415 |
1 |
y += charHeight - 1; |
416 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
417 |
|
false, 0); |
418 |
1 |
pos = testee.findMousePosition(evt); |
419 |
1 |
assertEquals(pos.seqIndex, -1); |
420 |
1 |
assertEquals(pos.annotationIndex, -1); |
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
|
425 |
1 |
y += 1; |
426 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
427 |
|
false, 0); |
428 |
1 |
pos = testee.findMousePosition(evt); |
429 |
1 |
assertEquals(pos.seqIndex, 0); |
430 |
1 |
assertEquals(pos.annotationIndex, -1); |
431 |
|
} |
432 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (102) |
Complexity: 2 |
Complexity Density: 0.02 |
1PASS
|
|
433 |
1 |
@Test(groups = "Functional")... |
434 |
|
public void testFindMousePosition_wrapped_scaleAbove() |
435 |
|
{ |
436 |
1 |
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "true"); |
437 |
1 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true"); |
438 |
1 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( |
439 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
440 |
1 |
AlignViewportI av = alignFrame.getViewport(); |
441 |
1 |
av.setScaleAboveWrapped(true); |
442 |
1 |
av.setScaleLeftWrapped(false); |
443 |
1 |
av.setScaleRightWrapped(false); |
444 |
1 |
alignFrame.alignPanel.updateLayout(); |
445 |
|
|
446 |
1 |
final int charHeight = av.getCharHeight(); |
447 |
1 |
final int charWidth = av.getCharWidth(); |
448 |
1 |
final int alignmentHeight = av.getAlignment().getHeight(); |
449 |
|
|
450 |
|
|
451 |
1 |
assertTrue(charHeight > 0); |
452 |
1 |
assertTrue(charWidth > 0); |
453 |
1 |
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0); |
454 |
|
|
455 |
1 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
456 |
1 |
int x = 0; |
457 |
1 |
int y = 0; |
458 |
|
|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
|
463 |
1 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, |
464 |
|
0, 0, 0, false, 0); |
465 |
1 |
MousePos pos = testee.findMousePosition(evt); |
466 |
1 |
assertEquals(pos.column, 0); |
467 |
1 |
assertEquals(pos.seqIndex, -1); |
468 |
1 |
assertEquals(pos.annotationIndex, -1); |
469 |
|
|
470 |
|
|
471 |
|
|
472 |
|
|
473 |
|
|
474 |
1 |
y = 2 * charHeight - 1; |
475 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
476 |
|
false, 0); |
477 |
1 |
pos = testee.findMousePosition(evt); |
478 |
1 |
assertEquals(pos.seqIndex, -1); |
479 |
1 |
assertEquals(pos.annotationIndex, -1); |
480 |
|
|
481 |
|
|
482 |
|
|
483 |
|
|
484 |
1 |
y += 1; |
485 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
486 |
|
false, 0); |
487 |
1 |
pos = testee.findMousePosition(evt); |
488 |
1 |
assertEquals(pos.seqIndex, 0); |
489 |
1 |
assertEquals(pos.annotationIndex, -1); |
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
1 |
y += charHeight - 1; |
495 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
496 |
|
false, 0); |
497 |
1 |
pos = testee.findMousePosition(evt); |
498 |
1 |
assertEquals(pos.seqIndex, 0); |
499 |
1 |
assertEquals(pos.annotationIndex, -1); |
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
|
504 |
1 |
y += 1; |
505 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
506 |
|
false, 0); |
507 |
1 |
pos = testee.findMousePosition(evt); |
508 |
1 |
assertEquals(pos.seqIndex, 1); |
509 |
1 |
assertEquals(pos.annotationIndex, -1); |
510 |
|
|
511 |
|
|
512 |
|
|
513 |
|
|
514 |
1 |
y += charHeight - 1; |
515 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
516 |
|
false, 0); |
517 |
1 |
pos = testee.findMousePosition(evt); |
518 |
1 |
assertEquals(pos.seqIndex, 1); |
519 |
1 |
assertEquals(pos.annotationIndex, -1); |
520 |
|
|
521 |
|
|
522 |
|
|
523 |
|
|
524 |
|
|
525 |
1 |
y = charHeight * (2 + alignmentHeight) - 1; |
526 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
527 |
|
false, 0); |
528 |
1 |
pos = testee.findMousePosition(evt); |
529 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
530 |
1 |
assertEquals(pos.annotationIndex, -1); |
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
1 |
y += 1; |
536 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
537 |
|
false, 0); |
538 |
1 |
pos = testee.findMousePosition(evt); |
539 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
540 |
1 |
assertEquals(pos.annotationIndex, -1); |
541 |
|
|
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
1 |
y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; |
547 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
548 |
|
false, 0); |
549 |
1 |
pos = testee.findMousePosition(evt); |
550 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
551 |
1 |
assertEquals(pos.annotationIndex, -1); |
552 |
|
|
553 |
1 |
AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation(); |
554 |
5 |
for (int n = 0; n < annotationRows.length; n++) |
555 |
|
{ |
556 |
|
|
557 |
|
|
558 |
|
|
559 |
4 |
y += 1; |
560 |
4 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
561 |
|
false, 0); |
562 |
4 |
pos = testee.findMousePosition(evt); |
563 |
4 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
564 |
4 |
assertEquals(pos.annotationIndex, n); |
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
|
569 |
4 |
y += annotationRows[n].height - 1; |
570 |
4 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
571 |
|
false, 0); |
572 |
4 |
pos = testee.findMousePosition(evt); |
573 |
4 |
SeqCanvas sc = testee.seqCanvas; |
574 |
4 |
assertEquals(pos.seqIndex, alignmentHeight - 1, |
575 |
|
String.format("%s n=%d y=%d %d, %d, %d, %d", |
576 |
|
annotationRows[n].label, n, y, sc.getWidth(), |
577 |
|
sc.getHeight(), sc.wrappedRepeatHeightPx, |
578 |
|
sc.wrappedSpaceAboveAlignment)); |
579 |
4 |
assertEquals(pos.annotationIndex, n); |
580 |
|
} |
581 |
|
|
582 |
|
|
583 |
|
|
584 |
|
|
585 |
1 |
y += 1; |
586 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
587 |
|
false, 0); |
588 |
1 |
pos = testee.findMousePosition(evt); |
589 |
1 |
assertEquals(pos.seqIndex, -1); |
590 |
1 |
assertEquals(pos.annotationIndex, -1); |
591 |
|
|
592 |
|
|
593 |
|
|
594 |
|
|
595 |
1 |
y += charHeight - 1; |
596 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
597 |
|
false, 0); |
598 |
1 |
pos = testee.findMousePosition(evt); |
599 |
1 |
assertEquals(pos.seqIndex, -1); |
600 |
1 |
assertEquals(pos.annotationIndex, -1); |
601 |
|
|
602 |
|
|
603 |
|
|
604 |
|
|
605 |
1 |
y += 1; |
606 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
607 |
|
false, 0); |
608 |
1 |
pos = testee.findMousePosition(evt); |
609 |
1 |
assertEquals(pos.seqIndex, -1); |
610 |
1 |
assertEquals(pos.annotationIndex, -1); |
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
1 |
y += charHeight - 1; |
616 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
617 |
|
false, 0); |
618 |
1 |
pos = testee.findMousePosition(evt); |
619 |
1 |
assertEquals(pos.seqIndex, -1); |
620 |
1 |
assertEquals(pos.annotationIndex, -1); |
621 |
|
|
622 |
|
|
623 |
|
|
624 |
|
|
625 |
1 |
y += 1; |
626 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
627 |
|
false, 0); |
628 |
1 |
pos = testee.findMousePosition(evt); |
629 |
1 |
assertEquals(pos.seqIndex, 0); |
630 |
1 |
assertEquals(pos.annotationIndex, -1); |
631 |
|
} |
632 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (47) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
633 |
1 |
@Test(groups = "Functional")... |
634 |
|
public void testFindMousePosition_wrapped_noAnnotations() |
635 |
|
{ |
636 |
1 |
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", "false"); |
637 |
1 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true"); |
638 |
1 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( |
639 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
640 |
1 |
AlignViewportI av = alignFrame.getViewport(); |
641 |
1 |
av.setScaleAboveWrapped(false); |
642 |
1 |
av.setScaleLeftWrapped(false); |
643 |
1 |
av.setScaleRightWrapped(false); |
644 |
1 |
alignFrame.alignPanel.updateLayout(); |
645 |
|
|
646 |
1 |
final int charHeight = av.getCharHeight(); |
647 |
1 |
final int charWidth = av.getCharWidth(); |
648 |
1 |
final int alignmentHeight = av.getAlignment().getHeight(); |
649 |
|
|
650 |
|
|
651 |
1 |
assertTrue(charHeight > 0); |
652 |
1 |
assertTrue(charWidth > 0); |
653 |
1 |
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0); |
654 |
|
|
655 |
1 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
656 |
1 |
int x = 0; |
657 |
1 |
int y = 0; |
658 |
|
|
659 |
|
|
660 |
|
|
661 |
|
|
662 |
|
|
663 |
1 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, |
664 |
|
0, 0, 0, false, 0); |
665 |
1 |
MousePos pos = testee.findMousePosition(evt); |
666 |
1 |
assertEquals(pos.column, 0); |
667 |
1 |
assertEquals(pos.seqIndex, -1); |
668 |
1 |
assertEquals(pos.annotationIndex, -1); |
669 |
|
|
670 |
|
|
671 |
|
|
672 |
|
|
673 |
1 |
y = charHeight; |
674 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
675 |
|
false, 0); |
676 |
1 |
pos = testee.findMousePosition(evt); |
677 |
1 |
assertEquals(pos.seqIndex, 0); |
678 |
1 |
assertEquals(pos.annotationIndex, -1); |
679 |
|
|
680 |
|
|
681 |
|
|
682 |
|
|
683 |
1 |
y = charHeight * (1 + alignmentHeight) - 1; |
684 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
685 |
|
false, 0); |
686 |
1 |
pos = testee.findMousePosition(evt); |
687 |
1 |
assertEquals(pos.seqIndex, alignmentHeight - 1); |
688 |
1 |
assertEquals(pos.annotationIndex, -1); |
689 |
|
|
690 |
|
|
691 |
|
|
692 |
|
|
693 |
1 |
y += 1; |
694 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
695 |
|
false, 0); |
696 |
1 |
pos = testee.findMousePosition(evt); |
697 |
1 |
assertEquals(pos.seqIndex, -1); |
698 |
1 |
assertEquals(pos.annotationIndex, -1); |
699 |
|
|
700 |
|
|
701 |
|
|
702 |
|
|
703 |
1 |
y += charHeight - 1; |
704 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
705 |
|
false, 0); |
706 |
1 |
pos = testee.findMousePosition(evt); |
707 |
1 |
assertEquals(pos.seqIndex, -1); |
708 |
1 |
assertEquals(pos.annotationIndex, -1); |
709 |
|
|
710 |
|
|
711 |
|
|
712 |
|
|
713 |
1 |
y += 1; |
714 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0, |
715 |
|
false, 0); |
716 |
1 |
pos = testee.findMousePosition(evt); |
717 |
1 |
assertEquals(pos.seqIndex, 0); |
718 |
1 |
assertEquals(pos.annotationIndex, -1); |
719 |
|
} |
720 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (30) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
|
|
721 |
1 |
@Test(groups = "Functional")... |
722 |
|
public void testFindColumn_unwrapped() |
723 |
|
{ |
724 |
1 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "false"); |
725 |
1 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( |
726 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
727 |
1 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
728 |
1 |
int x = 0; |
729 |
1 |
final int charWidth = alignFrame.getViewport().getCharWidth(); |
730 |
1 |
assertTrue(charWidth > 0); |
731 |
1 |
ViewportRanges ranges = alignFrame.getViewport().getRanges(); |
732 |
1 |
assertEquals(ranges.getStartRes(), 0); |
733 |
|
|
734 |
|
|
735 |
|
|
736 |
|
|
737 |
1 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, |
738 |
|
0, 0, 0, false, 0); |
739 |
1 |
assertEquals(testee.findColumn(evt), 0); |
740 |
|
|
741 |
|
|
742 |
|
|
743 |
|
|
744 |
1 |
x = charWidth-1; |
745 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, |
746 |
|
0, 0, 0, false, 0); |
747 |
1 |
assertEquals(testee.findColumn(evt), 0); |
748 |
|
|
749 |
|
|
750 |
|
|
751 |
|
|
752 |
1 |
x = charWidth; |
753 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
754 |
|
false, 0); |
755 |
1 |
assertEquals(testee.findColumn(evt), 1); |
756 |
|
|
757 |
|
|
758 |
|
|
759 |
|
|
760 |
1 |
x = 2 * charWidth; |
761 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
762 |
|
false, 0); |
763 |
1 |
assertEquals(testee.findColumn(evt), 2); |
764 |
|
|
765 |
|
|
766 |
|
|
767 |
|
|
768 |
1 |
x = 20000; |
769 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
770 |
|
false, 0); |
771 |
1 |
SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas; |
772 |
1 |
int w = seqCanvas.getWidth(); |
773 |
|
|
774 |
|
|
775 |
1 |
int expected = w / charWidth; |
776 |
1 |
expected = Math.min(expected, ranges.getEndRes()); |
777 |
1 |
assertEquals(testee.findColumn(evt), expected); |
778 |
|
|
779 |
|
|
780 |
|
|
781 |
|
|
782 |
1 |
alignFrame.getViewport().hideColumns(4, 9); |
783 |
1 |
x = 5 * charWidth + 2; |
784 |
|
|
785 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
786 |
|
false, 0); |
787 |
1 |
assertEquals(testee.findColumn(evt), 11); |
788 |
|
} |
789 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (46) |
Complexity: 1 |
Complexity Density: 0.02 |
1PASS
|
|
790 |
1 |
@Test(groups = "Functional")... |
791 |
|
public void testFindColumn_wrapped() |
792 |
|
{ |
793 |
1 |
Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", "true"); |
794 |
1 |
AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( |
795 |
|
"examples/uniref50.fa", DataSourceType.FILE); |
796 |
1 |
AlignViewport av = alignFrame.getViewport(); |
797 |
1 |
av.setScaleAboveWrapped(false); |
798 |
1 |
av.setScaleLeftWrapped(false); |
799 |
1 |
av.setScaleRightWrapped(false); |
800 |
1 |
alignFrame.alignPanel.updateLayout(); |
801 |
1 |
SeqPanel testee = alignFrame.alignPanel.getSeqPanel(); |
802 |
1 |
int x = 0; |
803 |
1 |
final int charWidth = av.getCharWidth(); |
804 |
1 |
assertTrue(charWidth > 0); |
805 |
1 |
assertEquals(av.getRanges().getStartRes(), 0); |
806 |
|
|
807 |
|
|
808 |
|
|
809 |
|
|
810 |
1 |
MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, |
811 |
|
0, 0, 0, false, 0); |
812 |
1 |
assertEquals(testee.findColumn(evt), 0); |
813 |
|
|
814 |
|
|
815 |
|
|
816 |
|
|
817 |
1 |
x = charWidth-1; |
818 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, |
819 |
|
0, 0, 0, false, 0); |
820 |
1 |
assertEquals(testee.findColumn(evt), 0); |
821 |
|
|
822 |
|
|
823 |
|
|
824 |
|
|
825 |
1 |
x = charWidth; |
826 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
827 |
|
false, 0); |
828 |
1 |
assertEquals(testee.findColumn(evt), 1); |
829 |
|
|
830 |
|
|
831 |
|
|
832 |
|
|
833 |
1 |
av.setScaleLeftWrapped(true); |
834 |
1 |
alignFrame.alignPanel.updateLayout(); |
835 |
1 |
SeqCanvas seqCanvas = testee.seqCanvas; |
836 |
1 |
int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest"); |
837 |
1 |
assertTrue(labelWidth > 0); |
838 |
1 |
x = labelWidth - 1; |
839 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
840 |
|
false, 0); |
841 |
1 |
assertEquals(testee.findColumn(evt), -1); |
842 |
|
|
843 |
1 |
x = labelWidth; |
844 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
845 |
|
false, 0); |
846 |
1 |
assertEquals(testee.findColumn(evt), 0); |
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
|
851 |
1 |
int residuesWide = av.getRanges().getViewportWidth(); |
852 |
1 |
assertTrue(residuesWide > 0); |
853 |
1 |
x = labelWidth + charWidth * residuesWide - 1; |
854 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
855 |
|
false, 0); |
856 |
1 |
assertEquals(testee.findColumn(evt), residuesWide - 1); |
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
861 |
1 |
av.setScaleRightWrapped(true); |
862 |
1 |
alignFrame.alignPanel.updateLayout(); |
863 |
1 |
labelWidth = (int) PA.getValue(seqCanvas, "labelWidthEast"); |
864 |
1 |
assertTrue(labelWidth > 0); |
865 |
1 |
int residuesWide2 = av.getRanges().getViewportWidth(); |
866 |
1 |
assertTrue(residuesWide2 > 0); |
867 |
1 |
assertTrue(residuesWide2 < residuesWide); |
868 |
1 |
x += 1; |
869 |
1 |
evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0, |
870 |
|
false, 0); |
871 |
1 |
assertEquals(testee.findColumn(evt), -1); |
872 |
|
|
873 |
|
|
874 |
|
|
875 |
|
} |
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
876 |
1 |
@BeforeClass(alwaysRun = true)... |
877 |
|
public static void setUpBeforeClass() throws Exception |
878 |
|
{ |
879 |
|
|
880 |
|
|
881 |
|
|
882 |
1 |
Cache.loadProperties("test/jalview/io/testProps.jvprops"); |
883 |
1 |
Jalview.main(new String[] { "-nonews" }); |
884 |
|
} |
885 |
|
|
886 |
|
|
887 |
|
|
888 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 0.67 |
|
889 |
0 |
synchronized void waitForSwing()... |
890 |
|
{ |
891 |
0 |
try |
892 |
|
{ |
893 |
0 |
EventQueue.invokeAndWait(new Runnable() |
894 |
|
{ |
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
895 |
0 |
@Override... |
896 |
|
public void run() |
897 |
|
{ |
898 |
|
} |
899 |
|
}); |
900 |
|
} catch (InterruptedException | InvocationTargetException e) |
901 |
|
{ |
902 |
0 |
e.printStackTrace(); |
903 |
|
} |
904 |
|
} |
905 |
|
} |